Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarchitecture of the hearts in term and former‐preterm lambs using diffusion tensor imaging

Diffusion tensor imaging (DTI) is an MRI technique that can be used to map cardiomyocyte tracts and estimate local cardiomyocyte and sheetlet orientation within the heart. DTI measures diffusion distances of water molecules within the myocardium, where water diffusion generally occurs more freely along the long axis of cardiomyocytes and within the extracellular matrix, but is restricted by cell membranes such that transverse diffusion is limited. DTI can be undertaken in fixed hearts and it allows the three‐dimensional mapping of the cardiac microarchitecture, including cardiomyocyte organization, within the whole heart. The objective of this study was to use DTI to compare the cardiac microarchitecture and cardiomyocyte organization in archived fixed left ventricles of lambs that were born either preterm (n = 5) or at term (n = 7), at a postnatal timepoint equivalent to about 6 years of age in children. Although the findings support the feasibility of retrospective DTI scanning of fixed hearts, several hearts were excluded from DTI analysis because of poor scan quality, such as ghosting artifacts. The preliminary findings from viable DTI scans (n = 3/group) suggest that the extracellular compartment is altered and that there is an immature microstructural phenotype early in postnatal life in the LV of lambs born preterm. Our findings support a potential time‐efficient imaging role for DTI in detecting abnormal changes in the microstructure of fixed hearts of former‐preterm neonates, although further investigation into factors that affect scan quality is required.
Itacitinib (INCB039110), a JAK1 Inhibitor, Reduces Cytokines Associated with Cytokine Release Syndrome Induced by CAR T-cell Therapy

Purpose: T cells engineered to express a chimeric antigen receptor (CAR) are a promising cancer immunotherapy. Such targeted therapies have shown long-term relapse-free survival in patients with B-cell leukemia and lymphoma. However, cytokine release syndrome (CRS) represents a serious, potentially life-threatening side effect often associated with CAR T-cell therapy. CRS manifests as a rapid (hyper)immune reaction driven by excessive inflammatory cytokine release, including IFNγ and IL6. Experimental Design: Many cytokines implicated in CRS are known to signal through the JAK-STAT pathway. Here we study the effect of blocking JAK pathway signaling on CAR T-cell proliferation, antitumor activity, and cytokine levels in in vitro and in vivo models. Results: We report that itacitinib, a potent, selective JAK1 inhibitor, was able to significantly and dose-dependently reduce levels of multiple cytokines implicated in CRS in several in vitro and in vivo models. Importantly, we also report that at clinically relevant doses that mimic human JAK1 pharmacologic inhibition, itacitinib did not significantly inhibit proliferation or antitumor killing capacity of three different human CAR T-cell constructs (GD2, EGFR, and CD19). Finally, in an in vivo model, antitumor activity of CD19-CAR T cells adoptively transferred into CD19+ tumor-bearing immunodeficient animals was unabated by oral itacitinib treatment. Conclusions: Together, these data suggest that itacitinib has potential as a prophylactic agent for the prevention of CAR T cell–induced CRS, and a phase II clinical trial of itacitinib for prevention of CRS induced by CAR T-cell therapy has been initiated (NCT04071366).
User Independent Estimations of Gait Events With Minimal Sensor Data

Goal: The purpose of this study was to provide an initial examination of the utility of the Beta Process - Auto Regressive - Hidden Markov Model (BP-AR-HMM) for the prior identification of gait events. A secondary objective was to determine whether the output of the model could be used for classification and prediction of locomotion states. Methods: In this study we utilized the output of the BP-AR-HMM to develop user-independent identification of gait events and gait classification from an idealized three-dimensional acceleration signal. The input acceleration data were collected from two walking (1.4 and 1.6 ms−1) and two running (2.6 and 3.0 ms−1) steady state speeds, and during two dynamic walk to run and run to walk transitions (1.8–2.4 and 2.4–1.8 ms−1) on an instrumented force treadmill. Results: The BP-AR-HMM identified 9 unique states. Of these, two states, 4 and 1, were utilized to estimate initial contact and toe off, respectively. The lead time from the first instance of state 4 to initial contact was 0.13 ± 0.02 s. Similarly, the first instance of state 1 occurred 0.14 ± 0.03 s before toe off. Two other states (3 and 7) were examined for possible utilization in a probabilistic model for the prediction of pending locomotion state transitions. Conclusion: The identification of gait events prior to their occurrence by the BP-AR-HMM appears to be an approach that can minimize the quantity of sensor data in an offline approach. Furthermore, there is evidence it could also be used as a basis to build a probabilistic model to estimate locomotion transitions.
A Fast Image Thresholding Algorithm for Infrared Images Based on Histogram Approximation and Circuit Theory

Image thresholding is one of the fastest and most effective methods of detecting objects in infrared images. This paper proposes an infrared image thresholding method based on the functional approximation of the histogram. The one-dimensional histogram of the image is approximated to the transient response of a first-order linear circuit. The threshold value for the image segmentation is formulated using combinational analogues of standard operators and principles from the concept of the transient behavior of the first-order linear circuit. The proposed method is tested on infrared images gathered from the standard databases and the experimental results are compared with the existing state-of-the-art infrared image thresholding methods. We realized through the experimental results that our method is well suited to perform infrared image thresholding.
Modeling the activation of the alternative complement pathway and its effects on hemolysis in health and disease

The complement system is a powerful mechanism of innate immunity poised to eliminate foreign cells and pathogens. It is an intricate network of >35 proteins, which, once activated, leads to the tagging of the surface to be eliminated, produces potent chemoattractants to recruit immune cells, and inserts cytotoxic pores into nearby lipid surfaces. Although it can be triggered via different pathways, its net output is largely based on the direct or indirect activation of the alternative pathway. Complement dysregulation or deficiencies may cause severe pathologies, such as paroxysmal nocturnal hemoglobinuria (PNH), where a lack of complement control proteins leads to hemolysis and life-threatening anemia. The complexity of the system poses a challenge for the interpretation of experimental data and the design of effective pharmacological therapies. To address this issue, we developed a mathematical model of the alternative complement pathway building on previous modelling efforts. The model links complement activation to the hemolytic activity of the terminal alternative pathway, providing an accurate description of pathway activity as observed in vitro and in vivo, in health and disease. Through adjustment of the parameters describing experimental conditions, the model was capable of reproducing the results of an array of standard assays used in complement research. To demonstrate its clinical applicability, we compared model predictions with clinical observations of the recovery of hematological biomarkers in PNH patients treated with the complement inhibiting anti-C5 antibody eculizumab. In conclusion, the model can enhance the understanding of complement biology and its role in disease pathogenesis, help identifying promising targets for pharmacological intervention, and predict the outcome of complement-targeting pharmacological interventions.
Collecting e‐cigarette aerosols for in vitro applications: A survey of the biomedical literature and opportunities to increase the value of submerged cell culture‐based assessments

Electronic nicotine delivery systems (ENDS) are being developed as potentially reduced‐risk alternatives to the continued use of combustible tobacco products. Because of the widespread uptake of ENDS—in particular, e‐cigarettes—the biological effects, including the toxic potential, of their aerosols are under investigation. Preclinically, collection of such aerosols is a prerequisite for testing in submerged cell culture‐based in vitro assays; however, despite the growth in this research area, there is no apparent standardized collection method for this application. To this end, through an Institute for in vitro Sciences, Inc. workshop initiative, we surveyed the biomedical literature catalogued in PubMed® to map the types of methods hitherto used and reported publicly. From the 47 relevant publications retrieved, we identified seven distinct collection methods. Bubble‐through (with aqueous solvents) and Cambridge filter pad (CFP) (with polar solvents) collection were the most frequently cited methods (57% and 18%, respectively), while the five others (CFP + bubble‐through; condensation; cotton filters; settle‐upon; settle‐upon + dry) were cited less often (2–10%). Critically, the collected aerosol fractions were generally found to be only minimally characterized chemically, if at all. Furthermore, there was large heterogeneity among other experimental parameters (e.g., vaping regimen). Consequently, we recommend that more comprehensive research be conducted to identify the method(s) that produce the fraction(s) most representative of the native aerosol. We also endorse standardization of the aerosol generation process. These should be regarded as opportunities for increasing the value of in vitro assessments in relation to predicting effects on human health.
A review of the systematics of the genus Bradypodion (Sauria: Chamaeleonidae), with the description of two new genera

The taxonomic history and composition of the genus Bradypodion as construed by Klaver & Bohme (1986) and new morphological and molecular data relevant to the taxonomy of the group is reviewed. The combined evidence strongly supports a formal rearrangement of the group into three distinct genera. Bradypodion, type species Chamaeleo pumilus Daudin 1802, is retained for the southern African species. Two new genera are erected to accommodate additional well-diagnosed clades within central and east African species previously referred to Bradypodion. Species of the “fischeri complex” are assigned to Kinyongia gen. nova, whilst the endemic Mulanje chameleon is placed in the monotypic genus Nadzikambia gen. nova.
The comparative gene expression concern to the seed pigmentation in maize (Zea mays L.)

Maize seed pigmentation is one of the important issue to develop maize seed breeding. The differently gene expression was characterized and compared for three inbred lines, such as the pigment accumulated seed (CM22) and non-pigmented seed (CM5 and CM19) at 10 days after pollination. We obtained a total of 63,870, 82,496, and 54,555 contigs by de novo assembly to identify gene expression in the CM22, CM5, and CM19, respectably. In differentially expressed gene analysis, it was revealed that 7,044 genes were differentially expressed by at least two-fold, with 4,067 upregulated in colored maize inbred lines and 2,977 upregulated in colorless maize inbred lines. Of them,18 genes were included to the anthocyanin biosynthesis pathways, while 15 genes were upregulated in both CM22/5 and CM22/19. Additionally, 37 genes were detected in the metabolic pathway concern to the seed pigmentation by BINs analysis using MAPMAN software. Finally, these differently expressed genes may aid in the research on seed pigmentation in maize breeding programs.
Strain modulated carrier mobility and optical properties of graphene nanowiggles

Recently, synthesized Chevron graphene nanoribbons (CGNRs) and its laterally extended counterpart known as extended CGNRs (ECGNR) are constructed by making alternated regular cuts in pristine graphene nanoribbons (GNRs). First-principles calculations demonstrate that these GNRs are super-ductile and possess width-dependent mechanical properties. The Young’s modulus is calculated to be 389.4 GPa and 414.6 GPa for CGNR and ECGNR, respectively. The bandgap of these nanoribbons decreases on the application of tensile strain. The carrier effective masses are found to be highly sensitive towards mechanical strains. The holes (electrons) mobility of ECGNR is calculated to be 7.68 × 104 cm2 V−1 s−1 (1.69 × 104 cm2 V−1 s−1), which is higher than that of CGNR can be further enhanced by elongation. The prominent peaks of the imaginary part of dielectric function and electron energy loss spectra show redshift on increasing the tensile strain. The electron energy loss spectra show intense plasmonic structure in low energy spectrum indicating GNRs to be more sensitive to the visible region than ultra violet spectrum. Our results provide insight about the possible applications of GNRs in the fields of high-speed transistors, sensors, photonics, and optoelectronics.
Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries

Abstract Background Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. Methods We assessed the global status of Mtb WGS and developed a 3-week training course coupled with long-term mentoring and WGS infrastructure building. Training focused on genome sequencing, bioinformatics and development of a locally relevant WGS research project. The aim of the long-term mentoring was to support trainees in project implementation and funding acquisition. The focus of WGS infrastructure building was on the DNA extraction process and bioinformatics. Findings Compared to their TB burden, Asia and Africa are grossly underrepresented in Mtb WGS research. Challenges faced resulted in adaptations to the training, mentoring and infrastructure building. Out-of-date laptop hardware and operating systems were overcome by using online tools and a Galaxy WGS analysis pipeline. A case studies approach created a safe atmosphere for students to formulate and defend opinions. Because quality DNA extraction is paramount for WGS, a biosafety level 3 and general laboratory skill training session were added, use of commercial DNA extraction kits was introduced and a 2-week training in a highly equipped laboratory was combined with a 1-week training in the local setting. Interpretation By developing and sharing the components of and experiences with a sequencing and bioinformatics training program, we hope to stimulate capacity building programs for Mtb WGS and empower high-burden countries to play an important role in WGS-based TB surveillance and research.
A Systematic Review of Controlled-Trials for PTSD in Maltreated Children and Adolescents

Child maltreatment is associated with elevated risk of post-traumatic stress disorder (PTSD), which can often present alongside comorbidities. While evidence-based treatments for PTSD in young people already exist, there remains ongoing clinical and academic debate about the suitability of these approaches, particularly cognitive-behavioral approaches, for young people who have been exposed to more complex traumatic experiences, such as maltreatment. We conducted an updated systematic review of the evidence-base for psychological treatments for PTSD, specifically for maltreated young people. Fifteen randomized controlled trials and five non-randomized controlled clinical trials satisfied the inclusion criteria. Trials included treatments ranging from trauma-focused CBT to creative-based therapies. Trauma-focused CBT remained the best supported treatment for children and adolescents following child maltreatment, with new evidence that symptom improvements are maintained at longer-term follow up. The evidence for other therapies remained limited, and there were concerns regarding methodological quality. Implications for treatment decision-making are discussed.
BIOLOGICAL Ecology A connectivity portfolio effect stabilizes marine reserve performance

Well-managed and enforced no-take marine reserves generate important larval subsidies 31 to neighboring habitats and thereby contribute to the long-term sustainability of fisheries. However, larval dispersal patterns are variable, which leads to temporal fluctuations in 33 the contribution of a single reserve to the replenishment of local populations. Identifying 34 management strategies that mitigate the uncertainty in larval supply will help ensure the 35 stability of recruitment dynamics and minimize the volatility in fishery catches. Here, we 36 use genetic parentage analysis to show extreme variability in both the dispersal patterns 37 and recruitment contribution of four individual marine reserves across six discrete 38 recruitment cohorts for coral grouper ( Plectropomus maculatus ) on the Great Barrier Reef. 39 Together though, the asynchronous contributions from multiple reserves create temporal 40 stability in recruitment via a connectivity portfolio effect. This dampening effect reduces 41 the variability in larval supply from individual reserves by a factor of 1.8, which effectively 42 halves the uncertainty in the recruitment contribution of individual reserves. Thus, not 43 only does the network of four marine reserves generate valuable larval subsidies to 44 neighboring habitats, the aggregate effect of individual reserves mitigates temporal 45 fluctuations in dispersal patterns and the replenishment of local populations. Our results indicate that small networks of marine reserves yield previously unrecognized stabilizing 47 benefits that ensure a consistent larval supply to replenish exploited fish stocks. Networks of marine reserves support fisheries supply and quantified temporal fluctuations in the recruitment contribution from a network of no- take marine reserves on the Great Barrier Reef. Although recruitment contributions from individual reserves are extremely variable, the reserve network generates a connectivity portfolio effect that successfully dampens the volatility of larval supply to nearby coral reefs. Our findings demonstrate that effective reserve networks can yield previously unrecognized stabilizing benefits that ensure a consistent replenishment of exploited fish stocks.
Depression screening in Surabaya Indonesia: Urgent need for better mental health care for high-risk communities and suicide prevention for men

Objectives: Despite its high prevalence and considerable burden, depression is not handled with the required urgency in Indonesia. Existing data from the government does not specifically note its prevalence and symptoms manifestation. This study screened depression in Surabaya, where the prevalence of mood disorder was reported to be higher than the national prevalence, in order to identify where action is most needed. Methods: Cross-sectional study with non-random sampling. Participants consisted of samples from general population categorised as non-high-risk group, and prisoners, sex workers and drug users categorised as high-risk group. Depression screening was done using MINI-ICD10 self-rated depression questionnaire. Correlation between screening results and demographic data was analysed using chi-square test. Results: Positive depression screening was significantly associated with grouping and educational background. High-risk group and participants with lower education background had significantly higher number of positive screening. Significantly higher proportion of participants in the high-risk group experience eight of the ten depression symptoms regardless of screening results. Higher proportion of depression positive male participants experienced suicidal/self-harm symptom. Limitations: This study used non-random sampling method, therefore the results may not fully represent the general population. The screening instrument used did not account for depression and symptoms severity. Conclusion: High-risk group with low educational background is in most urgent need of mental health help, and suicide prevention strategy is most needed for men.
Deamidation of Wheat-flour Gliadin with Ion-exchange Resin.

小麦粉グルテンのエタノール可溶性タンパク質であるグリアジンを陽イオン交換樹脂を用いて脱アミド化することを試みた. また,脱アミド化した試料と水との親和性は,低水分域では水分収着等温線の測定およびその熱力学的解析により,高水分域では溶解度の測定により評価した. (1) 陽イオン交換樹脂CE(COO-)を用い,樹脂量0. 2g/g-溶液で6時間処理することで,全アミド量の約28%に相当する1. 08mmol/g-タンパク質が脱アミド化されたグリアジンが得られた. (2) 水分収着等温線の測定により脱アミド化を行うことでグリアジンの水の収着量を高められることが分かった. (3) 水分収着等温線の熱力学的解析から,脱アミド化による水との親和性の向上の程度が定量化された. (4) 脱アミド化により,グリアジンの水および塩化ナトリウム水溶液に対する溶解性が増すことが明らかとなった.
Burnout in gastroenterology: Better awareness and research are needed

We read with interest the article by Buscarini et al. Although burnout is defined as an ‘occupational phenomenon’ rather than a mental health illness by the World Health Organization, we fully agree that it remains an important issue to address in gastroenterology, especially in the coronavirus disease 2019 era. Previous large-scale burnout studies in gastroenterology have originated mostly from the USA (pre-pandemic), and the current prevalence in the field remains poorly understood globally. Also, previous results cannot be reliably extrapolated across countries because of differences in health-care systems, working environment, study population, burnout detection tools and burnout criteria. Therefore, the scale of the problem must first be understood locally to compel organisational change. In managing burnout, we believe greater awareness of the syndrome is also needed amongst gastroenterologists to enable self-reporting, since a gold standard detection tool does not exist currently. Symptoms of emotional exhaustion and depersonalisation are telling of burnout. However, abnormal symptoms in only one domain can be reflective of an individual’s personality type. Symptoms of low personal accomplishment alone correlates poorly with burnout. These may exist in unaffected individuals and often have poor factor loading in detection tools. Nonetheless, the most extensively validated and commonly used tool to identify burnout in medical professionals – the 22-item Maslach Burnout Inventory (MBI) – has its limitations and can be costly as well as time-consuming to administer. Therefore, authorities must be prepared to allocate the time and resources to assess individuals holistically in order to achieve meaningful change. Abbreviated versions of the MBI can be inaccurate. So, we and other researchers advise against its use. If in doubt, or when burned-out individuals are identified, we also believe they should be referred to mental well-being support services where possible, since burnout may co-exist with undiagnosed mental health conditions such as depression. As such, comprehensive mental-health assessments should not be overlooked or replaced by ‘peer support’ alone. That said, support services must be well advertised and signposted for individuals to access. In a recent pilot study of gastroenterology trainees in the East of England, even though 35.3% had burnout or were at high risk of burnout, 51.6% of all trainees were unaware of available mental well-being services that existed within the training programme. In closing, we fully support Buscarini et al.’s call for better safeguards against burnout in gastroenterology. In addition, more research on burnout is also needed within the specialty.