Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity of NHE1, Receptor for Subgroup J Avian Leukosis Virus, in Domestic Chicken and Wild Anseriform Species

J subgroup avian leukosis virus (ALV-J) infects domestic chicken, jungle fowl, and turkey and enters the host cell through a receptor encoded by tvj locus and identified as Na+/H+ exchanger 1 (NHE1). The resistance to ALV-J in a great majority of examined galliform species was explained by deletions or substitutions of the critical tryptophan 38 in the first extracellular loop of NHE1, and genetic polymorphisms around this site predict the susceptibility or resistance of a given species or individual. In this study, we examined the NHE1 polymorphism in domestic chicken breeds and documented quantitative differences in their susceptibility to ALV-J in vitro. In a panel of chicken breeds assembled with the aim to cover the maximum variability encountered in domestic chickens, we found a completely uniform sequence of NHE1 extracellular loop 1 (ECL1) without any source of genetic variation for the selection of ALV-J-resistant poultry. In parallel, we studied the natural polymorphisms of NHE1 in wild ducks and geese because of recent reports on ALV-J positivity in feral Asian species. In anseriform species, we demonstrate a specific and highly conserved critical ECL1 sequence without any homologue of tryptophan 38 in accordance with the resistance of duck cells to prototype ALV-J. Last, we demonstrated that the new Asian strains of ALV-J have not evolved their envelope glycoprotein to the entry the duck cells. Our results contribute substantially to the current discussion of possible heterotransmission of ALV-J and its spill-over into the wild ducks and geese.
MIT Open Access

This paper introduces Copa, an end-to-end congestion control algorithm that uses three ideas. First, it shows that a target rate equal to 1 / ( δ d q ), where d q is the (measured) queueing delay, optimizes a natural function of throughput and delay under a Markovian packet arrival model. Second, it adjusts its congestion window in the direction of this target rate, converging quickly to the correct fair rates even in the face of significant flow churn. These two ideas enable a group of Copa flows to maintain high utilization with low queuing delay. However, when the bottleneck is shared with loss-based congestion-controlled flows that fill up buffers, Copa, like other delay-sensitive schemes, achieves low throughput. To combat this problem, Copa uses a third idea: detect the presence of buffer-fillers by observing the delay evolution, and respond with additive-increase/multiplicative decrease on the δ parameter. Experimental results show that Copa outperforms Cubic (similar throughput, much lower delay, fairer with diverse RTTs), BBR and PCC (significantly fairer, lower delay), and co-exists well with Cubic unlike BBR and PCC. Copa is also robust to non-congestive loss and large bottleneck buffers, and outperforms other schemes on long-RTT paths.
ICE AGE VEGETATION AND FLORA OF NEW MEXICO

A review of the glacial-age vegetation and flora of New Mexico concludes that, while the snowline was 3000 feet lower in elevation with glaciers on peaks above 12,000 feet, vegetation zones were compressed. The spruce-pine forests that today extend over 4000 feet of elevation in the mountains were reduced to 2000 feet. The lower glacial-age forest border was similar to or slightly lower than that of today, with tree and shrub taxa expanding their ranges into sagebrush grasslands along escarpments and rocky terrain. The broad basins and plains of New Mexico, including the High Plains of eastern New Mexico and adjacent Texas, were sagebrush grassland, a conclusion supported by vertebrate faunal studies and soil profiles. The plant-macrofossil record is from glacial-age woodrat middens that are located on rocky escarpments below 6000 feet elevation in southern New Mexico. The mix of montane tree and shrub taxa in these low-elevation sites suggests that the glacial-age spruce-pine forest was more homogeneous than
Quantifying antiviral activity optimizes drug combinations against hepatitis C virus infection

Significance Introduction of new anti-hepatitis C virus (HCV) agents, so-called direct-acting antivirals (DAAs), has greatly changed treatment for HCV, and a variety of choices for anti-HCV drug combinations are available. For better management and control of this worldwide infectious disease with anti-HCV agents, it is critical to develop a method for precisely profiling the antiviral efficacy of possible combination drug regimens and seek the “best treatment” based on scientific evidence. In this study, we showed how cell culture data can be combined with a mathematical model and computer simulation to quantify the anti-HCV drug efficacy of different drug concentrations and combinations in a preclinical setting, and hence develop a quantitative basis for selecting drug combinations prior to costly clinical trials. With the introduction of direct-acting antivirals (DAAs), treatment against hepatitis C virus (HCV) has significantly improved. To manage and control this worldwide infectious disease better, the “best” multidrug treatment is demanded based on scientific evidence. However, there is no method available that systematically quantifies and compares the antiviral efficacy and drug-resistance profiles of drug combinations. Based on experimental anti-HCV profiles in a cell culture system, we quantified the instantaneous inhibitory potential (IIP), which is the logarithm of the reduction in viral replication events, for both single drugs and multiple-drug combinations. From the calculated IIP of 15 anti-HCV drugs from different classes [telaprevir, danoprevir, asunaprevir, simeprevir, sofosbuvir (SOF), VX-222, dasabuvir, nesbuvir, tegobuvir, daclatasvir, ledipasvir, IFN-α, IFN-λ1, cyclosporin A, and SCY-635], we found that the nucleoside polymerase inhibitor SOF had one of the largest potentials to inhibit viral replication events. We also compared intrinsic antiviral activities of a panel of drug combinations. Our quantification analysis clearly indicated an advantage of triple-DAA treatments over double-DAA treatments, with triple-DAA treatments showing enhanced antiviral activity and a significantly lower probability for drug resistance to emerge at clinically relevant drug concentrations. Our framework provides quantitative information to consider in designing multidrug strategies before costly clinical trials.
The immediate effects of robot-assistance on energy consumption and cardiorespiratory load during walking compared to walking without robot-assistance: a systematic review

Abstract Purpose: The integration of sufficient cardiovascular stress into robot-assisted gait (RAG) training could combine the benefits of both RAG and aerobic training. The aim was to summarize literature data on the immediate effects of RAG compared to walking without robot-assistance on metabolic-, cardiorespiratory- and fatigue-related parameters. Methods: PubMed and Web of Science were searched for eligible articles till February 2016. Means, SDs and significance values were extracted. Effect sizes were calculated. Results: Fourteen studies were included, concerning 155 participants (85 healthy subjects, 39 stroke and 31 spinal cord injury patients), 9 robots (2 end-effectors, 1 treadmill-based and 6 wearable exoskeletons), and 7 outcome parameters (mostly oxygen consumption and heart rate). Overall, metabolic and cardiorespiratory parameters were lower during RAG compared to walking without robot-assistance (moderate to large effect sizes). In healthy subjects, when no body-weight support (BWS) was provided, RAG with an end-effector device was more energy demanding than walking overground (p > .05, large effect sizes). Conclusions: Generally, results suggest that RAG is less energy-consuming and cardiorespiratory stressful than walking without robot-assistance, but results depend on factors such as robot type, walking speed, BWS and effort. Additional research is needed to draw firm conclusions. Implications for Rehabilitation Awareness of the energy consumption and cardiorespiratory load of robot-assisted gait (RAG) training is important in the rehabilitation of (neurological) patients with impaired cardiorespiratory fitness and patients who are at risk of cardiovascular diseases. On the other hand, the integration of sufficient cardiometabolic stress in RAG training could combine the effects of both RAG and aerobic training. Energy consumption and cardiorespiratory load during walking with robot-assistance seems to depend on factors such as robot type, walking speed, body-weight support or amount of effort. These parameters could be adjusted in RAG rehabilitation to make RAG more or less energy-consuming and cardiorespiratory stressful. Overall, short duration exoskeleton walking seems less energy-consuming and cardiorespiratory stressful than walking without robot-assistance. This might implicate that the exercise intensity is safe for (neurological) patients at risk of cardiovascular diseases. How this changes in extended walking time is unclear.
Regulation of Blood Pressure by Targeting CaV1.2-Galectin-1 Protein Interaction

Background: L-type CaV1.2 channels play crucial roles in the regulation of blood pressure. Galectin-1 (Gal-1) has been reported to bind to the I-II loop of CaV1.2 channels to reduce their current density. However, the mechanistic understanding for the downregulation of CaV1.2 channels by Gal-1 and whether Gal-1 plays a direct role in blood pressure regulation remain unclear. Methods: In vitro experiments involving coimmunoprecipitation, Western blot, patch-clamp recordings, immunohistochemistry, and pressure myography were used to evaluate the molecular mechanisms by which Gal-1 downregulates CaV1.2 channel in transfected, human embryonic kidney 293 cells, smooth muscle cells, arteries from Lgasl1−/− mice, rat, and human patients. In vivo experiments involving the delivery of Tat-e9c peptide and AAV5-Gal-1 into rats were performed to investigate the effect of targeting CaV1.2-Gal-1 interaction on blood pressure monitored by tail-cuff or telemetry methods. Results: Our study reveals that Gal-1 is a key regulator for proteasomal degradation of CaV1.2 channels. Gal-1 competed allosterically with the CaV&bgr; subunit for binding to the I-II loop of the CaV1.2 channel. This competitive disruption of CaV&bgr; binding led to CaV1.2 degradation by exposing the channels to polyubiquitination. It is notable that we demonstrated that the inverse relationship of reduced Gal-1 and increased CaV1.2 protein levels in arteries was associated with hypertension in hypertensive rats and patients, and Gal-1 deficiency induces higher blood pressure in mice because of the upregulated CaV1.2 protein level in arteries. To directly regulate blood pressure by targeting the CaV1.2-Gal-1 interaction, we administered Tat-e9c, a peptide that competed for binding of Gal-1 by a miniosmotic pump, and this specific disruption of CaV1.2-Gal-1 coupling increased smooth muscle CaV1.2 currents, induced larger arterial contraction, and caused hypertension in rats. In contrasting experiments, overexpression of Gal-1 in smooth muscle by a single bolus of AAV5-Gal-1 significantly reduced blood pressure in spontaneously hypertensive rats. Conclusions: We have defined molecularly that Gal-1 promotes CaV1.2 degradation by replacing CaV&bgr; and thereby exposing specific lysines for polyubiquitination and by masking I-II loop endoplasmic reticulum export signals. This mechanistic understanding provided the basis for targeting CaV1.2-Gal-1 interaction to demonstrate clearly the modulatory role that Gal-1 plays in regulating blood pressure, and offering a potential approach for therapeutic management of hypertension.
Intelligent antenna solutions for UMTS: algorithms and simulation results

This article outlines the development of intelligent antenna (IA) solutions for UMTS, a third-generation W-CDMA system. Since the selection of an antenna configuration paired with realizable uplink/downlink algorithms that can satisfy all operating environments is a broad task, this article focus is on cost-effective antenna arrays for macrocells. Algorithms that exploit the antenna configurations and act at both the physical and MAC layers are highlighted and supported by simulation results. Two solutions stand out for UMTS: a universal beamforming algorithm that unifies user-specific and fixed beamforming under one framework, and multibeam scheduling (MBS) that significantly increases downlink packet data throughput using the concept of code reuse in conjunction with beamforming. The article summarizes the critical issues that were faced in the development of an IA solution capable of delivering the theoretically promised benefits to end users.
Gastroenteropancreatic neuroendocrine neoplasms: genes, therapies and models

ABSTRACT Gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) refer to a group of heterogeneous cancers of neuroendocrine cell phenotype that mainly fall into one of two subtypes: gastroenteropancreatic neuroendocrine tumors (GEP-NETs; well differentiated) or gastroenteropancreatic neuroendocrine carcinomas (GEP-NECs; poorly differentiated). Although originally defined as orphan cancers, their steadily increasing incidence highlights the need to better understand their etiology. Accumulating epidemiological and clinical data have shed light on the pathological characteristics of these diseases. However, the relatively low number of patients has hampered conducting large-scale clinical trials and hence the development of novel treatment strategies. To overcome this limitation, tractable disease models that faithfully reflect clinical features of these diseases are needed. In this Review, we summarize the current understanding of the genetics and biology of these diseases based on conventional disease models, such as genetically engineered mouse models (GEMMs) and cell lines, and discuss the phenotypic differences between the models and affected humans. We also highlight the emerging disease models derived from human clinical samples, including patient-derived xenograft models and organoids, which may provide biological and therapeutic insights into GEP-NENs. Summary: Gastroenteropancreatic neuroendocrine neoplasms have been an understudied entity with limited treatment options. We discuss the disease models, including emerging organoids, that may provide biological and therapeutic insight into these diseases.
Tensile and Morphological Properties of Hybrid Montmorillonite/Microcrystalline Cellulose Filled Polylactic Acid Composites: Effect of Filler Ratio

The objective of this study is to investigate the effect of partial replacement of montmorillonite (MMT) with microcrystalline cellulose (MCC) on the tensile and morphology properties of polylactic acid (PLA) composites. PLA composites reinforced with hybrid MMT/MCC were prepared by solution casting. Based on our previous study, tensile strength exhibited that the optimum MMT content in the PLA/MMT is 5 phr. Therefore, partial replacement of MMT with MCC was performed at 5 phr of filler content in order to produce PLA/MMT/MCC hybrid composites. Fourier transform infrared spectroscopy revealed some polar interaction between fillers and PLA matrix. Young’s modulus of the PLA/MMT/MCC hybrid composites increased gradually with increasing MCC filler in the hybrid composites and was higher than PLA/MMT nanocomposites. However, the highest tensile strength of hybrid composites was obtained at 4 phr MMT and 1 phr of MCC filler (~26 MPa), which was lower than optimum formulation of PLA/MMT nanocomposites. Interestingly, the percent elongation at break of the hybrid composites were higher than that of PLA/MMT nanocomposites; increased significantly from ~10 to ~58 %. Field emission scanning electron microscopy indicated the aggregation of MCC and the presence of some cracks in the PLA hybrid composites, resulted in decrease of the tensile strength.
Variability between Expected and Actual Outcome Following a Severe Traumatic Brain Injury

Traumatic brain injury remains a challenging and complicated disease process to care for, despite the advance of technology used to monitor and guide treatment. Currently the mainstay of treatment is aimed at limiting secondary brain injury, with the help of multiple specialties in a critical care setting. Prognosis after TBI is often even more challenging than the treatment itself, although there are various exam and imaging findings that are associated with poor outcome. These findings are important because they can be used to guide families and loved ones when making decisions about goals of care. However in this case report, we demonstrate the unanticipated recovery of a patient with a severe traumatic brain injury who presented with several exam and imaging findings that are statistically associated with increased mortality and morbidity.
Characterization and bacterial anti-adherent effect on modified PMMA denture acrylic resin containing platinum nanoparticles

PURPOSE This study characterized the synthesis of a modified PMMA (Polymethyl methacrylate) denture acrylic loading platinum nanoparticles (PtN) and assessed its bacterial inhibitory efficacy to produce novel antimicrobial denture base material. MATERIALS AND METHODS Polymerized PMMA denture acrylic disc (20 mm × 2 mm) specimens containing 0 (control), 10, 50, 100 and 200 mg/L of PtN were fabricated respectively. The obtained platinum-PMMA nanocomposite (PtNC) was characterized by TEM (transmission electron microscopy), SEM/EDX (scanning electron microscope/energy dispersive X-ray spectroscopy), thermogravimetric and atomic absorption spectrophotometer analysis. In antimicrobial assay, specimens were placed on the cell culture plate, and 100 µL of microbial suspensions of S. mutans (Streptococcus mutans) and S. sobrinus (Streptococcus sobrinus) were inoculated then incubated at 37℃ for 24 hours. The bacterial attachment was tested by FACS (fluorescence-activated cell sorting) analysis after staining with fluorescent probe. RESULTS PtN were successfully loaded and uniformly immobilized into PMMA denture acrylic with a proper thermal stability and similar surface morphology as compared to control. PtNC expressed significant bacterial anti-adherent effect rather than bactericidal effect above 50 mg/L PtN loaded when compared to pristine PMMA (P=.01) with no or extremely small amounts of Pt ion eluted. CONCLUSION This is the first report on the synthesis and its antibacterial activity of Pt-PMMA nanocomposite. PMMA denture acrylic loading PtN could be a possible intrinsic antimicrobial denture material with proper mechanical characteristics, meeting those specified for denture bases. For clinical application, future studies including biocompatibility, color stability and warranting the long-term effect were still required.
Observations and Analysis of the 10–11 June 1994 Coastally Trapped Disturbance

Abstract A coastally trapped disturbance (CTD), characterized by southerly flow at the surface on 10–11 June 1994, was observed from the California Bight to Bodega Bay during a field experiment along the California coast. (North–south approximates the coast-parallel direction.) Data from a special observational network of wind profilers, radio acoustic sounding systems, special surface data, balloon ascents, and a research aircraft were used with satellite and synoptic data to explore both the CTD structure and the regional-scale changes before the event. The disruption of the climatological northerly flow along the central California coast, which preconditioned the area for the development of a CTD, began with the eastward movement of a surface high into Washington and Oregon and the amplification of a thermal low in northern California. As with most CTDs in the region, this occurred over the 2–3 days preceding the CTD’s initiation. These large-scale changes caused westward advection of warm continental .
Demystifying coding for schools - what are we actually trying to teach?

As computer science enters school curricula around the world, many teachers are having to teach the topic of computer programming for the first time. For those who have little experience in the area it can be daunting, while those who are experienced programmers may be so familiar with the subject that it is hard to see what is dicult about it! This article explores the reality of what we need to be teaching in schools, and considers what the essence of the topic is.
The Periodontal Pathogen Porphyromonas gingivalis Preferentially Interacts with Oral Epithelial Cells in S Phase of the Cell Cycle

ABSTRACT Porphyromonas gingivalis, a key periodontal pathogen, is capable of invading a variety of cells, including oral keratinocytes, by exploiting host cell receptors, including alpha-5 beta-1 (α5β1) integrin. Previous studies have shown that P. gingivalis accelerates the cell cycle and prevents apoptosis of host cells, but it is not known whether the cell cycle phases influence bacterium-cell interactions. The cell cycle distribution of oral keratinocytes was characterized by flow cytometry and BrdU (5-bromo-2-deoxyuridine) staining following synchronization of cultures by serum starvation. The effect of cell cycle phases on P. gingivalis invasion was measured by using antibiotic protection assays and flow cytometry, and these results were correlated with gene and surface expression levels of α5 integrin and urokinase plasminogen activator receptor (uPAR). There was a positive correlation (R = 0.98) between the number of cells in S phase and P. gingivalis invasion, the organism was more highly associated with cells in S phase than with cells in G2 and G1 phases, and S-phase cells contained 10 times more bacteria than did cells that were not in S phase. Our findings also show that α5 integrin, but not uPAR, was positively correlated with cells in S phase, which is consistent with previous reports indicating that P. gingivalis invasion of cells is mediated by α5 integrin. This study shows for the first time that P. gingivalis preferentially associates with and invades cells in the S phase of the cell cycle. The mechanism of targeting stable dividing cells may have implications for the treatment of periodontal diseases and may partly explain the persistence of this organism at subgingival sites.
A Qualitative Study of African American/Black MSM’s Experiences of Participating in a Substance Use and Sexual Risk Reduction Intervention

The majority of new HIV infections in the United States are among men who have sex with men (MSM), and African American/Black MSM are especially affected. Employing a grounded theory approach, this study presents qualitative data from 21 African American/Black MSM who participated in a substance use and sexual risk reduction intervention trial (Project ROOM [men Reaching Out to Other Men]) in South Florida. African American/Black MSM from Project ROOM reduced their substance use and sexual risk behaviors at a faster rate than other men in the study. The present study examines how the experiences of participation in Project ROOM influenced the behavior change among African American/Black MSM. In-depth interviews indicate that study assessments enhanced African American/Black men’s mindfulness and self-realization of behaviors leading to behavior modification and changes in social relationships. Furthermore, these findings suggest that interventions tailored to the social environment of HIV transmission and substance use behaviors are key to reducing risk behaviors among this population.