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Ephrem Mebrahtu Araya,1 Haylay Araya Gebrezgabiher,1 Gebretsadkan Hintsa Tekulu,2 Niguse Meles Alema,1 Desalegn Getnet,1 Hirut Teame Gebru,3 Betelhem Anteneh Adamu4 1Department of Pharmacy, College of Medicine and Health Sciences, Adigrat University, Adigrat, Ethiopia; 2Department of Pharmacognosy, School of Pharmacy, College of Health Sciences, Mekelle University, Mekelle, Ethiopia; 3Department of Public Health, Colleges of Medicine and Health Sciences, Adigrat University, Adigrat, Ethiopia; 4Department of Pharmacognosy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, EthiopiaCorrespondence: Ephrem Mebrahtu ArayaDepartment of Pharmacy, College of Medicine and Health Sciences, Adigrat University, Adigrat, Tigrai, EthiopiaTel +251 914425760Email ephremcfc@gmail.comIntroduction: Medication non-adherence is a major public health problem among diabetes mellitus patients. However, there is a lack of data regarding its magnitude and the factors contributing to Ethiopia’s non-adherence, especially in the Tigrai region. This study was conducted to assess the magnitude of non-adherence and its contributing factors among diabetes mellitus patients in the Eastern Zone of Tigrai, Northern Ethiopia.Materials and Methods: A hospital-based cross-sectional study was conducted at Adigrat and Wukro General Hospitals using a pre-tested, self-administered, semi-structured questionnaire developed from the relevant literature and a checklist developed to review patient medical cards for the period of the 15th of March to the 15th of July, 2019. Data were analyzed using Statistical Package for Social Sciences version 20. Association between the dependent and the independent variable was performed using logistic regression and a p-value of < 0.05 was considered significant.Results: From a total of 321 study participants, 63.9% of the patients were non-adherent to their medications. Two-month dose issued on each visit (AOR = 2.865, 95% CI 1.380– 5.949), dose issued for more than three months (AOR = 4.314, 95% CI 1.526– 12.195), monthly income below 500 birr (AOR = 5.048, 95% CI 2.094– 12.168), monthly income between 500 and 2000 birr (AOR = 2.593, 95% CI 1.032– 6.517), distance greater than 24 kilometers from hospital to home (AOR = 10.091, 95% CI 3.509– 29.020), more than four prescribed medications per visit (AOR=7.192, 95% CI= 2.171– 23.824), never receiving counseling (AOR=22.334, 95% CI= 9.270– 53.810), and diabetes-related admission (AOR=0.248, 95% CI= 0.078– 0.789) were significantly associated with patients’ non-adherence to diabetes mellitus medications.Conclusion: The level of diabetic medication adherence was suboptimal, and our study highlights that better monthly earning, nearby health-care accessibility, fewer prescribed medication, and getting appropriate counseling about diabetes mellitus were predictive of adherence to medications. Hence, an urgent intervention targeting the development of guidelines that involve these determinates should be employed to improve health care.Keywords: diabetes mellitus, Ethiopia, medication non-adherence, patients

This study examined the effect of transactional leadership behaviors on research productivity in public universities, with organizational learning capability serving as a mediating factor. A quantitative research approach focusing on correlational design was utilized. Data were collected through a survey questionnaire administered to 519 respondents. Both measurement and structural model analyses were conducted, with deans, colleges, and individual academics serving as units of analysis. The findings revealed that deans’ contingent reward leadership behaviors significantly and positively influenced the research productivity of academics and colleges, even when controlling for workplace learning capability. Furthermore, the study demonstrated that deans’ contingent rewards and active-by-exception behaviors significantly and positively impacted workplace learning capability, accounting for 44.5% of the variance, with moderate and small effect sizes, respectively. Additionally, organizational learning capability exhibited a significant positive effect, explaining 54% of the variance in research productivity and demonstrating a moderate effect size, which indicates an unexplained variance of 46%. Bootstrapping tests confirmed that workplace learning capability partially and fully mediates the relationship between deans’ transactional leadership behaviors and research productivity. Consequently, it is imperative for college deans to enhance their contingent reward leadership behaviors and foster workplace learning capabilities to maximize their impact on research productivity.

Background and Aims Phosphorus (P) availability is often limiting for rice (Oryza sativa) production. Improving internal P-use efficiency (PUE) is crucial to sustainable food production, particularly in low-input systems. A critical aspect of PUE in plants, and one that remains poorly understood, is the investment of leaf P in different chemical P fractions (nucleic acid-P, lipid-P, inorganic-P, metabolite-P and residual-P). The overarching objective of this study was to understand how these key P fractions influence PUE. Methods Three high-PUE and two low-PUE rice genotypes were grown in hydroponics with contrasting P supplies. We measured PUE, total P, P fractions, photosynthesis and biomass. Key Results Low investment in lipid-P was strongly associated with increased photosynthetic PUE (PPUE), achieved by reducing total leaf P concentration while maintaining rapid photosynthetic rates. All low-P plants exhibited a low investment in inorganic-P and lipid-P, but not nucleic acid-P. In addition, whole-plant PUE was strongly associated with reduced total P concentration, increased biomass and increased preferential allocation of resources to the youngest mature leaves. Conclusions Lipid remodelling has been shown in rice before, but we show for the first time that reduced lipid-P investment improves PUE in rice without reducing photosynthesis. This presents a novel pathway for increasing PUE by targeting varieties with reduced lipid-P investment. This will benefit rice production in low-P soils and in areas where fertilizer use is limited, improving global food security by reducing P fertilizer demands and food production costs. [ABSTRACT FROM AUTHOR]

Background Assessment of quality of life (QoL) in cancer patients can provide an overall picture of the patient's adaptation to the disease and maintain long-term health and well-being. Determining the QoL in cancer patients could help with better care and could be as prognostic as medical factors and the survival benefit that pharmacological treatment could provide. The main objective of this review was to determine the prevalence of QoL among Ethiopian adult cancer patients. Methods A systematic review was conducted using the “Preferred Reporting Results of Systematic Reviews and Meta-Analyses” guidelines. Databases such as PubMed/Medline, CINAHL, AMED, Embase, the Cochrane Library, ScienceDirect, World Health Organization's Hinari portal, and African Journals Online databases were searched from January 2022 to June 2022. Google, Google Scholar, and university repositories were used to access unpublished studies. Two reviewers independently screened the data using a standardized data extraction format and appraised their quality using the Newcastle–Ottawa Scale. Results In this review, 10 studies were included. The prevalence of poor QoL ranged from 52 to 89.6. The physical, role, social, and emotional functioning were the most affected domains of QoL and have been significantly associated with QoL. Financial difficulty was the most important predictor of QoL among Ethiopian cancer patients. Pain, dyspnea, nausea, vomiting, and poor appetite were also reported as predictors of QoL. Low income, lower educational status, unmarried status, underweight, anxiety, and depression, advanced stage of cancer, patients with ≤2 cycles of chemotherapy, and the presence of comorbid diseases were significantly correlated with QoL. Conclusions The QoL of an Ethiopian cancer patient was low. Quality of life assessments, appropriate symptom management, integration of psycho-oncology care, and providing economic support shall be considered to improve their QoL.

Climate change and related extreme events have become global challenges in ensuring sustainable development. This affects water availability and agricultural production, particularly in developing countries. This study explored the factors affecting farmers' adaptation mechanisms to climate change in different agro-ecological zones of the Bure Zuria district of northwestern Ethiopia. A household survey, focus group discussion, key informant interviews, and observations were used to acquire primary data on farmers' socioeconomic and demographic characteristics, adaptation strategies and potential barriers. About 190 randomly selected households from different agro-ecologies were included in this study. Moreover, reports and published sources were used to acquire secondary data. Data were analyzed using a multinomial logit regression model and descriptive statistics. The results indicated that soil and water conservation practices (26.7%) were the main adaptation responses in highland agro-ecology. In contrast, supplementary feeding for livestock (56%) was the main adaptation response to the adverse effects of climate extremes in lowland agro-ecology. Farmers identified land scarcity (25.84%) and shortage of water for irrigation (28.57%) as major barriers to adaptation in the highland and lowland agro-ecologies, respectively. In addition, agro-ecology, education level, age, active labor, number of livestock (TLU), off-farm income, frequency of extension contacts, credit access, and market access were decisive factors affecting farmers’ adaptation mechanisms to withstand extreme climatic events. In conclusion, soil and water conservation practices are more practiced in highland areas than in lowland areas. Because the steepness of farmlands and erodible soils increase farmers' vulnerability to flood hazards in highland areas than in lowland areas. It is suggested that investigations on the climate change-induced gender-differentiated impacts shall be conducted to design all-inclusive and effective responses.

Abstract Background Though cervical cancer is largely preventable, it is still the second most common female cancer globally and the leading cause of cancer deaths among females in African. Though many efforts have been done to study the burden of the disease in Ethiopia, primary studies examining the prevalence of precancerous cervical lesions are fragmented. Hence, this systematic review and meta-analysis is aimed at estimating the pooled prevalence of precancerous cervical lesion and its trends in Ethiopia. Methods This systematic review and meta-analysis was conducted using the following electronic databases. PubMed, Web of Science, SCOPUS, Science Direct, Google Scholar, African Index Medicus (AIM), African Journals Online databases, and Addis Ababa and Bahir Dar Universities research repositories were searched following the Preferred Items for Systematic Review and Meta-analysis (PRISMA) Guideline. STATA 15 statistical software was used to analyze the data. The quality of the included studies was assessed using the Joanna Briggs Institute (JBI) quality appraisal tool for meta-analysis. Heterogeneity between studies was assessed using the Cochrane Q test and I 2 test statistics based on the random effects model. A random effects model was computed to estimate the pooled prevalence of precancerous cervical lesion in Ethiopia. Finally, the trend of precancerous cervical lesion in the country was presented. Result Seventeen studies with a total of 26,112 participants were included in the analysis. The pooled prevalence of precancerous cervical lesion was 15.16 (95% CI 10.16–19.70). The subgroup analysis by region showed the highest prevalence of precancerous cervical lesion at the Southern Nations and Nationalities Peoples Region (19.65%; 95% CI 15.51–23.80). The trend of precancerous cervical lesion prevalence showed an increased pattern over time. Conclusion Approximately one among six of the study participants had precancerous cervical lesion. The trend also showed that there is still an increasing precancerous cervical lesion in Ethiopia. Best practices in achieving high vaccination coverage shall be informed by practices in other successful countries.

Salinity is a global problem affecting agriculture that results in an estimated US$27 billion loss in revenue per year. Overexpression of vacuolar ATPase subunits has been shown to be beneficial in improving plant performance under saline conditions. Most studies, however, have not shown whether overexpression of genes encoding ATPase subunits results in improvements in grain yield, and have not investigated the physiological mechanisms behind the improvement in plant growth. In this study, we constitutively expressed Arabidopsis Vacuolar ATPase subunitC(AtVHA-C) in barley. Transgenic plants were assessed for agronomical and physiological characteristics, such as fresh and dry biomass, leaf pigment content, stomatal conductance, grain yield, and leaf Na+and K+ concentration, when grown in either 0 or 300mM NaCl. When compared with non-transformed barley, AtVHA-C expressing barley lines had a smaller reduction in both biomass and grain yield under salinity stress. The transgenic lines accumulated Na+ and K+ in leaves for osmotic adjustment. This in turn saves energy consumed in the synthesis of organic osmolytes that otherwise would be needed for osmotic adjustment. [ABSTRACT FROM AUTHOR]

BackgroundAnemia is a major public health problem worldwide which accounts 24.8% of the population. Subsequently, anemia is a leading killer of people living with human immunodeficiency virus and many of these deaths occur in developing countries including Ethiopia. Cross sectional studies have done on anemia and human immunodeficiency virus. However, there is limited study on incidence of anemia and its predictors among adults on HIV care, especially no survival study has been conducted in the study area.ObjectiveTo assess incidence and predictors of anemia among adults on Human immunodeficiency virus care.MethodsAn institution-based retrospective cohort study was conducted among 434 adults on HIV care from January 1st 2015 to December 30th 2019 at Debre Tabor Referral Hospital. A computer-generated simple random sampling technique was employed to select the study participants. Ethical clearance was obtained from the Institutional Review Board of Bahir Dar University, and also, we got implied consent to review charts from the concerned bodies in the hospital. Data were entered using Epi-data version 3.1 and analyzed by using STATA version 14.0. A Kaplan Meier survival curve was utilized to estimate anemia free survival time. Bivariable and Multivariable Cox proportional hazards model were fitted to identify predictors of anemia.ResultsThe overall incidence density rate of anemia was 6.27 (95% CI: 0.051, 0.077) per 100 person years. Clinical stage III/IV (AHR = 1.04; 95% CI = 1.02, 1.06), Body Mass Index less than 18.5 kg/m2 (AHR = 3.11; 95% CI = 1.56, 6.22), serum creatinine greater than 1.1 IU/L(AHR = 2.07; 95% CI = 1.12, 3.81) and fair/poor level of adherence(AHR = 1.05; 95% CI = 1.03, 1.07) were statistically significant predictors of anemia while increased anti-retroviral treatment duration (AHR = 0.98; 95% CI = 0.97, 0.99) decrease the risk of anemia at 95% confidence level.ConclusionThe overall incidence density rate of anemia was high. Patients with clinical stage III/IV, body mass index < 18.5 kg/m2, serum creatinine greater than 1.1 IU/L and fair/poor level of adherence were significant predictors of anemia while increased antiretroviral treatment duration had decreased the risk of anemia.RecommendationEven if the overall incidence rate of anemia was lower as compared to previous studies in Ethiopia, still the incidence of anemia was high. So, prevention measures should be taken beside with HIV care especially within 6-months ART initiation.

Abstract Background Ethiopia has been experiencing a high prevalence of communicable diseases, which resulted in high morbidity, mortality, and hospital admission rates. One of the highest contributing factors for this is lower level of latrine utilization. There had been significantly varying finding reports with regard to the level of latrine utilization and its association with education level from different pocket studies in the country. Therefore, this systematic review and meta-analysis was aimed to estimate the pooled prevalence of household latrine utilization and its association with education status of household heads, in Ethiopia using available studies. Methods This systematic review and meta-analysis was conducted using available data from the international databases, including PubMed, Google Scholar, Science direct, Cochrane library and unpublished reports. All observational studies reporting the prevalence of latrine utilization in Ethiopia were included. Four authors independently extracted all necessary data using a standardized data extraction format. STATA 13 statistical software was used to analyze the data. The Cochrane Q test statistics and I 2 test were used to assess the heterogeneity between the studies. A random effect model was computed to estimate the pooled level of latrine utilization in Ethiopia. In addition, the association between latrine utilization and the educational level of the users was analyzed. Results After reviewing of 1608 studies, 17 studies were finally included in our meta-analysis. The result of 16 studies revealed that the pooled prevalence of latrine utilization level in Ethiopia was 50.02% (95%CI: 40.23, 59.81%). The highest level (67.4%) of latrine utilization was reported from Southern Nations Nationality and People regional state, followed by Amhara regional state (50.1%). Participants who completed their high school and above education were more likely (OR: 1.79, 95%CI: 1.05, 3.05) to utilize latrine compared to those who did not attend formal education. Conclusion In Ethiopia, only half of the households utilize latrine and the level of utilization has significant association with educational status.

Introduction: Sepsis is one of the leading causes of death in military and civilian hospitals. Rapid identification of involved pathogens is a key step for appropriate diagnosis, treatment and ultimately survival. Current diagnostics tools are either very bulky and not deployment ready, or require a long time to provide results. Given these obstacles, new solutions are urgently needed. Optomagnetic Imaging Spectroscopy (OMIS) is novel technology successfully used for the detection of cancer cells and viruses. OMIS has high sensitivity due to recording the unpaired and paired electrons of sample material. Furthermore, machine learning that uses the algorithms random forest (RF) classifier and artificial neural network (ANN) is integrated into the technology to enhance detection. Here we evaluated the feasibility of OMIS for the detection of bacteria in blood. Methods: We used commercially available human blood spiked with a defined concentration multidrug resistant Staphylococcus aureus derived from a clinical isolate. Final concentrations of bacteria of 1 × 106, 1 × 105 and 1 × 104 CFU/mL corresponding to High (H), Medium (M) and Low (L) concentrations respectively. A total of 240 samples (60 samples per concentration as well as 60 samples of sterile blood (N)) was imaged, and the data were analyzed using random forest classifier and artificial neural network. Images for the training set and validation sets were separately obtained and used for comparison against true positive values (confirmatory plating on the nutrient agar). Results: The average score of classification samples in the correct category (N, L, M, H) one-by-one was 94% for the ANN algorithm, while for the RF algorithm accuracy was 93% (average means that three times different 40 samples (of 240 samples) were chosen, and each prediction test had different sample mixtures). The closeness of the two values of accuracy strongly indicates that the input data (interaction of light with paired and unpaired electrons) and output data (classification N, L, M, H concentration of bacteria) are correlated.

Phosphorus (P) is an essential macronutrient for plant growth and development. Phosphorus is usually applied as fertilizer obtained from rock phosphate which is a non-renewable resource. Therefore, developing rice varieties that can use P more efficiently is crucial. Here, we investigated genotypic differences in traits related to internal Phosphorus Utilization Efficiency (PUE) in five rice genotypes grown under P-deficient conditions. P-efficient rice genotypes showed higher total biomass. This was partly due to higher root biomass, which in turn relied on preferential allocation of P to roots in these genotypes. Changes in P content and tissue P concentrations were analyzed in individual leaves at different time points. Genotypes belonging to the high-PUE group responded more quickly to P starvation in terms of reducing leaf P concentrations and they were able to reduce these concentrations to a lower level compared to the low-PUE group. Changes in P concentrations were reflected in gene expression levels for genes involved in lipid remodeling. Sulfolipid (OsSQD2) and galactolipid (OsMGD and OsDGD) synthesis-related genes were generally induced due to P starvation with most pronounced up-regulation in OsDGD1 and OsMGD3, but patterns differed between genotypes. A significantly higher expression of OsDGD5 and OsMGD1 & 2 was detected in the youngest fully expanded leaf of the high-PUE genotype group, whereas expression levels were reversed in older leaves. This pattern would confirm that P efficient genotypes react faster to P starvation in terms of freeing P for redistribution to growing tissues and replacing phospholipids with galactolipids in younger leaves may contribute to this aspect.

BackgroundTuberculosis is a global public health problem. One of the overarching dilemmas and challenges facing most tuberculosis program is non-adherence to treatment. However, in Ethiopia there are few studies with variable and inconsistent findings regarding non-adherence to treatment for tuberculosis.MethodsThis systematic review and meta-analysis was conducted to determine the prevalence of non-adherence to tuberculosis treatment and its determinants in Ethiopia. Biomedical databases including PubMed, Google Scholar, Science Direct, HINARI, EMBASE and Cochrane Library were systematically and comprehensively searched. To estimate the pooled prevalence, studies reporting the prevalence of adherence or non-adherence to tuberculosis treatment and its determinants were included. Data were extracted using a standardized data extraction tool prepared in Microsoft Excel and transferred to STATA/se version-14 statistical software for further analyses. To assess heterogeneity, the Cochrane Q test statistics and I2 test were performed. Since the included studies exhibited high heterogeneity, a random effects model meta- analysis was used to estimate the pooled prevalence of non-adherence to tuberculosis treatment. Finally, the association between determinant factors and non-adherence to tuberculosis treatment was assessed.ResultsThe result of 13 studies revealed that the pooled prevalence of non-adherence to tuberculosis treatment in Ethiopia was found to be 21.29% (95% CI: 15.75, 26.68). In the subgroup analysis, the highest prevalence was observed in Southern Nations and Nationalities of Ethiopia, 23.61% (95% CI: 21.05, 26.17) whereas the lowest prevalence was observed in Amhara region, 10.0% (95% CI: 6.48, 13.17.0;). Forgetfulness (OR = 3.22, 95% CI = 2.28, 4.53), fear side effect of the drugs (OR = 1.93, 95% CI = 1.37, 2.74), waiting time ≥ 1 hour during service (OR = 4.88, 95% CI = 3.44, 6.91) and feeling distance to health institution is long (OR = 5.35, 95% CI = 4.00, 7.16) were found to be determinants of non-adherence to tuberculosis treatment.ConclusionIn this meta-analysis, the pooled prevalence of non-adherence to tuberculosis treatment in Ethiopia was high. Forgetfulness, fear of side effect of the drugs, long waiting time (≥1 hour) during service and feeling distance to health institution is long were the main risk factors for non-adherence to tuberculosis treatment in Ethiopia. Early monitoring of the side effects and other reasons which account for missing medication may increase medication adherence in patients with tuberculosis in Ethiopia.

Hypothermia in combination with infection presents a complex challenge in clinical and battlefield medicine. Multifaceted physiological and immunological consequences of hypothermia drastically change the risk, progression, and treatment of a concomitant infection. Managing hypothermia and infection in extreme cold settings is particularly relevant in an era with increased risk of military operations in Polar climates. Here, we discuss the elevated instance of infection during accidental and therapeutic hypothermia and speculate how a compromised immune system may contribute. We focus on skin and soft tissue infections and sepsis, which are among the serious infectious complications of hypothermia and battlefield injuries. We also present the challenges associated with treating infections under hypothermic conditions. Finally, we advocate for a renewed focus on identifying causal relationships between hypothermia and infection risk and assessing established infection treatment regiments in hypothermic patients to enhance trauma management and survival outcomes in hypothermia-related injuries., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: CPT Richard Kevorkian reports financial support was provided by US Department of Defense JPC-6 Combat Casualty Care Research Program. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Introduction: Extensive trauma, commonly seen in wounded military Service Members, often leads to a severe sterile inflammation termed systemic inflammatory response syndrome (SIRS), which can progress to multiple organ dysfunction syndrome (MODS) and death. MODS is a serious threat to wounded Service Members, historically causing 10% of all deaths in trauma admissions at a forward deployed combat hospital. The importance of this problem will be exacerbated in large-scale combat operations, in which evacuation will be delayed and care of complex injuries at lower echelons of care may be prolonged. The main goal of this study was to optimize an existing mouse model of lethal SIRS/MODS as a therapeutic screening platform for the evaluation of immunomodulatory drugs., Materials and Methods: Male C57BL/6 mice were euthanized, and the bones and muscles were collected and blended into a paste termed tissue-bone matrix (TBX). The TBX at 12.5%-20% relative to body weight of each recipient mouse was implanted into subcutaneous pouches created on the dorsum of anesthetized animals. Mice were observed for clinical scores for up to 48 hours postimplantation and euthanized at the preset point of moribundity. To test effects of anesthetics on TBX-induced mortality, animals received isoflurane or ketamine/xylazine (K/X). In a separate set of studies, mice received TBX followed by intraperitoneal injection with 20 mg/kg or 40 mg/kg Eritoran or a placebo carrier. All Eritoran studies were performed in a blinded fashion., Results: We observed that K/X anesthesia significantly increased the lethality of the implanted TBX in comparison to inhaled anesthetics. Although all the mice anesthetized with isoflurane and implanted with 12.5% TBX survived for 24 hours, 60% of mice anesthetized with K/X were moribund by 24 hours postimplantation. To mimic more closely the timing of lethal SIRS/MODS following polytrauma in human patients, we extended observation to 48 hours. We performed TBX dose-response studies and found that as low as 15%, 17.5%, and 20% TBX caused moribundity/mortality in 50%, 80%, and 100% mice, respectively, over a 48-hour time period. With 17.5% TBX, we tested if moribundity/mortality could be rescued by anti-inflammatory drug Eritoran, a toll-like receptor 4 antagonist. Neither 20 mg/kg nor 40 mg/kg doses of Eritoran were found to be effective in this model., Conclusions: We optimized a TBX mouse model of SIRS/MODS for the purpose of evaluating novel therapeutic interventions to prevent trauma-related pathophysiologies in wounded Service Members. Negative effects of K/X on lethality of TBX should be further evaluated, particularly in the light of widespread use of ketamine in treatment of pain. By mimicking muscle crush, bone fracture, and necrosis, the TBX model has pleiotropic effects on physiology and immunology that make it uniquely valuable as a screening tool for the evaluation of novel therapeutics against trauma-induced SIRS/MODS., (Published by Oxford University Press on behalf of the Association of Military Surgeons of the United States 2024. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

Wound-invasive fungal diseases (WIFDs), especially mucormycosis, have emerged as life-threatening infections during recent military combat operations. Many combat-relevant fungal pathogens are refractory to current antifungal therapy. Therefore, animal models of WIFDs are urgently needed to investigate new therapeutic solutions. Our study establishes combat-relevant murine models of wound mucormycosis using Rhizopus arrhizus and Lichtheimia corymbifera , two Mucorales species that cause wound mucormycosis worldwide. These models recapitulate the characteristics of combat-related wounds from explosions, including blast overpressure exposure, full-thickness skin injury, fascial damage, and muscle crush. The independent inoculation of both pathogens caused sustained infections and enlarged wounds. Histopathological analysis confirmed the presence of necrosis and fungal hyphae in the wound bed and adjacent muscle tissue. Semi-quantification of fungal burden by colony-forming units corroborated the infection. Treatment with liposomal amphotericin B, 30 mg/kg, effectively controlled R. arrhizus growth and significantly reduced residual fungal burden in infected wounds ( p < 0.001). This study establishes the first combat-relevant murine model of wound mucormycosis, paving the way for developing and evaluating novel antifungal therapies against combat-associated WIFDs.

Introduction: Combat injuries are complex and multimodal. Most injuries to the extremities occur because of explosive devices such as improvised explosive devices. Blast exposure dramatically increases the risk of infection in combat wounds, and there is limited available information on the best antibiotic treatments for these injuries. We previously demonstrated that mice exposed to blast displayed a delayed clearance of cefazolin from the plasma and liver; further semi-mechanistic modeling determined that cefazolin concentrations in the skin of these mice were reduced. Our objective was to investigate the effects of blast on the pharmacokinetics of antibiotics of different types used for the treatment of combat wounds in the rat model., Materials and Methods: Male Sprague Dawley rats were exposed to blast overpressure followed by injection of a bolus of animal equivalent doses of an antibiotic (cefazolin, cefepime, ertapenem, or clindamycin) into the tail vein at 1-hour post-blast exposure. Blood was collected at predetermined time points via repeated sampling from the tail vein. Animals were also euthanized at predetermined time points, at which time liver, kidney, skin, and blood via cardiac puncture were collected. Antibiotic concentrations were determined by ultra-performance liquid chromatography-tandem mass spectrometry., Results: Blast-exposed rats exhibited a similar rate of clearance compared to non-blasted rats in the blood, liver, kidney, and skin, which is inconsistent with the data regarding cefazolin in blast-exposed mice., Conclusions: Our results in rats do not recapitulate our previous observation of delayed cefazolin clearance in mice following the blast overpressure exposure. Although using rats permitted us to collect multiple blood samples from the same animals, rats may not be a suitable model for measuring the pharmacokinetics of antibiotics following blast. The interpretation of the results may be challenging because of variation in data among rat subjects in the same sample groups., (Published by Oxford University Press on behalf of the Association of Military Surgeons of the United States 2023. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

Antibiotic resistance, when it comes to bacterial infections, is not a problem that is going to disappear anytime soon. With the lack of larger investment in novel antibiotic research and the ever-growing increase of resistant isolates amongst the ESKAPEE pathogens ( Enterobacter cloacae , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa , Enterococcus sp., and Escherichia coli ), it is inevitable that more and more infections caused by extensively drug-resistant (XDR) and pandrug-resistant (PDR) strains will arise. One strategy to counteract the growing threat is to use antibiotic adjuvants, a drug class that on its own lacks significant antibiotic activity, but when mixed with another antibiotic, can potentiate increased killing of bacteria. Antibiotic adjuvants have various mechanisms of action, but polymyxins and polymyxin-like molecules can disrupt the Gram-negative outer membrane and allow other drugs better penetration into the bacterial periplasm and cytoplasm. Previously, we showed that SPR741 had this adjuvant effect with regard to rifampin; however, rifampin is often not used clinically because of easily acquired resistance. To find additional, appropriate clinical partners for SPR741 with respect to pulmonary and wound infections, we investigated tetracyclines and found a previously undocumented synergy with minocycline in vitro and in vivo in murine models of infection.

Modern combat-related injuries are often associated with acute polytrauma. As a consequence of severe combat-related injuries, a dysregulated immune response results in serious infectious complications. The gram-negative bacterium Pseudomonas aeruginosa is an opportunistic pathogen that often causes life-threatening bloodstream, lung, bone, urinary tract, and wound infections following combat-related injuries. The rise in the number of multidrug-resistant P. aeruginosa strains has elevated its importance to civilian clinicians and military medicine. Development of novel therapeutics and treatment options for P. aeruginosa infections is urgently needed. During the process of drug discovery and therapeutic testing, in vivo testing in animal models is a critical step in the bench-to-bedside approach, and required for Food and Drug Administration approval. Here, we review current and past literature with a focus on combat injury-relevant animal models often used to understand infection development, the interplay between P. aeruginosa and the host, and evaluation of novel treatments. Specifically, this review focuses on the following animal infection models: wound, burn, bone, lung, urinary tract, foreign body, and sepsis., (Published 2021. This article is a U.S. Government work and is in the public domain in the USA.)

Providencia rettgeri is an emerging opportunistic Gram-negative pathogen with reports of increasing antibiotic resistance. Pan-drug resistant (PDR) P. rettgeri infections are a growing concern, demonstrating a need for the development of alternative treatment options which is fueling a renewed interest in bacteriophage (phage) therapy. Here, we identify and characterize phage vB&#95;PreP&#95;EPr2 (EPr2) with lytic activity against PDR P. rettgeri MRSN 845308, a clinical isolate that carries multiple antibiotic resistance genes. EPr2 was isolated from an environmental water sample and belongs to the family Autographiviridae , subfamily Studiervirinae and genus Kayfunavirus , with a genome size of 41,261 base pairs. Additional phenotypic characterization showed an optimal MOI of 1 and a burst size of 12.3 ± 3.4 PFU per bacterium. EPr2 was determined to have a narrow host range against a panel of clinical P. rettgeri strains. Despite this fact, EPr2 is a promising lytic phage with potential for use as an alternative therapeutic for treatment of PDR P. rettgeri infections.

Explosive devices, either conventional or improvised, are common sources of injuries during combat, civil unrest, and terror attacks, resulting in trauma from exposure to blast. A blast wave (BW), a near-instantaneous rise in pressure followed by a negative pressure, propagates through the body in milliseconds and can affect physiology for days/months after exposure. Epidemiological data show that blast-related casualties result in significantly higher susceptibility to wound infections, suggesting long-lasting immune modulatory effects from blast exposure. The mechanisms involved in BW-induced immune changes are poorly understood. We evaluated the effects of BW on the immune system using an established murine model. Animals were exposed to BWs (using an Advanced Blast Simulator), followed by longitudinally sampling for 14 days. Blood, bone marrow, and spleen were analyzed for changes in the 1) complete blood count (CBC), and 2) composition of bone marrow cells (BMC) and splenocytes, and 3) concentrations of systemic cytokines/chemokines. Our data demonstrate that BW results in transient bone marrow failure and long-term changes in the frequency and profile of progenitor cell populations. Viability progressively decreased in hematopoietic stem cells and pluripotent progenitor cells. Significant decrease of CD4 + T cells in the spleen indicates reduced functionality of adaptive immune system. Dynamic changes in the concentrations of several cytokines and chemokines such as IL-1α and IL-17 occurred potentially contributing to dysregulation of immune response after trauma. This work lays the foundation for identifying the potential mechanisms behind BW's immunosuppressive effects to inform the recognition of this compromised status is crucial for the development of therapeutic interventions for infections to reduce recovery time of wounded patients injured by explosive devices., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Bergmann-Leitner, Bobrov, Bolton, Rouse, Heyburn, Pavlovic, Garry, Alamneh, Long, Swierczewski, Tyner, Getnet, Sajja and Antonic.)

Cefazolin is a first-line antibiotic to treat infection related to deployment-associated blast injuries. Prior literature demonstrated a 331% increase cefazolin liver area under the curve (AUC) in mice exposed to a survivable blast compared with controls. We repeated the experiment, validated the findings, and established a semimechanistic two-compartment pharmacokinetic (PK) model with effect compartments representing the liver and skin. We found that blast statistically significantly increased the pseudo-partition coefficient to the liver by 326% (95% confidence interval: 76-737%), which corresponds to the observed 331% increase in cefazolin liver AUC described previously. To a lesser extent, plasma AUC in blasted mice increased 14-45% compared with controls. Nevertheless, the effects of blast on cefazolin PK were transient, normalizing by 10 hours after the dose. It is unclear as to how this blast effect t emporally translates to humans; however, given the short-lived effect on PK, there is insufficient evidence to recommend cefazolin dosing changes based on blast overpressure injury alone. Clinicians should be aware that cefazolin may cause drug-induced liver injury with a single dose and the risk may be higher in patients with blast overpressure injury based on our findings. SIGNIFICANCE STATEMENT: Blast exposure significantly, but transiently, alters cefazolin pharmacokinetics in mice. The questions of whether other medications or potential long-term consequences in humans need further exploration., (U.S. Government work not protected by U.S. copyright.)

Post-traumatic stress disorder (PTSD) is a heterogeneous condition evidenced by the absence of objective physiological measurements applicable to all who meet the criteria for the disorder as well as divergent responses to treatments. This study capitalized on biological diversity observed within the PTSD group observed following epigenome-wide analysis of a well-characterized Discovery cohort (N = 166) consisting of 83 male combat exposed veterans with PTSD, and 83 combat veterans without PTSD in order to identify patterns that might distinguish subtypes. Computational analysis of DNA methylation (DNAm) profiles identified two PTSD biotypes within the PTSD+ group, G1 and G2, associated with 34 clinical features that are associated with PTSD and PTSD comorbidities. The G2 biotype was associated with an increased PTSD risk and had higher polygenic risk scores and a greater methylation compared to the G1 biotype and healthy controls. The findings were validated at a 3-year follow-up (N = 59) of the same individuals as well as in two independent, veteran cohorts (N = 54 and N = 38), and an active duty cohort (N = 133). In some cases, for example Dopamine-PKA-CREB and GABA-PKC-CREB signaling pathways, the biotypes were oppositely dysregulated, suggesting that the biotypes were not simply a function of a dimensional relationship with symptom severity, but may represent distinct biological risk profiles underpinning PTSD. The identification of two novel distinct epigenetic biotypes for PTSD may have future utility in understanding biological and clinical heterogeneity in PTSD and potential applications in risk assessment for active duty military personnel under non-clinician-administered settings, and improvement of PTSD diagnostic markers., (© 2020. The Author(s).)

Here, we describe genome sequences of 17 Pseudomonas aeruginosa phages, including therapeutic candidates. They belong to the families Myoviridae , Podoviridae , and Siphoviridae and six different genera. The genomes ranged in size from 42,788 to 88,805 bp, with G+C contents of 52.5% to 64.3% and numbers of coding sequences from 58 to 179.

Diabetes is a serious threat to global health and among the top 10 causes of death, with nearly half a billion people living with it worldwide. Treating patients with diabetes tend to become more challenging due to the progressive nature of the disease. The role and benefits of combination therapies for the management of type 2 diabetes are well-documented, while the comparative safety and efficacy among the different combination options have not been elucidated. We aimed to systematically synthesize the evidence on the comparative cardiovascular safety and efficacy of combination therapy with metformin-sodium-glucose cotransporter-2 inhibitors versus metformin-sulfonylureas in patients with type 2 diabetes. We searched MEDLINE-PubMed, Embase, Cochrane Library, and ClinicalTrials.gov up to 15 August 2019 without restriction in the year of publication. We included randomized controlled trials of patients with type 2 diabetes who were on metformin-sodium-glucose cotransporter-2 inhibitors or metformin-sulphonylureas combination therapy at least for a year. The primary endpoints were all-cause mortality and serious adverse events, and the secondary endpoints were cardiovascular mortality, non-fatal myocardial infarction, non-fatal stroke, hypoglycemia, and changes in glycated hemoglobin A1c (HbA1c), body weight, fasting plasma glucose, blood pressure, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol. We used a random-effects meta-analysis model to estimate mean differences for continuous outcomes and risk ratio for dichotomous outcomes. We followed PICOS description model for defining eligibility and the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) 2015 guidelines for reporting results. Of 3,190 citations, we included nine trials involving 10,974 participants. The pooled analysis showed no significant difference in all-cause mortality (risk ration [RR] = 0.93, 95% CI [0.52, 1.67]), serious adverse events (RR = 0.96, 95% CI [0.79, 1.17]) and adverse events (RR = 1.00, 95% CI [0.99, 1.02]) between the two, but in hypoglycemia (RR = 0.13, 95% CI [0.10, 0.17], P < 0.001). Participants taking metformin-sodium glucose cotransporter-2 inhibitors showed a significantly greater reduction in HbA1c (mean difference [MD] = - 0.10%, 95% CI [- 0.17, - 0.03], body weight (MD = - 4.57 kg, 95% CI [- 4.74, - 4.39], systolic blood pressure (MD = - 4.77 mmHg, 95% CI [- 5.39, - 4.16]), diastolic blood pressure (MD = - 2.07 mmHg, 95% CI [- 2.74, - 1.40], and fasting plasma glucose (MD = - 0.55 mmol/L, 95% CI [- 0.69, - 0.41]), p < 0.001. Combination therapy of metformin and sodium-glucose cotransporter-2 inhibitors is a safe and efficacious alternative to combination therapy of metformin and sulphonylureas for patients with type 2 diabetes who are at risk of cardiovascular comorbidity. However, there remains a need for additional long-term randomized controlled trials as available studies are very limited and heterogeneous.

Khat plant ( Catha edulis Forsk) is an evergreen perennial cash crop cultivated in east Africa, southwest Arabia, and Madagascar. The plant is known for its production of stimulant fresh leaves, and expanding as expense of other land uses for its short-term financial returns. We, therefore, developed allometric equations for estimating aboveground biomass and carbon (C) removal of khat grown in farmlands of Raya Valley, Northern Ethiopia. A total of 31 plant individuals were harvested destructively on the basis of their diameters and age ranges. The equations were parametrized using biometric variables such as basal diameter ( d 10 ), diameter at breast height ( d ), dominate height ( doh ) and mean height ( h ). Results of the analysis showed that, stem accounted for 58%, branch 32% and foliage 10% of the aboveground biomass (AGB). Commercial foliage biomass C removal ranged from 2.3 to 2.7 Mg ha -1 . The power equation, AGB = b 1 ×d 10 b2 ×doh b3 , was the best (highest ranked using goodness-of-fit statistics), explaining 96% of the variation in aboveground biomass ( p < 0.01) . Models comparisons showed that our best ranked equation (M6) improved the aboveground biomass estimate by 44% and 48 % that of generic and other species-site specific equations developed in the tropics, respectively. Thus, our best species-site specific equation developed in this study can accurately estimate aboveground of khat plant biomass in the study region., Competing Interests: The authors declare no conflict of interest., (© 2020 The Author(s).)

Background: Despite global containment measures to fight the coronavirus disease 2019 (COVID-19), the pandemic continued to rise, rapidly spread across the world, and resulting in 2.6 million confirmed cases and 185 061 deaths worldwide as of 23 April 2020. Yet, there are no approved vaccines or drugs to make the disease less deadly, while efforts are underway. Remdesivir, a nucleotide-analogue antiviral drug developed for Ebola, is determined to prevent and stop infections with COVID-19, while results are yet controversial. Here, we aim to conduct a systematic review and meta-analysis of randomised controlled trials (RCTs) to evaluate the efficacy of remdesivir in patients with COVID-19., Method and Analysis: We will search MEDLINE-PubMed, Embase, Cochrane Library, ClinicalTrials.gov and Google scholar databases for articles published as of 30 June 2020 and we will complete the study on 30 August 2020. We will follow the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) 2015 guidelines for the design and reporting of the results. We will include RCTs that assessed the efficacy of remdesivir versus placebo or standard of care. The primary endpoint will be time to clinical recovery. The secondary endpoints will be proportion of participants relieved from clinical symptoms defined at the time (in hours) from initiation of the study treatment, all-cause mortality, discharged date, frequency of respiratory progression and treatment-emergent adverse events. RevMan V.5.3 software will be used for statistical analysis. Random effects model will be carried out to calculate mean differences for continuous outcome data and risk ratio for dichotomous outcome data between remdesivir and placebo or standard of care., Ethics and Dissemination: There are no ethical considerations associated with this study as we will use publicly available data from previously published studies. We plan to publish results in open-access peer-reviewed journals and present at international and national conferences., Prospero Registration Number: CRD42020177953., Competing Interests: Competing interests: All review authors declare that they have no competing interests. The funder has no role in the design, syntheses and report of the study., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Life science research is moving quickly towards large-scale experimental designs that are comprised of multiple tissues, time points, and samples. Omic time-series experiments offer answers to three big questions: what collective patterns do most analytes follow, which analytes follow an identical pattern or synchronize across multiple cohorts, and how do biological functions evolve over time. Existing tools fall short of robustly answering and visualizing all three questions in a unified interface., Results: Functional Heatmap offers time-series data visualization through a Master Panel page, and Combined page to answer each of the three time-series questions. It dissects the complex multi-omics time-series readouts into patterned clusters with associated biological functions. It allows users to identify a cascade of functional changes over a time variable. Inversely, Functional Heatmap can compare a pattern with specific biology respond to multiple experimental conditions. All analyses are interactive, searchable, and exportable in a form of heatmap, line-chart, or text, and the results are easy to share, maintain, and reproduce on the web platform., Conclusions: Functional Heatmap is an automated and interactive tool that enables pattern recognition in time-series multi-omics assays. It significantly reduces the manual labour of pattern discovery and comparison by transferring statistical models into visual clues. The new pattern recognition feature will help researchers identify hidden trends driven by functional changes using multi-tissues/conditions on a time-series fashion from omic assays.

The experimental pathophysiology of organophosphorus (OP) chemical exposure has been extensively reported. Here, we describe an altered fecal bacterial biota and urine metabolome following intoxication with soman, a lipophilic G class chemical warfare nerve agent. Nonanesthetized Sprague-Dawley male rats were subcutaneously administered soman at 0.8 (subseizurogenic) or 1.0 (seizurogenic) of the 50% lethal dose (LD 50 ) and evaluated for signs of toxicity. Animals were stratified based on seizing activity to evaluate effects of soman exposure on fecal bacterial biota and urine metabolites. Soman exposure reshaped fecal bacterial biota by altering Facklamia , Rhizobium , Bilophila , Enterobacter , and Morganella genera of the Firmicutes and Proteobacteria phyla, some of which are known to hydrolyze OP chemicals. However, analogous changes were not observed in the bacterial biota of the ileum, which remained the same irrespective of dose or seizing status of animals after soman intoxication. However, at 75 days after soman exposure, the bacterial biota stabilized and no differences were observed between groups. Interestingly, in considering just the seizing status of animals, we found that the urine metabolomes were markedly different. Leukotriene C 4 , kynurenic acid, 5-hydroxyindoleacetic acid, norepinephrine, and aldosterone were excreted at much higher rates at 72 h in seizing animals, consistent with early multiorgan involvement during soman poisoning. These findings demonstrate the feasibility of using the dysbiosis of fecal bacterial biota in combination with urine metabolome alterations as forensic evidence for presymptomatic OP exposure temporally to enable administration of neuroprotective therapies of the future. IMPORTANCE The paucity of assays to determine physiologically relevant OP exposure presents an opportunity to explore the use of fecal bacteria as sentinels in combination with urine to assess changes in the exposed host. Recent advances in sequencing technologies and computational approaches have enabled researchers to survey large community-level changes of gut bacterial biota and metabolomic changes in various biospecimens. Here, we profiled changes in fecal bacterial biota and urine metabolome following a chemical warfare nerve agent exposure. The significance of this work is a proof of concept that the fecal bacterial biota and urine metabolites are two separate biospecimens rich in surrogate indicators suitable for monitoring OP exposure. The larger value of such an approach is that assays developed on the basis of these observations can be deployed in any setting with moderate clinical chemistry and microbiology capability. This can enable estimation of the affected radius as well as screening, triage, or ruling out of suspected cases of exposures in mass casualty scenarios, transportation accidents involving hazardous materials, refugee movements, humanitarian missions, and training settings when coupled to an established and validated decision tree with clinical features.

Introduction: Adverse drug interaction is a major cause of morbidity and mortality. Its occurrence is influenced by a multitude of factors. The influences of drug-drug interactions (DDIs) can be minimized through creation of awareness to health care professionals., Objective: The objective of this study was to assess DDIs in Ayder Comprehensive Specialized Hospital (ACSH)., Methodology: A retrospective study design was employed on patient prescriptions available in the outpatient department of pharmacy and filled from September 2016 to February 2017 in ACSH., Result: From the 600 prescription records assessed, the average number of drugs on single prescription was 2.73. Regarding the interaction observed 34 (9.63%) prescriptions with major drug-drug interaction, 210 (59.5%) moderate, 87 (24.65%) minor, and 22 (6.22%) unknown were identified. Age category showed significant association to affect the occurrence of DDIs and polypharmacy had statistically significant association with DDIs in bivariate analysis which was lost in adjusted OR., Conclusion: From the current study it can be concluded that nearly half of the prescription ordered in ACSH contained DDIs and from the prescription with interacting medications majority of them had moderate DDIs.

Background: Cellular function and diversity are orchestrated by complex interactions of fundamental biomolecules including DNA, RNA and proteins. Technological advances in genomics, epigenomics, transcriptomics and proteomics have enabled massively parallel and unbiased measurements. Such high-throughput technologies have been extensively used to carry out broad, unbiased studies, particularly in the context of human diseases. Nevertheless, a unified analysis of the genome, epigenome, transcriptome and proteome of a single human cell type to obtain a coherent view of the complex interplay between various biomolecules has not yet been undertaken. Here, we report the first multi-omic analysis of human primary naïve CD4+ T cells isolated from a single individual., Results: Integrating multi-omics datasets allowed us to investigate genome-wide methylation and its effect on mRNA/protein expression patterns, extent of RNA editing under normal physiological conditions and allele specific expression in naïve CD4+ T cells. In addition, we carried out a multi-omic comparative analysis of naïve with primary resting memory CD4+ T cells to identify molecular changes underlying T cell differentiation. This analysis provided mechanistic insights into how several molecules involved in T cell receptor signaling are regulated at the DNA, RNA and protein levels. Phosphoproteomics revealed downstream signaling events that regulate these two cellular states. Availability of multi-omics data from an identical genetic background also allowed us to employ novel proteogenomics approaches to identify individual-specific variants and putative novel protein coding regions in the human genome., Conclusions: We utilized multiple high-throughput technologies to derive a comprehensive profile of two primary human cell types, naïve CD4+ T cells and memory CD4+ T cells, from a single donor. Through vertical as well as horizontal integration of whole genome sequencing, methylation arrays, RNA-Seq, miRNA-Seq, proteomics, and phosphoproteomics, we derived an integrated and comparative map of these two closely related immune cells and identified potential molecular effectors of immune cell differentiation following antigen encounter.

Interleukin-17 (IL-17) belongs to a relatively new family of cytokines that has garnered attention as the signature cytokine of Th17 cells. This cytokine family consists of 6 ligands, which bind to 5 receptor subtypes and induce downstream signaling. Although the receptors are ubiquitously expressed, cellular responses to ligands vary across tissues. The cytokine family is associated with various autoimmune disorders including rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, asthma and psoriasis in addition to being implicated in the pathogenesis of cancer. In addition, this family plays a role in host defense against bacterial and fungal infections. The signaling mechanisms of the IL-17 family of proinflammatory cytokines are not well explored. In this study, we present a resource of literature-annotated reactions induced by IL-17. The reactions are catalogued under 5 categories, namely; molecular association, catalysis, transport, activation/inhibition and gene regulation. A total of 93 molecules and 122 reactions have been annotated. The IL-17 pathway is freely available through NetPath, a resource of signal transduction pathways previously developed by our group.

Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ∼ 69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes., (© 2014 by The American Society for Biochemistry and Molecular Biology, Inc.)

Anopheles gambiae has a well-adapted system for host localization, feeding, and mating behavior, which are all governed by neuronal processes in the brain. However, there are no published reports characterizing the brain proteome to elucidate neuronal signaling mechanisms in the vector. To this end, a large-scale mapping of the brain proteome of An. gambiae was carried out using high resolution tandem mass spectrometry, revealing a repertoire of >1800 proteins, of which 15% could not be assigned any function. A large proportion of the identified proteins were predicted to be involved in diverse biological processes including metabolism, transport, protein synthesis, and olfaction. This study also led to the identification of 10 GPCR classes of proteins, which could govern sensory pathways in mosquitoes. Proteins involved in metabolic and neural processes, chromatin modeling, and synaptic vesicle transport associated with neuronal transmission were predominantly expressed in the brain. Proteogenomic analysis expanded our findings with the identification of 15 novel genes and 71 cases of gene refinements, a subset of which were validated by RT-PCR and sequencing. Overall, our study offers valuable insights into the brain physiology of the vector that could possibly open avenues for intervention strategies for malaria in the future.

The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here we present a draft map of the human proteome using high-resolution Fourier-transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples, including 17 adult tissues, 7 fetal tissues and 6 purified primary haematopoietic cells, resulted in identification of proteins encoded by 17,294 genes accounting for approximately 84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading frames. This large human proteome catalogue (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.

Purpose: To optimize the combination of ionizing radiation and cellular immunotherapy using a preclinical autochthonous model of prostate cancer., Methods and Materials: Transgenic mice expressing a model antigen under a prostate-specific promoter were treated using a platform that integrates cone-beam CT imaging with 3-dimensional conformal therapy. Using this technology we investigated the immunologic and therapeutic effects of combining ionizing radiation with granulocyte/macrophage colony-stimulating factor-secreting cellular immunotherapy for prostate cancer in mice bearing autochthonous prostate tumors., Results: The combination of ionizing radiation and immunotherapy resulted in a significant decrease in pathologic tumor grade and gross tumor bulk that was not evident with either single-modality therapy. Furthermore, combinatorial therapy resulted in improved overall survival in a preventive metastasis model and in the setting of established micrometastases. Mechanistically, combined therapy resulted in an increase of the ratio of effector-to-regulatory T cells for both CD4 and CD8 tumor-infiltrating lymphocytes., Conclusions: Our preclinical model establishes a potential role for the use of combined radiation-immunotherapy in locally advanced prostate cancer, which warrants further exploration in a clinical setting., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Background: The FDA recently approved an anti-CTLA-4 antibody (Iplimumab) for the treatment of metastatic melanoma. This decision was based on Phase III results, which demonstrate that blocking this immune checkpoint provides a survival advantage in patients with advanced disease. As a single agent, ipilimumab is also being clinically evaluated in advanced (metastatic, castrate-resistant) prostate cancer and two randomized, placebo-controlled Phase III studies have recently completed accrual., Methods: We used a well-described genetically engineered mouse (GEM), autochronous prostate cancer model (Pro-TRAMP) to explore the relative sequencing and dosing of anti-CTLA-4 antibody when combined with a cell-based, GM-CSF-secreting vaccine (GVAX)., Results: Our results show that combined treatment results in a dramatic increase in effector CD8 T cells in the prostate gland, and enhanced tumor-antigen directed lytic function. These effects are maximized when CTLA-4 blockade is applied after, but not before, vaccination. Additional experiments, using models of metastatic disease, show that incorporation of low-dose cyclophosphamide into this combined treatment regimen results in an additional pre-clinical benefit., Conclusions: Together these studies define a combination regimen using anti-CTLA-4/GVAX immunotherapy and low-dose chemotherapy for potential translation to a clinical trial setting.

Tissue microarrays have become a valuable tool for high-throughput analysis using immunohistochemical labeling. However, the large majority of biochemical studies are carried out in cell lines to further characterize candidate biomarkers or therapeutic targets with subsequent studies in animals or using primary tissues. Thus, cell line-based microarrays could be a useful screening tool in some situations. Here, we constructed a cell microarray (CMA) containing a panel of 40 pancreatic cancer cell lines available from American Type Culture Collection in addition to those locally available at Johns Hopkins. As proof of principle, we performed immunocytochemical labeling of an epithelial cell adhesion molecule (Ep-CAM), a molecule generally expressed in the epithelium, on this pancreatic cancer CMA. In addition, selected molecules that have been previously shown to be differentially expressed in pancreatic cancer in the literature were validated. For example, we observed strong labeling of CA19-9 antigen, a prognostic and predictive marker for pancreatic cancer. We also carried out a bioinformatics analysis of a literature curated catalog of pancreatic cancer biomarkers developed previously by our group and identified two candidate biomarkers, HLA class I and transmembrane protease, serine 4 (TMPRSS4), and examined their expression in the cell lines represented on the pancreatic cancer CMAs. Our results demonstrate the utility of CMAs as a useful resource for rapid screening of molecules of interest and suggest that CMAs can become a universal standard platform in cancer research.

Thymic stromal lymphopoietin (TSLP) is a cytokine that plays diverse roles in the regulation of immune responses. TSLP requires a heterodimeric receptor complex consisting of IL-7 receptor α subunit and its unique TSLP receptor (gene symbol CRLF2) to transmit signals in cells. Abnormal TSLP signaling (e.g. overexpression of TSLP or its unique receptor TSLPR) contributes to the development of a number of diseases including asthma and leukemia. However, a detailed understanding of the signaling pathways activated by TSLP remains elusive. In this study, we performed a global quantitative phosphoproteomic analysis of the TSLP signaling network using stable isotope labeling by amino acids in cell culture. By employing titanium dioxide in addition to antiphosphotyrosine antibodies as enrichment methods, we identified 4164 phosphopeptides on 1670 phosphoproteins. Using stable isotope labeling by amino acids in cell culture-based quantitation, we determined that the phosphorylation status of 226 proteins was modulated by TSLP stimulation. Our analysis identified activation of several members of the Src and Tec families of kinases including Btk, Lyn, and Tec by TSLP for the first time. In addition, we report TSLP-induced phosphorylation of protein phosphatases such as Ptpn6 (SHP-1) and Ptpn11 (Shp2), which has also not been reported previously. Co-immunoprecipitation assays showed that Shp2 binds to the adapter protein Gab2 in a TSLP-dependent manner. This is the first demonstration of an inducible protein complex in TSLP signaling. A kinase inhibitor screen revealed that pharmacological inhibition of PI-3 kinase, Jak family kinases, Src family kinases or Btk suppressed TSLP-dependent cellular proliferation making them candidate therapeutic targets in diseases resulting from aberrant TSLP signaling. Our study is the first phosphoproteomic analysis of the TSLP signaling pathway that greatly expands our understanding of TSLP signaling and provides novel therapeutic targets for TSLP/TSLPR-associated diseases in humans.

Dicer is a ribonuclease whose major role is to generate mature microRNAs, although additional functions have been proposed. Deletion of Dicer leads to embryonic lethality in mice. To study the role of Dicer in adults, we generated mice in which administration of tamoxifen induces deletion of Dicer. Surprisingly, disruption of Dicer in adult mice induced lipid accumulation in the small intestine. To dissect the underlying mechanisms, we carried out miRNA, mRNA, and proteomic profiling of the small intestine. The proteomic analysis was done using mice metabolically labeled with heavy lysine (SILAC mice) for an in vivo readout. We identified 646 proteins, of which 80 were up-regulated >2-fold and 75 were down-regulated. Consistent with the accumulation of lipids, Dicer disruption caused a marked decrease of microsomal triglyceride transfer protein, long-chain fatty acyl-CoA ligase 5, fatty acid binding protein, and very-long-chain fatty acyl-CoA dehydrogenase, among others. We validated these results using multiple reaction monitoring (MRM) experiments by targeting proteotypic peptides. Our data reveal a previously unappreciated role of Dicer in lipid metabolism. These studies demonstrate that a systems biology approach by integrating mouse models, metabolic labeling, gene expression profiling, and quantitative proteomics can be a powerful tool for understanding complex biological systems.