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Abstract CRISPR/Cas9 is widely used for precise mutagenesis through targeted DNA double-strand breaks (DSBs) induction followed by error-prone repair. A better understanding of this process requires measuring the rates of cutting, error-prone, and precise repair, which have remained elusive so far. Here, we present a molecular and computational toolkit for multiplexed quantification of DSB intermediates and repair products by single-molecule sequencing. Using this approach, we characterize the dynamics of DSB induction, processing and repair at endogenous loci along a 72 h time-course in tomato protoplasts. Combining this data with kinetic modeling reveals that indel accumulation is determined by the combined effect of the rates of DSB induction processing of broken ends, and precise versus error repair. In this study, 64–88% of the molecules were cleaved in the three targets analyzed, while indels ranged between 15–41%. Precise repair accounts for most of the gap between cleavage and error repair, representing up to 70% of all repair events. Altogether, this system exposes flux in the DSB repair process, decoupling induction and repair dynamics, and suggesting an essential role of high-fidelity repair in limiting the efficiency of CRISPR-mediated mutagenesis.

Abstract Background Malfunction of astrocytes is implicated as one of the pathological factors of ALS. Thus, intrathecal injection of healthy astrocytes in ALS can potentially compensate for the diseased astrocytes. AstroRx® is an allogeneic cell-based product, composed of healthy and functional human astrocytes derived from embryonic stem cells. AstroRx® was shown to clear excessive glutamate, reduce oxidative stress, secrete various neuroprotective factors, and act as an immunomodulator. Intrathecal injection of AstroRx® to animal models of ALS slowed disease progression and extended survival. Here we report the result of a first-in-human clinical study evaluating intrathecal injection of AstroRx® in ALS patients. Methods We conducted a phase I/IIa, open-label, dose-escalating clinical trial to evaluate the safety, tolerability, and therapeutic effects of intrathecal injection of AstroRx® in patients with ALS. Five patients were injected intrathecally with a single dose of 100 × 106 AstroRx® cells and 5 patients with 250 × 106 cells (low and high dose, respectively). Safety and efficacy assessments were recorded for 3 months pre-treatment (run-in period) and 12 months post-treatment (follow-up period). Results A single administration of AstroRx® at either low or high doses was safe and well tolerated. No adverse events (AEs) related to AstroRx® itself were reported. Transient AEs related to the Intrathecal (IT) procedure were all mild to moderate. The study demonstrated a clinically meaningful effect that was maintained over the first 3 months after treatment, as measured by the pre-post slope change in ALSFRS-R. In the 100 × 106 AstroRx® arm, the ALSFRS-R rate of deterioration was attenuated from − 0.88/month pre-treatment to − 0.30/month in the first 3 months post-treatment (p = 0.039). In the 250 × 106 AstroRx® arm, the ALSFRS-R slope decreased from − 1.43/month to − 0.78/month (p = 0.0023). The effect was even more profound in a rapid progressor subgroup of 5 patients. No statistically significant change was measured in muscle strength using hand-held dynamometry and slow vital capacity continued to deteriorate during the study. Conclusions Overall, these findings suggest that a single IT administration of AstroRx® to ALS patients at a dose of 100 × 106 or 250 × 106 cells is safe. A signal of beneficial clinical effect was observed for the first 3 months following cell injection. These results support further investigation of repeated intrathecal administrations of AstroRx®, e.g., every 3 months. Trial Registration: NCT03482050.

Abstrak Hasil observasi menunjukkan bahwa kemampuan siswa dalam menyelesaikan soal cerita matematika dalam kategori rendah. Maka solusi dari permasalahan tersebut digunakan Geogebra sebagai media interaktif. Studi ini bertujuan untuk melihat pengaruh dari penggunaan media interaktif Geogebra terhadap kemampuan menyelesaikan soal cerita yang disajikan dalam materi SPLDV. Dalam studi ini digunakan pendekatan kuantitatif jenis Quasi-Eksperimental Design. Sampel ditentukan dengan Purposive Sampling, sedangkan Independent Sample T-Test telah digunakan sebagai analisis data dalam studi ini dengan uji prasyarat normalitas dan homogenitas. Hasil studi menunjukkan bahwa thitung = 2,729 > ttabel= 2,052 (sig. 0,009) artinya terdapat perbedaan kemampuan penyelesaian soal cerita siswa antara kelas eksperimen dan kelas kontrol dimana nilai rata-rata kelas eksperimen lebih tinggi dari pada kelas kontrol. Dapat disimpulkan bahwa media interaktif Geogebra berpengaruh positif serta signifikan terhadap kemampuan siswa dalam menyelesaikan soal cerita matematika materi SPLDV. Kata kunci: Penyelesaian soal cerita matematika; media interaktif Geogebra; SPLDV Abstract The observation results show that students' ability to solve math word problems is in a low category. Then the solution to this problem is using Geogebra as an interactive medium. This study aims to determine the effect of using Geogebra's interactive media on mathematical word problems on SPLDV material. This study employs a quantitative approach by using a Quasi-Experimental Design. The sample was determined by Purposive Sampling, while the Independent Sample T-Test was used as data analysis in this study with normality and homogeneity prerequisite tests. The results showed that tcount = 2,729 > ttable = 2,052 (sig. 0,009) this means that there are differences in the ability to solve student’s word problems between the experimental and control class where the average value of the experimental class is higher than that of the control class. It can be concluded that the Geogebra interactive media has a positive and significant effect on students' ability to solve math word problems on SPLDV material. Keywords: Completion of mathematical word problems; Geogebra interactive media; SPLDV

IntroductionPeople living with HIV (PLHIV) are characterized by functional reprogramming of innate immune cells even after long-term antiretroviral therapy (ART). In order to assess technical feasibility of omics technologies for application to larger cohorts, we compared multiple omics data layers.MethodsBulk and single-cell transcriptomics, flow cytometry, proteomics, chromatin landscape analysis by ATAC-seq as well as ex vivo drug stimulation were performed in a small number of blood samples derived from PLHIV and healthy controls from the 200-HIV cohort study.ResultsSingle-cell RNA-seq analysis revealed that most immune cells in peripheral blood of PLHIV are altered in their transcriptomes and that a specific functional monocyte state previously described in acute HIV infection is still existing in PLHIV while other monocyte cell states are only occurring acute infection. Further, a reverse transcriptome approach on a rather small number of PLHIV was sufficient to identify drug candidates for reversing the transcriptional phenotype of monocytes in PLHIV.DiscussionThese scientific findings and technological advancements for clinical application of single-cell transcriptomics form the basis for the larger 2000-HIV multicenter cohort study on PLHIV, for which a combination of bulk and single-cell transcriptomics will be included as the leading technology to determine disease endotypes in PLHIV and to predict disease trajectories and outcomes.

A combination of surgery and chemotherapy is the most effective treatment available for Malignant Pleural Mesothelioma (MPM). However, both cause significant collateral damage and cannot eliminate residual microscopic disease. This investigation aimed to compare and determine the feasibility of utilizing Radiofrequency Ablation (RFA) and Magnetic-Resonance-guided Focused Ultrasound Surgery (MRgFUS) as alternative treatments for MPM. A large animal tumor model was developed in 13 Yorkshire female pigs using the MSTO211H cell line. Two pigs were initially used to determine the cyclosporine dose required for immunosuppression and tumor development. Subsequently, 11 other pigs underwent tumor development. Of these 11, 2 died during cell inoculation. Small tumor masses and adhesions were present in the other 9, indicating mesothelioma development. Five pigs then received RFA treatment, and 4 pigs received MRgFUS treatment. Tumor model development and effect of the two treatments were examined using MRI and by necropsy. RFA and MRgFUS both successfully ablated approximately the same sized area in the same treatment time. This study demonstrates that RFA and MRgFUS are feasible for tumor debulking, and while MRgFUS requires more pretreatment planning compared to RFA, MRgFUS is a completely noninvasive procedure.

Summary: Systemic inflammation is established as part of late-stage severe lung disease, but molecular, functional, and phenotypic changes in peripheral immune cells in early disease stages remain ill defined. Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small-airway inflammation, emphysema, and severe breathing difficulties. Using single-cell analyses we demonstrate that blood neutrophils are already increased in early-stage COPD, and changes in molecular and functional neutrophil states correlate with lung function decline. Assessing neutrophils and their bone marrow precursors in a murine cigarette smoke exposure model identified similar molecular changes in blood neutrophils and precursor populations that also occur in the blood and lung. Our study shows that systemic molecular alterations in neutrophils and their precursors are part of early-stage COPD, a finding to be further explored for potential therapeutic targets and biomarkers for early diagnosis and patient stratification.

Synthetic embryo models have arisen as an approach to probe early development in vitro, facilitating the study of difficult to access stages. Here the authors present a simple system for generating embryo-like structures that resemble peri-implantation mouse embryos.

Omics-based technologies are driving major advances in precision medicine, but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development of 3-chloropiperidines, a new class of candidate anticancer agents. Combined analyses of transcriptome and chromatin accessibility elucidated the mechanisms underlying sensitivity to test agents. Furthermore, we implemented a new versatile strategy for the integration of RNA- and ATAC-seq (Assay for Transposase-Accessible Chromatin) data, able to accelerate and extend the standalone analyses of distinct omic layers. This platform guided the construction of a perturbation-informed basal signature predicting cancer cell lines’ sensitivity and to further direct compound development against specific tumor types. Overall, this approach offers a scalable pipeline to support the early phases of drug discovery, understanding of mechanisms, and potentially inform the positioning of therapeutics in the clinic.

Abstract Background The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system. Methods In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings. Results Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host. Conclusions Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.

BackgroundCell therapy of diabetes aims at restoring the physiological control of blood glucose by transplantation of functional pancreatic islet cells. A potentially unlimited source of cells for such transplantations would be islet cells derived from an in vitro differentiation of human pluripotent stem cells (hESC/hiPSC). The islet-like clusters (ILC) produced by the known differentiation protocols contain various cell populations. Among these, the β-cells that express both insulin and the transcription factor Nkx6.1 seem to be the most efficient to restore normoglycemia in diabetes animal models. Our aim was to find markers allowing selection of these efficient cells.MethodsFunctional Cell-Capture Screening (FCCS) was used to identify markers that preferentially capture the cells expressing both insulin and Nkx6.1, from hESC-derived ILC cells. In order to test whether selection for such markers could improve cell therapy in diabetic mouse models, we used ILC produced from a clinical-grade line of hESC by a refined differentiation protocol adapted to up-scalable bioreactors. Re-aggregated MACS sorted cells were encapsulated in microspheres made of alginate modified to reduce foreign body reaction. Implantation was done intraperitoneally in STZ-treated C57BL/6 immuno-competent mice.ResultsCD49A (integrin alpha1) was identified by FCCS as a marker for cells that express insulin (or C-peptide) as well as Nkx6.1 in ILC derived by hESC differentiation. The ILC fraction enriched in CD49A+ cells rapidly reduced glycemia when implanted in diabetic mice, whereas mice receiving the CD49A depleted population remained highly diabetic. CD49A-enriched ILC cells also produced higher levels of human C-peptide in the blood of transplanted mice. However, the difference between CD49A-enriched and total ILC cells remained small. Another marker, CD26 (DPP4), was identified by FCCS as binding insulin-expressing cells which are Nkx6.1 negative. Depletion of CD26+ cells followed by enrichment for CD49A+ cells increased insulin+/Nkx6.1+ cells fraction to ~70%. The CD26-/CD49A+ enriched ILC exhibited improved function over non-sorted ILC or CD49A+ cells in diabetic mice and maintain prolonged blood C-peptide levels.ConclusionsRefining the composition of ILC differentiated from hPSC by negative selection to remove cells expressing CD26 and positive selection for CD49A expressing cells could enable more effective cell therapy of diabetes.

Background: Medial branch (MB) targeting during RF ablation for facetogenic back pain is usually performed with flouroscopic guidance yet no specific measurements on the target depth have been published. In order to understand candidacy for other potential ablation methods, we sought to determine the actual MB depth and measurements of adjacent osseous structures. Methods: CT scans without contrast of the lumbar spine performed in the supine position were retrospectively analyzed in 100 patients. Axial slices less than or equal to 2.5 mm with sagittal and coronal reformations were evaluated. The following distances were measured bilaterally at the L2-L5 levels: The depth from the skin to the MB nerve (anatomic target for RF ablation) at a 15° angulation, the smallest width of the pedicle, and the length, height and width of the transverse process. Age, gender, weight, height, and BMI were correlated with the above measurements. Results: The average distance and 95% CI from skin-to-MB in mm at a 15°angle to the skin increased as the lumbar level increased measuring 64.4 (62.4–66.5) at L2, 72.0 (69.7–74.3) at L3, 79.2 (76.9–81.6) at L4, and 79.1 (76.7–81.5) at L5. The average thickness of the pedicles also increased as the lumbar level increased measuring 9.2 mm at L2 and 16.1 mm at L5. Body weight, lumbar level, and female gender were associated with increased MB depth. Taller stature was associated with more superficial MB depth. We eliminated mild interaction effects between height, weight, and gender by substituting BMI for height and weight without affecting r2. Linear regression revealed the following equation: MB Depth (mm) = 2.2*BMI + 4.9*lumbar vertebral level + 3.6 (if female) – 5.4, which fit the data well (P 95% of patients and the distance increases as the lumbar level increases.

Abstract Background Amyotrophic lateral sclerosis (ALS) is a motor neuron (MN) disease characterized by the loss of MNs in the central nervous system. As MNs die, patients progressively lose their ability to control voluntary movements, become paralyzed and eventually die from respiratory/deglutition failure. Despite the selective MN death in ALS, there is growing evidence that malfunctional astrocytes play a crucial role in disease progression. Thus, transplantation of healthy astrocytes may compensate for the diseased astrocytes. Methods We developed a good manufacturing practice-grade protocol for generation of astrocytes from human embryonic stem cells (hESCs). The first stage of our protocol is derivation of astrocyte progenitor cells (APCs) from hESCs. These APCs can be expanded in large quantities and stored frozen as cell banks. Further differentiation of the APCs yields an enriched population of astrocytes with more than 90% GFAP expression (hES-AS). hES-AS were injected intrathecally into hSOD1G93A transgenic mice and rats to evaluate their therapeutic potential. The safety and biodistribution of hES-AS were evaluated in a 9-month study conducted in immunodeficient NSG mice under good laboratory practice conditions. Results In vitro, hES-AS possess the activities of functional healthy astrocytes, including glutamate uptake, promotion of axon outgrowth and protection of MNs from oxidative stress. A secretome analysis shows that these hES-AS also secrete several inhibitors of metalloproteases as well as a variety of neuroprotective factors (e.g. TIMP-1, TIMP-2, OPN, MIF and Midkine). Intrathecal injections of the hES-AS into transgenic hSOD1G93A mice and rats significantly delayed disease onset and improved motor performance compared to sham-injected animals. A safety study in immunodeficient mice showed that intrathecal transplantation of hES-AS is safe. Transplanted hES-AS attached to the meninges along the neuroaxis and survived for the entire duration of the study without formation of tumors or teratomas. Cell-injected mice gained similar body weight to the sham-injected group and did not exhibit clinical signs that could be related to the treatment. No differences from the vehicle control were observed in hematological parameters or blood chemistry. Conclusion Our findings demonstrate the safety and potential therapeutic benefits of intrathecal injection of hES-AS for the treatment of ALS.

In vitro gas production technique (IVGPT) is a routine method in nutritional sciences to determine energy content, organic matter (OM) digestibility, and fermentation kinetics of feedstuffs. After collecting from two ruminally cannulated Holstein heifers (350 kg), rumen liquors were used either fresh or cryopreserved form in the inoculums for IVGPT. Starch- (barley, wheat, and corn) and protein-rich (sunflower meal, cotton seed meal, and soybean meal) feedstuffs were evaluated for gas production kinetics, fermentation pattern, and energy content in 5 replicates. pH, NH3-N concentration and volatile fatty acids (VFA) profile, gas production, and fermentation kinetics parameters were measured. Data were analyzed by 2-way ANOVA. Viable protozoa rate was found to be 70.8% in cryopreserved rumen liquor after thawing. Decrease in pH in thawed rumen liquor was less than fresh rumen liquor as the incubation period advanced. Utilization of frozen rumen liquor after thawing in IVGPT was associated with lower VFA and NH3-N concentration, cumulative gas production, and metabolisable energy estimate for all feedstuffs. In conclusion, despite high correlation between in vitro data obtained from fresh and thawed rumen liquors to predict gas production, further experiments should cope with improving cryopreservation protocol for rumen liquors in order to optimize microbial activity for maintaining fermentation pattern.

Background: Middle income countries are facing an epidemic of non-communicable diseases, especially coronary heart disease (CHD). We used a validated CHD mortality model (IMPACT) to explain recent trends in Tunisia, Syria, the occupied Palestinian territory (oPt) and Turkey., Methods: Data on populations, mortality, patient numbers, treatments and risk factor trends from national and local surveys in each country were collated over two time points (1995-97; 2006-09); integrated and analysed using the IMPACT model., Results: Risk factor trends: Smoking prevalence was high in men, persisting in Syria but decreasing in Tunisia, oPt and Turkey. BMI rose by 1-2 kg/m(2) and diabetes prevalence increased by 40%-50%. Mean systolic blood pressure and cholesterol levels increased in Tunisia and Syria. Mortality trends: Age-standardised CHD mortality rates rose by 20% in Tunisia and 62% in Syria. Much of this increase (79% and 72% respectively) was attributed to adverse trends in major risk factors, occurring despite some improvements in treatment uptake. CHD mortality rates fell by 17% in oPt and by 25% in Turkey, with risk factor changes accounting for around 46% and 30% of this reduction respectively. Increased uptake of community treatments (drug treatments for chronic angina, heart failure, hypertension and secondary prevention after a cardiac event) accounted for most of the remainder., Discussion: CHD death rates are rising in Tunisia and Syria, whilst oPt and Turkey demonstrate clear falls, reflecting improvements in major risk factors with contributions from medical treatments. However, smoking prevalence remains very high in men; obesity and diabetes levels are rising dramatically., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)

Background: Coronary heart disease (CHD) mortality rates have been decreasing in Turkey since the early 1990s. Our study aimed to determine how much of the CHD mortality decrease in Turkey between 1995 and 2008 could be attributed to temporal trends in major risk factors and how much to advances in medical and surgical treatments., Methods: The validated IMPACT CHD mortality model was used to combine and analyse data on uptake and effectiveness of CHD treatments and risk factor trends in Turkey in adults aged 35-84 years between 1995 and 2008.Data sources were identified, searched and appraised on population, mortality and major CHD risk factors for adults those aged 35-84 years. Official statistics, electronic databases, national registers, surveys and published trials were screened from 1995 onwards., Results: Between 1995 and 2008, coronary heart disease mortality rates in Turkey decreased by 34% in men and 28% in women 35 years and over. This resulted in 35,720 fewer deaths in 2008.Approximately 47% of this mortality decrease was attributed to treatments in individuals (including approximately 16% to secondary prevention, 3% angina treatments, 9% to heart failure treatments, 5% to initial treatments of acute myocardial infarction, and 5% to hypertension treatments) and approximately 42% was attributable to population risk factor reductions (notably blood pressure 29%; smoking 27%; and cholesterol 1%). Adverse trends were seen for obesity and diabetes (potentially increasing mortality by approximately 11% and 14% respectively). The model explained almost 90% of the mortality fall., Conclusion: Reduction in major cardiovascular risk factors explained approximately 42% and improvements in medical and surgical treatments explained some 47% of the CHD mortality fall. These findings emphasize the complimentary value of primary prevention and evidence-based medical treatments in controlling coronary heart disease.

Background: Cardiovascular disease (CVD) mortality increased in developed countries until the 1970s then started to decline. Turkey is about to complete its demographic transition, which may also influence mortality trends. This study evaluated trends in coronary heart disease (CHD) and stroke mortality between 1988 and 2008., Methods: The number of deaths by cause (ICD-8), age and sex were obtained from the Turkish Statistical Institute (TurkStat) annually between 1988 and 2008. Population statistics were based on census data (1990 and 2000) and Turkstat projections. European population standardised mortality rates for CHD and stroke were calculated for men and women over 35 years old. Joinpoint Regression was used to identify the points at which a statistically significant (p < 0.05) change of the trend occurred., Results: The CHD mortality rate increased by 2.9% in men and 2.0% in women annually from 1988 to 1994, then started to decline. The annual rate of decline for men was 1.7% between 1994-2008, whilst in women it was 2.8% between 1994-2000 and 6.7% between 2005-2008 (p < 0.05 for all periods).Stroke mortality declined between 1990-1994 (annual fall of 3.8% in both sexes), followed by a slight increase between 1994-2004 (0.6% in men, 1.1% in women), then a further decline until 2008 (annual reduction of 4.4% in men, 7.9% in women) (p < 0.05 for all periods)., Conclusions: A decrease in CVD mortality was observed from 1995 onwards in Turkey. The causes need to be explored in detail to inform future policy priorities in noncommunicable disease control.

Objectives: Turkey is facing increasing rates of cardiovascular disease (CVD). The study is designed to meet the growing need to obtain information about the recent status and trends of CVD risk factors and their impact on mortality., Methods: Balcova heart study (BHS) is a prospective cohort study, focusing on reducing the CVD risk factors of people over 30 years old living in Balcova District, Izmir, Turkey. Information about risk factors, anthropometric and biochemical measurements was collected in community centers. Interventions were planned, based on the 10-year coronary heart disease (CHD) risk and lifestyle characteristics with the collaboration of university and municipality., Results: Mean age of the 16,080 participants was 52 years. The percentage of current smoking was 41.6 in men and 31.1 in women. One-third of the men were physically inactive. Hypertension was reported as 25% in men and 33% in women., Conclusions: The project is unique for being the first community-based cohort on CVD risk factors in a Turkish setting. This project will have a valuable contribution on not only determining CVD risks, but also incorporating interventions for prevention.