Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide SNP-Genotyping Array to Study the Evolution of the Human Pathogen Vibrio vulnificus Biotype 3

Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae, horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen.
Evidence for Deficits in the Temporal Attention Span of Poor Readers

Background While poor reading is often associated with phonological deficits, many studies suggest that visual processing might also be impaired. In particular, recent research has indicated that poor readers show impaired spatial visual attention spans in partial and whole report tasks. Given the similarities between competition-based accounts for reduced visual attention span and similar explanations for impairments in sequential object processing, the present work examined whether poor readers show deficits in their “temporal attention span” – that is, their ability to rapidly and accurately process sequences of consecutive target items. Methodology/Principal Findings Poor and normal readers monitored a sequential stream of visual items for two (TT condition) or three (TTT condition) consecutive target digits. Target identification was examined using both unconditional and conditional measures of accuracy in order to gauge the overall likelihood of identifying a target and the likelihood of identifying a target given successful identification of previous items. Compared to normal readers, poor readers showed small but consistent deficits in identification across targets whether unconditional or conditional accuracy was used. Additionally, in the TTT condition, final-target conditional accuracy was poorer than unconditional accuracy, particularly for poor readers, suggesting a substantial cost arising from processing the previous two targets that was not present in normal readers. Conclusions/Significance Mirroring the differences found between poor and normal readers in spatial visual attention span, the present findings suggest two principal differences between the temporal attention spans of poor and normal readers. First, the consistent pattern of reduced performance across targets suggests increased competition amongst items within the same span for poor readers. Second, the steeper decline in final target performance amongst poor readers in the TTT condition suggests a reduction in the extent of their temporal attention span.
Early intervention (mobilization or active exercise) for critically ill adults in the intensive care unit (Review)

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The Neighborhood Voice

The Neighborhood Voice is a vehicle customized for conducting health research in community settings. It brings research studies into neighborhoods affected most by health disparities and reaches groups often underrepresented in research samples. This paper reports on the experience and satisfaction of 599 African American women who participated in research on board the Neighborhood Voice. Using bivariate, psychometric, and logistic regression analyses, we examined responses to a brief post-research survey. Most women (71%) reported that they had never previously participated in research, and two-thirds (68%) rated their Neighborhood Voice experience as excellent. Satisfaction scores were highest among first-time research participants (p < .05). Women’s ratings of the Neighborhood Voice on Comfort (OR = 4.9; 95% CI = 3.0, 7.9) and Convenience (OR = 1.8; 95% CI = 1.2, 2.9) significantly predicted having an excellent experience. Mobile research facilities may increase participation among disadvantaged and minority populations. Our brief survey instrument is a model for evaluating such outreach.
Micro injection molding simulation based on SPH method

Micro injection molding is an efficient and low cost process for the large-scale replication of thermoplastic polymer microparts.Numerical simulation in cavity filling is important to mold design and process parameters setting before mold manufacture.A meshfree-based method for solving viscosity equations was proposed to simulate the filling process of micro injection molding.The N-S governing equations were discretized by using a particle approximate method of smooth particle hydrodynamics.Some physical properties,such as velocity,pressure,and temperature were investigated in the filling process.As an example,mold cavity filling simulation for a microneedle used in biomedical application was performed,and the results were consistent with experiment.Compared with the traditional mesh method,such as three dimensional finite element method,with corresponding node or particle number and process condition,the proposed meshfree method showed advantages of higher accuracy and calculation efficiency.
Effect of Processing Method on Thermal Behavior in PLA/PEG Melt Blending

The dispersion of PEG acts as plasticizer in PLA blends were investigated using thermal analysis. The comparisons were made between two melt processing method, twin screw extruder and two-roll mills to study how it will affect the Tg, Tc and Tm of blends in DSC analysis. The TGA behavior was also studied for two-roll mills processing method to confirm the effect of PEG loading in PLA on degradation and amount of residue left after analysis. In DSC analysis, it can be seen clearly, the PEG loading decreased the glass transition temperature in all blends compares to neat PLA. For twin screw extruder blending, the crystallization peak existed for some blend. It was difference for two-roll mills blends where the crystallization peak absent in all blends with PEG loading. The presence of PEG gave no significant variation on melting temperature peak for both processing method.
Ratiometric sensing of BiP-client versus BiP levels by the unfolded protein response determines its signaling amplitude

Insufficient folding capacity of the endoplasmic reticulum (ER) activates the unfolded protein response (UPR) to restore homeostasis. Yet, how the UPR achieves ER homeostatic readjustment is poorly investigated, as in most studies the ER stress that is elicited cannot be overcome. Here we show that a proteostatic insult, provoked by persistent expression of the secretory heavy chain of immunoglobulin M (µs), is well-tolerated in HeLa cells. Upon µs expression, its levels temporarily eclipse those of the ER chaperone BiP, leading to acute, full-geared UPR activation. Once BiP is in excess again, the UPR transitions to chronic, submaximal activation, indicating that the UPR senses ER stress in a ratiometric fashion. In this process, the ER expands about three-fold and becomes dominated by BiP. As the UPR is essential for successful ER homeostatic readjustment in the HeLa-µs model, it provides an ideal system for dissecting the intricacies of how the UPR evaluates and alleviates ER stress.
Overview on Polystyrene/Nanoclay Composite: Physical Properties and Application

ABSTRACT This article reviews the research and progress on polystyrene and nanoclay-based nanocomposite. Polystyrene is one of the most extensively used commercial polymers in the world. This review is designed to be an expansive source for polystyrene–clay nanocomposite research, including synthesis, characterization, structure/property relationship, manufacturing techniques, and applications considering thermal, mechanical, barrier, electrical conductivity, non-flammability, and biodegradability. The frequently used clays with polystyrene are montmorillonite, bentonite, hectorite, and kaolinite. The polystyrene–clay nanocomposite has several interesting commercial significances in packaging, automotive, fuel cell, construction, and electrical materials. Finally, future challenges toward the technical applications of these advance materials have been discussed. GRAPHICAL ABSTRACT
A three-dimensional ex vivo tri-culture model mimics cell-cell interactions between acute myeloid leukemia and the vascular niche

Ex vivo studies of human disease, such as acute myeloid leukemia, are generally limited to the analysis of two-dimensional cultures which often misinterpret the effectiveness of chemotherapeutics and other treatments. Here we show that matrix metalloproteinase-sensitive hydrogels prepared from poly(ethylene glycol) and heparin functionalized with adhesion ligands and pro-angiogenic factors can be instrumental to produce robust three-dimensional culture models, allowing for the analysis of acute myeloid leukemia development and response to treatment. We evaluated the growth of four leukemia cell lines, KG1a, MOLM13, MV4-11 and OCI-AML3, as well as samples from patients with acute myeloid leukemia. Furthermore, endothelial cells and mesenchymal stromal cells were co-seeded to mimic the vascular niche for acute myeloid leukemia cells. Greater drug resistance to daunorubicin and cytarabine was demonstrated in three-dimensional cultures and in vascular co-cultures when compared with two-dimensional suspension cultures, opening the way for drug combination studies. Application of the C-X-C chemokine receptor type 4 (CXCR4) inhibitor, AMD3100, induced mobilization of the acute myeloid leukemia cells from the vascular networks. These findings indicate that the three-dimensional tri-culture model provides a specialized platform for the investigation of cell-cell interactions, addressing a key challenge of current testing models. This ex vivo system allows for personalized analysis of the responses of patients’ cells, providing new insights into the development of acute myeloid leukemia and therapies for this disease.
Blocking landing techniques in volleyball and the possible association with anterior cruciate ligament injury

ABSTRACT The number and type of landings performed after blocking during volleyball matches has been related to the potential risk of ACL injury. The aim of the present study was to determine whether gender affects the frequency of specific blocking landing techniques with potential risk of ACL injury from the perspective of foot contact and subsequent movement after the block used by volleyball players during competitive matches. Three matches involving four female volleyball teams (fourteen sets) and three matches involving four male volleyball teams (thirteen sets) in the Czech Republic were analyzed for this study. A Pearson chi-square test of independence was used to detect the relationship between gender and different blocking techniques. The results of the present study showed that gender affected single-leg landings with subsequent movement in lateral direction and double-leg landings. Although the total number of landings was lower for male athletes than for female athletes, a larger portion of male athletes demonstrated single leg landings with a subsequent movement than female athletes. Single leg landings with a subsequent movement have a higher potential risk of ACL injury.
Efficient bio-production of citramalate using an engineered Escherichia coli strain

Citramalic acid is a central intermediate in a combined biocatalytic and chemocatalytic route to produce bio-based methylmethacrylate, the monomer used to manufacture Perspex and other high performance materials. We developed an engineered E. coli strain and a fed-batch bioprocess to produce citramalate at concentrations in excess of 80 g l−1 in only 65 h. This exceptional efficiency was achieved by designing the production strain and the fermentation system to operate synergistically. Thus, a single gene encoding a mesophilic variant of citramalate synthase from Methanococcus jannaschii, CimA3.7, was expressed in E. coli to convert acetyl-CoA and pyruvate to citramalate, and the ldhA and pflB genes were deleted. By using a bioprocess with a continuous, growth-limiting feed of glucose, these simple interventions diverted substrate flux directly from central metabolism towards formation of citramalate, without problematic accumulation of acetate. Furthermore, the nutritional requirements of the production strain could be satisfied through the use of a mineral salts medium supplemented only with glucose (172 g l−1 in total) and 1.4 g l−1 yeast extract. Using this system, citramalate accumulated to 82±1.5 g l−1, with a productivity of 1.85 g l−1 h−1 and a conversion efficiency of 0.48 gcitramalate g−1glucose. The new bioprocess forms a practical first step for integrated bio- and chemocatalytic production of methylmethacrylate.
Breaking Up Sitting with Light-Intensity Physical Activity: Implications for Shift-Workers

Prolonged sitting, restricted sleep, and circadian disruption are all independent risk factors for non-communicable diseases. Previous research has demonstrated that breaking up sitting with light-intensity physical activity has clear benefits for the health of day workers, but these findings may not apply in the presence of sleep restriction and/or circadian disruption—both of which are commonly experienced by shift-workers. Specifically, sleep restriction, and circadian disruption result in acute physiological changes that may offset the benefits of breaking up sitting. This commentary will explore the potential benefits of breaking up sitting for health, work performance, and subsequent sleep in shift-workers. Future areas of research designed to understand the mechanisms by which prolonged sitting and shift work impact worker health and safety and to support the design of effective occupational health and safety interventions are proposed.
Decentralised management of drug-resistant tuberculosis (MDR- and XDR-TB) in South Africa: an alternative model of care.

SETTING A growing number of cases of extensively drug-resistant tuberculosis (XDR-TB) have been reported from KwaZulu-Natal, South Africa. OBJECTIVE To propose an alternative model to centralised care that can be implemented to alleviate the current emergency. DISCUSSION The current failing TB programme could be improved by borrowing strategies such as decentralisation of care, treatment expertise, high levels of treatment adherence and successful outcomes, all of which have been successfully implemented in the human immunodeficiency virus programme. Patients with multidrug-resistant or XDR-TB could be admitted to institutions closer to their homes for treatment with subsequent discharge to home-based care. CONCLUSION The longer we support a failed system or wait for a perfect solution, the more the current devastation will continue to grow.
Atrial fibrillation in the Middle East: unmapped, underdiagnosed, undertreated

ABSTRACT Introduction: Atrial fibrillation (AF) is the commonest persistent cardiac arrhythmia with an estimated incidence rate of between 1.5–2% and an important cause of strokes. Few epidemiological studies and clinical trials on the management of AF have been conducted outside Europe and North America. These gaps in our understanding of AF likely lead to sub-optimal management of patients with AF in the rest of the world. Areas covered: We discuss the epidemiology, treatment and clinical outcomes for AF in the Middle East after systematic review of published work for AF from the Middle East. We also discuss important clinical trials on AF conducted in the West in the same period to help contextualize our findings. Expert commentary: The few available Middle East studies suggest important epidemiological differences between Middle Eastern and Western AF populations. In particular, the Middle Eastern AF population is younger and have more co-morbidities than patients in the West. We find that significant numbers of moderate to high risk patients with AF are either undertreated or untreated placing them at increased risk of complications such as stroke. More studies in the Middle Eastern population are required to aid the development of region-specific clinical guidelines to improve patient care.
Edoxaban Plus Aspirin vs Dual Antiplatelet Therapy in Endovascular Treatment of Patients With Peripheral Artery Disease: Results of the ePAD Trial

Purpose: To report a randomized study that investigated the safety (risk of major bleeds) and potential efficacy of edoxaban, an oral anticoagulant that targets the major components of arterial thrombi, to prevent loss of patency following endovascular treatment (EVT). Methods: Between February 2012 and June 2014, 203 patients who underwent femoropopliteal EVT were randomized to receive aspirin plus edoxaban or aspirin plus clopidogrel for 3 months in the Edoxaban in Peripheral Arterial Disease (ePAD) study (ClinicalTrials.gov identifier NCT01802775). Randomization assigned 101 patients (mean age 68.0±10.4 years; 67 men) to the edoxaban group and 102 patients (mean age 66.7±8.6 years; 78 men) to the clopidogrel group. The primary safety endpoint was bleeding as classified by the TIMI (Thrombolysis in Myocardial Infarction) criteria and ISTH (International Society of Thrombosis and Hemostasis) criteria; the efficacy endpoint was the rate of restenosis/reocclusion. Results: There were no major or life-threatening bleeding events in the edoxaban group, while there were 2 major and 2 life-threatening bleeding events in the clopidogrel group by the TIMI criteria. By the ISTH classification, there was 1 major and 1 life-threatening bleeding event vs 5 major and 2 life-threatening bleeding events, respectively [relative risk (RR) 0.20, 95% confidence interval (CI) 0.02 to 1.70]. The bleeding risk was not statistically different with either treatment when assessed by TIMI or ISTH. Following 6 months of observation, there was a lower incidence of restenosis/reocclusion with edoxaban compared with clopidogrel (30.9% vs 34.7%; RR 0.89, 95% CI 0.59 to 1.34, p=0.643). Conclusion: These results suggest that patients who have undergone EVT have similar risks for major and life-threatening bleeding events with edoxaban and aspirin compared with clopidogrel and aspirin. The incidence of restenosis/reocclusion events, while not statistically different, was lower with edoxaban and aspirin, but an adequately sized trial will be needed to confirm these findings.
Biomechanical deformable image registration of longitudinal lung CT images using vessel information

Spatial correlation of lung tissue across longitudinal images, as the patient responds to treatment, is a critical step in adaptive radiotherapy. The goal of this work is to expand a biomechanical model-based deformable registration algorithm (Morfeus) to achieve accurate registration in the presence of significant anatomical changes. Six lung cancer patients previously treated with conventionally fractionated radiotherapy were retrospectively evaluated. Exhale CT scans were obtained at treatment planning and following three weeks of treatment. For each patient, the planning CT was registered to the follow-up CT using Morfeus, a biomechanical model-based deformable registration algorithm. To model the complex response of the lung, an extension to Morfeus has been developed: an initial deformation was estimated with Morfeus consisting of boundary conditions on the chest wall and incorporating a sliding interface with the lungs. It was hypothesized that the addition of boundary conditions based on vessel tree matching would provide a robust reduction of the residual registration error. To achieve this, the vessel trees were segmented on the two images by thresholding a vesselness image based on the Hessian matrix’s eigenvalues. For each point on the reference vessel tree centerline, the displacement vector was estimated by applying a variant of the Demons registration algorithm between the planning CT and the deformed follow-up CT. An expert independently identified corresponding landmarks well distributed in the lung to compute target registration errors (TRE). The TRE was: 5.8±2.9, 3.4±2.3 and 1.6±1.3 mm after rigid registration, Morfeus and Morfeus with boundary conditions on the vessel tree, respectively. In conclusion, the addition of boundary conditions on the vessels significantly improved the accuracy in modeling the response of the lung and tumor over the course of radiotherapy. Minimizing and modeling these geometrical uncertainties will enable future plan adaptation strategies.
Fire and Grazing Influences on Rates of Riparian Woody Plant Expansion along Grassland Streams

Grasslands are threatened globally due to the expansion of woody plants. The few remaining headwater streams within tallgrass prairies are becoming more like typical forested streams due to rapid conversion of riparian zones from grassy to wooded. Forestation can alter stream hydrology and biogeochemistry. We estimated the rate of riparian woody plant expansion within a 30 m buffer zone surrounding the stream bed across whole watersheds at Konza Prairie Biological Station over 25 years from aerial photographs. Watersheds varied with respect to experimentally-controlled fire and bison grazing. Fire frequency, presence or absence of grazing bison, and the historical presence of woody vegetation prior to the study time period (a proxy for proximity of propagule sources) were used as independent variables to predict the rate of riparian woody plant expansion between 1985 and 2010. Water yield was estimated across these years for a subset of watersheds. Riparian woody encroachment rates increased as burning became less frequent than every two years. However, a higher fire frequency (1–2 years) did not reverse riparian woody encroachment regardless of whether woody vegetation was present or not before burning regimes were initiated. Although riparian woody vegetation cover increased over time, annual total precipitation and average annual temperature were variable. So, water yield over 4 watersheds under differing burn frequencies was quite variable and with no statistically significant detected temporal trends. Overall, burning regimes with a frequency of every 1–2 years will slow the conversion of tallgrass prairie stream ecosystems to forested ones, yet over long time periods, riparian woody plant encroachment may not be prevented by fire alone, regardless of fire frequency.