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Natural language processing (NLP) has become an essential technique in various fields, offering a wide range of possibilities for analyzing data and developing diverse NLP tasks. In the biomedical domain, understanding the complex relationships between compounds and proteins is critical, especially in the context of signal transduction and biochemical pathways. Among these relationships, protein–protein interactions (PPIs) are of particular interest, given their potential to trigger a variety of biological reactions. To improve the ability to predict PPI events, we propose the protein event detection dataset (PEDD), which comprises 6823 abstracts, 39 488 sentences and 182 937 gene pairs. Our PEDD dataset has been utilized in the AI CUP Biomedical Paper Analysis competition, where systems are challenged to predict 12 different relation types. In this paper, we review the state-of-the-art relation extraction research and provide an overview of the PEDD's compilation process. Furthermore, we present the results of the PPI extraction competition and evaluate several language models' performances on the PEDD. This paper's outcomes will provide a valuable roadmap for future studies on protein event detection in NLP. By addressing this critical challenge, we hope to enable breakthroughs in drug discovery and enhance our understanding of the molecular mechanisms underlying various diseases. [ABSTRACT FROM AUTHOR]

Background: Taiwan has a substantial number of veterans, but knowledge regarding their emergency department (ED) visits during the coronavirus disease 2019 (COVID-19) pandemic remains limited. This study examined the characteristics of veterans' ED visits during Taiwan's COVID-19 epidemic. Methods: This was a cross-sectional study conducted at the ED of a large veteran medical center located in Taipei, Taiwan, from May 2018 to October 2021. We analyzed the numbers and features of visits in summer and autumn according to the first wave of the COVID-19 epidemic in Taiwan in 2021. Results: Medical institutions were positively associated with veteran status. Emergency department complaints of trauma (adjusted odds ratio [AOR] = 1.15, 95% CI: 1.06-1.25; summer P < .01) and chest pain/tightness (AOR = 1.65, 95% CI: 1.45-1.87; summer P < .01; AOR = 1.4, 95% CI: 1.26-1.55; P < .01) were associated with increased odds of being a veteran. Triage levels above 2 were positively associated with veteran status in the autumn model (AOR = 1.14, 95% CI: 1.07-1.22; P < .01). Patients hospitalized after ED visits were associated with reduced odds of veteran status (P < .01). Those who spent a long time in the ED were more likely to be veterans than those who spent a shorter time in the ED (P < .01). Veterans were less likely to visit the ED regardless of the time frame of the study period (P < .01), except during the COVID-19 outbreak in the autumn (2019-2020). Conclusions: The distinctions in ED visits highlighted the individuality of veterans' medical needs. Our findings suggest that the veteran medical system can add to the focus on improving senior-friendly care, fall prevention, quality of life of institutionalized veterans, access for homeless veterans, and care for ambulatory care–sensitive conditions. [ABSTRACT FROM AUTHOR]

Objectives RA is an autoimmune disease characterized by chronic inflammation and joint destruction. Biologics are crucial to achieving treat-to-target goals in patients with RA. The global spread and continuous variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitate the monitoring of variant-specific humoral responses post-vaccination. The aim of this study was to investigate how different biologic treatments for vaccinated RA patients might affect their neutralizing antibodies against multiple SARS-CoV-2 variants. Methods We recruited RA patients who had received three doses of conventional SARS-CoV-2 vaccines and were treated with various biologics, e.g. TNF inhibitor (etanercept), IL-6 inhibitor (tocilizumab), CTLA4-Ig (abatacept) or anti-CD20 (rituximab). Serum samples were used to profile the binding and neutralizing antibodies using our own SARS-CoV-2 variant (CoVariant) protein array, developed previously. Results Compared with healthy controls, only RA therapy with rituximab showed a reduction in neutralizing antibodies capable of targeting spike proteins in SARS-CoV-2 wild-type and most variants. This reduction was not observed in binding antibodies against SARS-CoV-2 wild-type or its variants. Conclusion After receiving three doses of SARS-CoV-2 vaccination, RA patients who underwent rituximab treatment generated sufficient antibodies but exhibited lower neutralizing activities against wild-type and multiple variants, including current Omicron. Other biological DMARDs, e.g. TNF inhibitor, IL-6 inhibitor and CTLA4-Ig, did not show obvious inhibition. [ABSTRACT FROM AUTHOR]

Background Acute kidney injury (AKI) is associated with an increased incidence of poor liver graft and renal outcomes in patients who have undergone liver transplantation (LT). To date, no comprehensive study has compared patients with and without post-LT AKI and analyzed patients who recovered from AKI versus those who did not. Methods Patients who received living LT between January 2003 and January 2019 were enrolled. We diagnosed and classified AKI patients based on AKI-KDIGO guidelines by increment of creatinine after surgery when compared with serum creatinine on the day of surgery. The recovered AKI subgroup included recipients whose estimated glomerular filtration rate (eGFR) recovered more than 90% of baseline eGFR within 90 days after surgery. The risk of chronic kidney disease (CKD; eGFR <60 mL/min/1.73 m2) was investigated. Results A total of 392 patients, 77.3% men and mean ± standard deviation age 54.1 ± 8.4 years, met the eligible criteria and were divided into two groups (AKI vs non-AKI) and 243 (62%) patients developed AKI within 7 days after surgery. Compared with the non-AKI group, the AKI group was associated with an adjusted hazard ratio of 1.55 (95% CI 1.12–2.14) for the risk of incident CKD. Among AKI patients, 160 (65.8%) patients recovered renal function and 83 (34.2%) patients did not. Compared with the non-AKI group, the AKI non-recovery group was associated with an adjusted hazard ratio of 2.87 (95% CI 1.95–4.21) for the risk of incident CKD, while the AKI recovery group had no significant difference in the adjusted risk of incident CKD. Conclusions Post-LT AKI is associated with subsequent risk of CKD development. Taking into account recovery status, AKI was no longer associated with a higher risk of CKD if renal function recovered within 90 days after surgery. Identification and implementation of targeted and individualized therapies for patients at risk for AKI, particularly non-recovery AKI, is of paramount importance to reduce incident CKD during follow-up. [ABSTRACT FROM AUTHOR]

Recent studies have increasingly pointed to microRNAs (miRNAs) as the agent of gene regulatory network (GRN) stabilization as well as developmental canalization against constant but small environmental perturbations. To analyze mild perturbations, we construct a Dicer-1 knockdown line (dcr-1 KD) in Drosophila that modestly reduces all miRNAs by, on average, ∼20%. The defining characteristic of stabilizers is that, when their capacity is compromised, GRNs do not change their short-term behaviors. Indeed, even with such broad reductions across all miRNAs, the changes in the transcriptome are very modest during development in stable environment. By comparison, broad knockdowns of other regulatory genes (esp. transcription factors) by the same method should lead to drastic changes in the GRNs. The consequence of destabilization may thus be in long-term development as postulated by the theory of canalization. Flies with modest miRNA reductions may gradually deviate from the developmental norm, resulting in late-stage failures such as shortened longevity. In the optimal culture condition, the survival to adulthood is indeed normal in the dcr-1 KD line but, importantly, adult longevity is reduced by ∼90%. When flies are stressed by high temperature, dcr-1 KD induces lethality earlier in late pupation and, as the perturbations are shifted earlier, the affected stages are shifted correspondingly. Hence, in late stages of development with deviations piling up, GRN would be increasingly in need of stabilization. In conclusion, miRNAs appear to be a solution to weak but constant environmental perturbations. [ABSTRACT FROM AUTHOR]

Portal vein cannulation is a very rare complication of endoscopic retrograde cholangiopancreatography (ERCP). In most reported cases, the event was managed safely with immediate catheter, guidewire withdrawn and procedure termination. Here, we report an unusual case of portobiliary fistula created during ERCP. To our knowledge, this is the first report of such case managed with immediate surgical biliary exposure. [ABSTRACT FROM AUTHOR]

The Red Queen hypothesis depicts evolution as the continual struggle to adapt. According to this hypothesis, new genes, especially those originating from nongenic sequences (i.e. de novo genes), are eliminated unless they evolve continually in adaptation to a changing environment. Here, we analyze two Drosophila de novo miRNAs that are expressed in a testis-specific manner with very high rates of evolution in their DNA sequence. We knocked out these miRNAs in two sibling species and investigated their contributions to different fitness components. We observed that the fitness contributions of miR-975 in Drosophila simulans seem positive, in contrast to its neutral contributions in D. melanogaster , whereas miR-983 appears to have negative contributions in both species, as the fitness of the knockout mutant increases. As predicted by the Red Queen hypothesis, the fitness difference of these de novo miRNAs indicates their different fates. [ABSTRACT FROM AUTHOR]

Natural language processing (NLP) is widely applied in biological domains to retrieve information from publications. Systems to address numerous applications exist, such as biomedical named entity recognition (BNER), named entity normalization (NEN) and protein–protein interaction extraction (PPIE). High-quality datasets can assist the development of robust and reliable systems; however, due to the endless applications and evolving techniques, the annotations of benchmark datasets may become outdated and inappropriate. In this study, we first review commonlyused BNER datasets and their potential annotation problems such as inconsistency and low portability. Then, we introduce a revised version of the JNLPBA dataset that solves potential problems in the original and use state-of-the-art named entity recognition systems to evaluate its portability to different kinds of biomedical literature, including protein–protein interaction and biology events. Lastly, we introduce an ensembled biomedical entity dataset (EBED) by extending the revised JNLPBA dataset with PubMed Central full-text paragraphs, figure captions and patent abstracts. This EBED is a multi-task dataset that covers annotations including gene, disease and chemical entities. In total, it contains 85000 entity mentions, 25000 entity mentions with database identifiers and 5000 attribute tags. To demonstrate the usage of the EBED, we review the BNER track from the AI CUP Biomedical Paper Analysis challenge. Availability: The revised JNLPBA dataset is available at https://iasl-btm.iis.sinica.edu.tw/BNER/Content/Re vised_JNLPBA.zip. The EBED dataset is available at https://iasl-btm.iis.sinica.edu.tw/BNER/Content/AICUP _EBED_dataset.rar. Contact: Email: thtsai@g.ncu.edu.tw , Tel. 886-3-4227151 ext. 35203, Fax: 886-3-422-2681 Email: hsu@iis.sinica.edu.tw , Tel. 886-2-2788-3799 ext. 2211, Fax: 886-2-2782-4814 Supplementary information: Supplementary data are available at Briefings in Bioinformatics online. [ABSTRACT FROM AUTHOR]

Mapping of disease incidence has long been of importance to epidemiology and public health. In this paper, we consider identification of clusters of spatial units with elevated disease rates and develop a new approach that estimates the relative disease risk in association with potential risk factors and simultaneously identifies clusters corresponding to elevated risks. A heterogeneity measure is proposed to enable the comparison of a candidate cluster and its complement under a pair of complementary models. A quasi‐likelihood procedure is developed for estimating the model parameters and identifying the clusters. An advantage of our approach over traditional spatial clustering methods is the identification of clusters that can have arbitrary shapes due to abrupt or noncontiguous changes while accounting for risk factors and spatial correlation. Asymptotic properties of the proposed methodology are established and a simulation study shows empirically sound finite‐sample properties. The mapping and clustering of enterovirus 71 infections in Taiwan are carried out for illustration. [ABSTRACT FROM AUTHOR]

The aim of the study was to estimate organ dose rate reduction to a female anthropomorphic phantom, which simulated the cardiologist, during percutaneous coronary interventions (PCI) when the patient's arm support was covered with 0.4-mm lead foil. Organ dose rates were determined using five radiation detectors inserted into the left eye, left thyroid, left breast, left liver lobe and uterus of the phantom. A male anthropomorphic phantom was placed on the examination table of an angiography system. Heart images of the patient phantom were acquired under 10 gantry angulations typical for PCI. The lead-covered arm support did not interfere with any of the cardiac images. The median organ dose rate reductions to the left eye, left thyroid, left breast, left liver lobe and uterus were 7.8, 36.0, 28.8, 35.7 and 33.5%, respectively. The lead-covered arm support substantially reduced scattered radiation to the female cardiologist without interfering with clinical environments. [ABSTRACT FROM AUTHOR]

Background: The form of microsatellite instability (MSI) affecting tetranucleotide repeats known as elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) has emerged as a new potential biomarker in multiple cancers. In colorectal cancer (CRC), the correlation between EMAST and MSI mutations remain inconclusive. Materials and Methods: We evaluated 1,505 patients with CRC using five EMAST markers (D20S82, D20S85, D8S321, D9S242, and MYCL1) and the Bethesda panel of MSI markers. Most commonly, mutations involved in CRCs were identified by MassArray Assay, and DNA repair genes were analyzed by next‐generation sequencing. Clinical characteristics and prognostic relevance were correlated with EMAST and MSI. Results: Tumors that were EMAST positive and MSI high (MSI‐H) were detected in 159 (10.6%) and 154 (10.2%) of 1,505 patients with CRC. Patients were divided into four groups according to EMAST and MSI status (EMAST‐positive and MSI‐H, EMAST‐positive and microsatellite‐stable [MSS], EMAST‐negative and MSI‐H, and EMAST‐negative and MSS). The EMAST‐positive and MSI‐H group was associated with female predominance, higher prevalence of proximal colon tumors, early stage tumors, poorly differentiated tumors, mucinous histology, and higher incidence of mutations in PI3KCA, BRAF, TGFBR, PTEN, and AKT1 compared with other groups. Furthermore, compared with only EMAST‐positive tumors or only MSI‐H tumors, tumors that were both EMAST‐positive and MSI‐H had a higher frequency of MLH1, MSH3, MSH6, PMS2, and EXO1 gene mutations. Finally, the presence of EMAST‐positive and MSI‐H tumors was a good prognostic indicator in CRC. Conclusion: High mutations in several DNA repair genes in EMAST‐positive and MSI‐H tumors suggest that this subtype of CRC might be more suitable for treatment with immune therapy. Implications for Practice: Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) is a unique molecular subtype of colorectal cancer (CRC). The current study demonstrated that the EMAST‐positive and MSI‐high (MSI‐H) group was associated with female predominance, higher prevalence of proximal colon tumors, early stage tumors, poorly differentiated tumors, mucinous histology, and higher incidence of mutations in PI3KCA, BRAF, TGFBR, PTEN, and AKT1 compared with other groups. Most importantly, high mutations in DNA repair genes and MSI‐related genes in EMAST‐positive and MSI‐H tumors suggest that this subtype of CRC might be more suitable for treatment with immune therapy compared with MSI‐H tumors alone. EMAST (elevated microsatellite alterations at selected tetranucleotide repeats) is a potential biomarker for many cancer types. This article compares clinical and tumor‐specific factors in cases of colorectal cancer evaluated using both EMAST markers and the Bethesda panel of markers of microsatellite instability mutations. [ABSTRACT FROM AUTHOR]

Food web and gene regulatory networks (GRNs) are large biological networks, both of which can be analyzed using the May–Wigner theory. According to the theory, networks as large as mammalian GRNs would require dedicated gene products for stabilization. We propose that microRNAs (miRNAs) are those products. More than 30% of genes are repressed by miRNAs, but most repressions are too weak to have a phenotypic consequence. The theory shows that (i) weak repressions cumulatively enhance the stability of GRNs, and (ii) broad and weak repressions confer greater stability than a few strong ones. Hence, the diffuse actions of miRNAs in mammalian cells appear to function mainly in stabilizing GRNs. The postulated link between mRNA repression and GRN stability can be seen in a different light in yeast, which do not have miRNAs. Yeast cells rely on non-specific RNA nucleases to strongly degrade mRNAs for GRN stability. The strategy is suited to GRNs of small and rapidly dividing yeast cells, but not the larger mammalian cells. In conclusion, the May–Wigner theory, supplanting the analysis of small motifs, provides a mathematical solution to GRN stability, thus linking miRNAs explicitly to 'developmental canalization'. [ABSTRACT FROM AUTHOR]

Background The genetic background of patients with hemoglobin (Hb) H disease in Taiwan has been investigated; however, the clinical features and treatment outcomes were not reported. Objective To analyze the clinical features and genotypes of patients with HbH who reside in Taiwan. Methods We conducted a retrospective analysis of the clinical and molecular characteristics of 38 patients with HbH disease who were undergoing treatment at Kaohsiung Medical University Hospital, Taiwan. Results Initial Hb levels were lower and the numbers of patients requiring iron-chelation therapy were higher in the nondeletional HbH group than in the deletional HbH group (P <.05). Compared with the healthy population, the patients with HbH disease exhibited short body length, low body weight, and low body mass index (BMI). Conclusions Patients with nondeletional HbH disease had lower Hb levels and a higher requirement for splenectomy and iron-chelation therapy than did those with deletional HbH disease. Also, growth status was compromised in patients with HbH disease. [ABSTRACT FROM AUTHOR]

Arsenic and its compounds are toxic environmental pollutants and known carcinogens. We investigated here the mechanism of arsenite-induced damage in renal cells. Treating human embryonic kidney cells (HEK293) with sodium arsenite reduces cell viability in a dose- and time-dependent manner. The decline of cell viability is due to apoptotic death since arsenite treatment reduces Akt activity and the Bcl2 level but increases caspase 3 activity and the cytochrome c level. These effects can be reverted by the addition of an apoptosis inhibitor. PTEN, the upstream negative regulator of Akt activity, was also reduced with arsenite treatment. Noticeably, PTEN markedly increased in the insoluble fraction of the cells, suggesting a cell failure in removing the damaged proteins. Arsenite treatment activates a variety of signaling factors. Among them, ERK and JNK are associated with autophagy via regulating the levels of LC3 and p62. With arsenite administration, the LC3 and p62 levels increased. However, lysosomal activity was decreased and led to the decline of autophagic activity. The addition of rapamycin, the mTOR inhibitor, activated the autophagic pathway that accelerated the removal of damaged proteins. The recovery of autophagy increased the viability of arsenite-treated cells. Similar to rapamycin treatment, the knockdown of mTOR expression also enhanced the viability of arsenite-treated cells. Both rapamycin treatment and mTOR knockdown enhanced ERK activity further, but reduced JNK activity and the p62 level in arsenite-treated cells. Lysosomal activity increased with the depletion of mTOR, indicating an increase of autophagic activity. These results reveal the critical role of mTOR in regulating the cell fate of arsenite-exposed renal cells. [ABSTRACT FROM AUTHOR]

Level Of Evidence5: [ABSTRACT FROM AUTHOR]

Each animal microRNA (miRNA) targets many genes for repression. Down-regulation of most of these targets is weak and has no detectable individual phenotypic effect. Whether this extensive weak repression is biologically relevant is a central issue in the debate on miRNA functionality. In the "small (target) pool" view, weak repression is nonfunctional and should be gradually removed during evolution. However, since the selective advantage of removing individual targets is small, testing this hypothesis is a challenge. We propose a novel approach by using miRNAs we call twin-miRs, which produce two mature products from the hairpin of the same miRNA precursor. Loss of the minor miR partner would affect all its targets and thus could be visible to selection. Since the minor miRs repress all their targets weakly, the "small pool" hypothesis would predict the elimination of twin-miRs over time. Surveying and sequencing 45 small RNA libraries in Drosophila , we found that nearly 40% of miRNAs produce twin-miRs. The minor forms are expressed in nontrivial abundance and repress their targets weakly. Interestingly, twin-miRs are often evolutionarily old, highly conserved, and comparable to solo-miRs in expression. Since there is no measurable trend toward reduction in target pool size, we conclude that at least some of the weak repression interactions are functional. A companion study using the May–Wigner theory of network stability suggests that distributed weak repression cumulatively contributes to stability of gene regulatory networks. [ABSTRACT FROM AUTHOR]

Background. Relapsed or refractory mantle cell lymphoma (MCL) has a poor prognosis. The best outcome is achieved in patients who have a partial or complete response to salvage treatment and proceed to allogeneic stem cell transplant. Patients and Methods. Twenty-one patients were given a combination regimen of bortezomib, cyclophosphamide, and rituximab at MD Anderson Cancer Center as part of a single-arm, prospective, open-label phase II clinical trial. The median age was 66 years, with a median number of prior treatments of three. Sixty-seven percent had failed intensive chemoimmunotherapy and 43% were intermediate/high risk according to the MCL international prognostic index score, with a median Ki-67 proliferation index of 45% in those who were tested. Results. The rates of overall and complete response achieved were 74% and 42%, respectively, with median progression-free and overall survivals of 9 months and 36.4months, respectively. The regimen's toxicity profile was acceptable; only 25% of the cycles resulted in grade 3 or 4 neutropenia or thrombocytopenia, and only 3% of cycles produced grade 3-4 fatigue. There were no episodes of grade 3-4 neuropathy. Conclusion. The combination of bortezomib with cyclophosphamide and rituximab is an effective and well-tolerated regimen in patients with relapsed/refractory MCL. Because of its low toxicity, future combinations of this regimen with other promising drugs that have different mechanisms of action offer a realistic possibility that may improve outcomes for patients who have MCL. [ABSTRACT FROM AUTHOR]

In applying scan statistics for public health research, it would be valuable to develop a detection method for multiple clusters that accommodates spatial correlation and covariate effects in an integrated model. In this article, we connect the concepts of the likelihood ratio (LR) scan statistic and the quasi-likelihood (QL) scan statistic to provide a series of detection procedures sufficiently flexible to apply to clusters of arbitrary shape. First, we use an independent scan model for detection of clusters and then a variogram tool to examine the existence of spatial correlation and regional variation based on residuals of the independent scan model. When the estimate of regional variation is significantly different from zero, a mixed QL estimating equation is developed to estimate coefficients of geographic clusters and covariates. We use the Benjamini-Hochberg procedure (1995) to find a threshold for p-values to address the multiple testing problem. A quasi-deviance criterion is used to regroup the estimated clusters to find geographic clusters with arbitrary shapes. We conduct simulations to compare the performance of the proposed method with other scan statistics. For illustration, the method is applied to enterovirus data from Taiwan. [ABSTRACT FROM AUTHOR]

Objectives: Mantle cell lymphoma (MCL) may present de novo or undergo progression to a clinically aggressive variant, known as a blastoid or pleomorphic variant. We report an unusual case of classic MCL in a 78-year-old man with a typical immunophenotype, including CD5 positivity, who subsequently relapsed with CD5-negative pleomorphic variant MCL.Methods: Biopsy specimens were evaluated using Wright-Giemsa-stained or H&E-stained sections, flow cytometry, immunohistochemistry, conventional cytogenetic, next-generation sequencing, and fluorescence in situ hybridization.Results: The patient continued to be refractory to intensive chemotherapy and radiation therapy. Initial conventional cytogenetic analysis showed a complex karyotype with amplification of the CCND1-IGH fusion gene on the der(14): 44, Y, t(X;2)(p22.3;q21), del(2)(p21), del(6)(p23), add(7)(p22),-9, del(9)(p22), add(11)(q13),-13, add(14)(p11.2), der(14)t(11;14)(q13;q32)hsr(14)(q32), add(18)(q23), add(21)(p11.1),-22,+mar[12]. A repeat biopsy revealed MCL, pleomorphic variant, with loss of CD5 expression and extra copies of the MYC CONCLUSIONS: CCND1-IGH fusion-amplification with MYC copy number gain is extremely rare and may play a role in disease progression in a subset of MCL cases. [ABSTRACT FROM AUTHOR]

ALL is a malignant disorder and the disease relapse also exhibit high mortality to child. In this study, we demonstrated that Wls was highly expressed and correlated with disease relapse and survival outcome in BCP ALL.B-cell precursor acute lymphoblastic leukemia (BCP ALL) is the most common childhood leukemia, with a cure rate of 80%. Nevertheless, disease relapse is the most important prognostic factor for the disease outcome. We aimed to elucidate the role of Wnt secretion-regulating protein, Wntless (Wls)/GPR177, on disease outcome in pediatric patients with BCP ALL, and assess its pathogenetic role in the regulation of the disease. Wls expression was characterized and correlated with Wnt pathway signaling in the bone marrow leukemia cells isolated from 44 pediatric patients with BCP ALL. The overexpression of Wls was detected in leukemia cells and was significantly correlated with the disease relapse and poor survival in the patients. The high expression of Wls also correlated with the Wnt expression and consequent downstream signaling activation, which was shown to provide essential proliferation, transformation and anti-apoptotic activity during leukemogenesis. These results indicated that Wls played an essential role in disease relapse and poor survival in patients with BCP ALL. Therefore, Wls may provide a potential future therapeutic target, particularly for patients who do not respond to existing therapies and suffer relapse. [ABSTRACT FROM AUTHOR]

Objective To study the effectiveness of a very brief advice (<30 s) on smoking cessation. Design A ‘proof-of-principle’ single-blind, randomized controlled trial (RCT). Setting Medical outpatient clinics of a general hospital in Guangzhou, China. Participants One hundred and twenty-six male current smokers randomly allocated into an intervention (n = 74) and a control group (n = 52). Intervention A health warning by physicians that half of all smokers would be killed by smoking, an advice to quit immediately and referral to a cessation clinic. The control group received none. Outcomes Primary: seven-day quitting point prevalence at 6 months. Secondary: 7-day point prevalence at 1, 3 and 12 months, sustained abstinence at 3, 6 and 12 months, smoking reduction by half and cessation clinic attendance. Results By intention-to-treat analysis, 7-day quitting point prevalence rates at four follow-ups were 27.0, 23.0, 21.6 and 18.9% in the intervention group, compared with 5.8, 3.8, 5.8 and 5.8% in the control group (first three P < 0.05). At 3, 6 and 12 months, sustained abstinence prevalence rates were 18.9, 17.6 and 14.9% versus 3.8, 3.8 and 3.8% (P = 0.035, 0.046, 0.074). More smokers in the intervention group had reduced smoking. Almost no participants attended the cessation clinic. Conclusion Our findings support the need for large RCTs on minimal interventions with the ‘one in two’ warning. [ABSTRACT FROM AUTHOR]

Refractory anemia with ring sideroblasts associated with marked thrombocytosis (RARS-T) is a provisional entity in the current World Health Organization classification and is thought to be a myelodysplastic/myeloproliferative neoplasm (MDS/MPN). We analyzed 18 cases of RARS-T. All patients had thrombocytosis (platelet count, 515-1,100 × 10(3)/μL [515-1,100 × 10(9)/L]) and anemia (hemoglobin level, 7.2-12.6 g/dL [72-126 g/L]). Three patients had mild leukocytosis (WBC count, 3,900-16,300/μL [3.9-16.3 × 10(9)/L]). Ring sideroblasts were 8% to 75% in the bone marrow. Megakaryocytes showed a spectrum of morphologic findings. JAK2(V617F) was identified in 9 of 15 cases, including 7 of 9 with thrombocytosis (platelet count, >600 × 10(3)/μL [600 × 10(9)/L]) and 1 with 8% ring sideroblasts. The MPL(W515L) mutation was not detected (n = 9). We conclude that RARS-T is a pathogenetically heterogeneous group of limited diagnostic usefulness. Approximately 60% of cases carry JAK2(V617F)and seem to be closer to an MPN in which ring sideroblasts may be a secondary phenomenon. The remaining cases usually lack the JAK2(V617F)mutation, have a platelet count less than 600 × 10(3)/μL (600 × 10(9)/L), and may represent an MDS or MPN with thrombocytosis of unknown mechanisms. [ABSTRACT FROM AUTHOR]

Waldenström macroglobulinemia (WM) is currently defined as lymphoplasmacytic lymphoma involving bone marrow (BM) associated with a serum IgM paraprotein. WM is typically composed of small lymphocytes, plasmacytoid lymphocytes, and plasma cells in variable proportions, which can change after therapy. In this study, we assessed 41 WM cases that required chemotherapy, 39 showing persistent disease in restaging BM specimens. In 10 cases, there was persistent monotypic plasmacytosis in BM in the absence of demonstrable monotypic B cells. The monotypic plasma cells represented 0.5% to 46% of the cellularity and persisted 1 to 50 months after the last course of chemotherapy. The plasma cells were best quantified by immunohistochemical analysis on paraffin sections. We conclude that WM can persist as a pure plasma cell population after therapy. This finding has implications for the immunophenotypic assessment of WM after therapy and may explain persistent IgM paraproteinemia in patients with WM with no evidence of a clonal B-lymphocyte population. [ABSTRACT FROM AUTHOR]

Primary myelofibrosis (PMF) is a myeloproliferative neoplasm that may display a variable degree of cytopenia and dysplasia sometimes difficult to distinguish from myelodysplastic syndrome with myelofibrosis (MDS-MF). We reviewed flow cytometric features of bone marrow from 70 cases of PMF and compared them with those from 17 cases of MDS-MF and 20 nonneoplastic control cases. The results were correlated with JAK2(V617F) and cytogenetic findings. Granulocytes and monocytes from PMF cases exhibited multiple dysplastic features overlapping with those of MDS-MF at a comparable or higher frequency: low side scattering, aberrant CD56 expression in granulocytes and monocytes, and an abnormal CD13/CD16 maturation pattern. Unique to PMF was the small granulocyte size compared with that of MDS-MF and control cases. Although the percentage of CD56+ granulocytes and monocytes did not correlate with JAK2(V617F) or cytogenetic abnormalities, a subset analysis of 36 cases revealed that median fluorescence intensity of CD56 expression correlated positively with the presence of cytogenetic abnormalities. Our findings indicate that although there is considerable overlap between PMF and MDS-MF, the smaller granulocytes observed in PMF are a useful distinguishing feature. [ABSTRACT FROM AUTHOR]

To determine if therapy-related acute myeloid leukemia (t-AML) with t(8;21)(q22;q22) [t-AML-t(8;21)] harbors similar characteristic clinicopathologic features as de novo AML-t(8;21) (q22;q22), we studied 13 cases of t-AML-t(8;21) and 38 adult cases of de novo AML-t(8;21) diagnosed and treated at our hospital (1995-2008). Of 13 t-AML-t(8;21) cases, 11 had previously received chemotherapy with or without radiation for malignant neoplasms and 2 received radiation alone. The median latency to t-AML onset was 37 months (range, 11-126 months). Compared with patients with de novo AML-t(8;21), patients with t-AML-t(8;21) were older (P = .001) and had a lower WBC count (P = .039), substantial morphologic dysplasia, and comparable CD19/CD56 expression. The AML1-ETO (RUNX1-RUNX1T1) fusion was demonstrated in all 10 cases assessed. Class I mutations analyzed included FLT3 (0/10 [0%]), RAS (0/10 [0%]), JAK2 V617 (0/11 [0%]), and KIT (4/11 [36%]). With a median follow-up of 13 months, 10 patients with t-AML-t(8;21) died; the overall survival was significantly inferior to that of patients with de novo AML-t(8;21) (19 months vs not reached; P = .002). These findings suggest that t-AML-t(8;21) shares many features with de novo AML-t(8;21)(q22;q22), but affected patients have a worse outcome. [ABSTRACT FROM AUTHOR]

: Until recently, environmental factors were considered of greatest importance in the etiology of esophageal cancer. Recent studies, however, have suggested that genetic factors also have a role. : Since no formal genetic study of this cancer has been previously reported, we carried out a statistical analysis to determine how important genetic factors are in the etiology of esophageal cancer in high-incidence areas of North China. : Using a logistic regressive model, we performed a segregation analysis on 221 high-risk nuclear families from the Yaocun Commune, Linxian, Henan Province of China, with at least one affected family member and with all offspring aged 40 years or older. Three models, the mendelian, the environmental, and the no-transmission models, were each compared with the general-transmission model that incorporated both genetic and environmental factors. : According to Akaike's Information Criterion, the mendelian model provided the best fit for the data. By the chi-square test, the mendelian inheritance model was not rejected, but the environmental and the no-transmission models were both rejected. : The segregation analysis indicated an autosomal recessive mendelian inheritance, with the alleged mendelian gene present at a frequency of 19%, causing 4% of this population to be predisposed to develop esophageal cancer. Large, unmeasured, residual familial factors, however, were also significant. : Both an autosomal recessive gene and unexplained environmental factors appear to be important in the etiology of esophageal cancer in the subpopulation studied. [J Natl Cancer Inst 84: 771–776, 1992] [ABSTRACT FROM PUBLISHER]

Summary: Identifying biological functions and molecular networks in a gene list and how the genes may relate to various topics is of considerable value to biomedical researchers. Here, we present a web-based text-mining server, GenCLiP 2.0, which can analyze human genes with enriched keywords and molecular interactions. Compared with other similar tools, GenCLiP 2.0 offers two unique features: (i) analysis of gene functions with free terms (i.e. any terms in the literature) generated by literature mining or provided by the user and (ii) accurate identification and integration of comprehensive molecular interactions from Medline abstracts, to construct molecular networks and subnetworks related to the free terms.Availability and implementation: http://ci.smu.edu.cn.Contact: zxhuang@smu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

The article discussed the study about the treatment of lung adenocarcinoma through RNA-sequencing prognostic signature. Topics discussed include the use of the Cancer Genome Atlas (TCGA) lung adenocarcinoma data set, the four-gene signature generated in the Stepwise regression and the risk stratification ability of the four-gene signature on patients with lung adenocarcinoma.

Background: Human neutrophil peptides (HNPs) are small cationic proteins primarily released from activated and degranulated neutrophils. HNPs function to inhibit bacteria, virus, fungi, and parasites. Additionally, HNPs are prothrombotic by enhancing platelet aggregation and fibrin formation, and inhibiting proteolytic cleavage of von Willebrand factor (VWF) by ADAMTS13. However, the role of HNPs in inhibition of thrombus formation under more physiological conditions (eg, under flow) has not been determined.Objective: To investigate the effects of synthetic HNP1 on platelet adhesion/aggregation on VWF/collagen surface under arterial shears.Methods: Whole blood was obtained from C57/BL6 wild type and Adamts13–/– mice, and anticoagulated with a potent thrombin inhibitor D-phenylalanyl-L-prolyl-L-arginine chloromethyl ketone (PPACK) and PGE1, and platelets were labeled with FITC antimouse CD41 IgG. After incubation with varying concentrations of purified and synthetic HNP1 for 30 minutes, the whole-blood samples were then perfused through a fibrillar collagen-coated surface in a microfluidic system at 100 dyne/cm2 for 180 seconds. The rate and extent of accumulation of platelets were determined under inverted fluorescent microscope at a 4-second interval. The images were analyzed offline with Montage to evaluate the area of platelet coverage over time. This process was repeated with the addition of N-ethylmaleimide (NEM) or NEM-treated synthetic HNP1 to the samples to probe the effect of free cysteine residues.Results: Purified native HNPs at the final concentrations of 15 µmol/L and 30 µmol/L exhibited no or little effect on the adhesion and aggregation of murine platelets on VWF/collagen surface under arterial shears (100 dyne/cm2). Surprisingly, synthetic HNP1 at the same concentrations (15-30 μmol/L) resulted in a dramatic reduction in the rate and surface coverage of murine platelets on VWF/collagen surface under the same conditions. This inhibitory activity of synthetic HNP1 was abolished after pretreatment with NEM that reacts with free thiols (-SH). Aliphatic HNP1 with all 6 cysteine residues chemically modified also showed no effect on inhibiting the adhesion and aggregation of murine platelets on VWF/collagen surface under flow.Conclusions: These results suggest that higher concentrations of native HNPs may be required for inhibiting ADAMTS13 activity in vivo. However, synthetic HNP1 exhibits a differential activity by reducing platelet and VWF interaction and thrombus formation under arterial shear via a disulfide bond reduction mechanism. [ABSTRACT FROM AUTHOR]