Miracle-dz/UniFAR-FTUs huggingface dataset:
Interplay between membrane tension and the actin cytoskeleton determines shape changes

The ability of mammalian cells to deform their membrane relies on the action of the cytoskeleton. In particular, the dynamics of the actin cytoskeleton, assembling at the plasma membrane, plays a crucial role in controlling cell shape. Many proteins are involved to ensure proper growth of the actin network at the cell membrane. The detailed structure of this network regulates the force that is necessary for membrane deformation. We address here how the presence of capping proteins, which limit the length of actin filaments and thus affects network topology, influences membrane shape. We use a system of liposomes, activated to polymerize actin at their surface, and placed in a mixture of purified proteins that reconstitutes actin dynamics. Our system also allows the variation of membrane tension by deflating the liposomes. We show that membrane deformations are clearly favored in the presence of capping proteins in the actin network. Moreover, in the absence of capping proteins, membrane deformations appear only when the liposomes are deflated. Our results unveil that the interplay between membrane tension and actin network structure and dynamics governs cell shape.
Supplementary Material for ICCV 2015 Paper # 1007 RIDE : Reversal Invariant Descriptor Enhancement

This document is the supplementary material of the ICCV paper #1007 [5]. We provide the proof of gradient estimation of SIFT, and the generalization of RIDE to deal with more types of reversal and rotation invariance. 1. Orientation Estimation of Dense SIFT In this section, we aim at proving an approximated estimation of SIFT orientation based on its local gradient values. The approximation is used in Section 3.3 of the main article. 1.1. Implementation of SIFT The implementation of SIFT is based on the original paper [2]. In the following paragraphs, we briefly review the process of orientation assignment and descriptor representation. First let us assume that the assignment of descriptor scale is finished, which fits the case of dense sampling [1] where all the descriptors have the same, fixed window size. Denote an image as I = [L(x, y)]W×H . The gradient magnitude, m(x, y), and orientation, θ(x, y), is pre-computed for each pixel: m(x, y) = [ (L(x+ 1, y)− L(x− 1, y)) + (L(x, y + 1)− L(x, y − 1)) ]1/2 (1) θ(x, y) = arctan [(L(x, y + 1)− L(x, y − 1)) / (L(x+ 1, y)− L(x− 1, y))] (2) The magnitude and orientation on each pixel are then used to estimate the dominant orientation of that descriptor. An orientation histogram is formed from gradient orientation of the pixels within a region around the keypoint. Each sample added to the histogram is weighted by its gradient magnitude and by a Gaussian-weighted circular window with a σ that is 1.5 times that of the scale of the keypoint. Peaks in the orientation histogram correspond to dominant orientations of local gradients. The highest peak in the histogram is detected, and then any other local peak that is within 80% of the highest peak is used to also create a keypoint with that orientation. Therefore, for locations with multiple peaks of similar magnitude, there will be multiple keypoints created at the same location and scale but different orientations. The above method works well on image matching and retrieval [2], but we do not need to assign multiple orientations for a descriptor in the classification tasks. As an alternation, it is also suggested to estimate a unique accumulated orientation ∗This work was done when Lingxi Xie was an intern at Microsoft Research.
Understanding Tendons: Lessons from Transgenic Mouse Models

Tendons and ligaments are connective tissues that have been comparatively less studied than muscle and cartilage/bone, even though they are crucial for proper function of the musculoskeletal system. In tendon biology, considerable progress has been made in identifying tendon-specific genes (Scleraxis, Mohawk, and Tenomodulin) in the past decade. However, besides tendon function and the knowledge of a small number of important players in tendon biology, neither the ontogeny of the tenogenic lineage nor signaling cascades have been fully understood. This results in major drawbacks in treatment and repair options following tendon degeneration. In this review, we have systematically evaluated publications describing tendon-related genes, which were studied in depth and characterized by using knockout technologies and the subsequently generated transgenic mouse models (Tg) (knockout mice, KO). We report in a tabular manner, that from a total of 24 tendon-related genes, in 22 of the respective knockout mouse models, phenotypic changes were detected. Additionally, in some of the models it was described at which developmental stages these changes appeared and progressed. To summarize, only loss of Scleraxis and TGFβ signaling led to severe tendon developmental phenotypes, while mice deficient for various proteoglycans, Mohawk, EGR1 and 2, and Tenomodulin presented mild phenotypes. These data suggest that the tendon developmental system is well organized, orchestrated, and backed up; this is even more evident among the members of the proteoglycan family, where the compensatory effects are much clearer. In future, it will be of great importance to discover additional master tendon transcription factors and the genes that play crucial roles in tendon development. This would improve our understanding of the genetic makeup of tendons, and will increase the chances of generating tendon-specific drugs to advance overall treatment strategies.
Effects of Low Energy Availability on Reproductive Functions and Their Underlying Neuroendocrine Mechanisms

It is known that metabolic disturbances suppress reproductive functions in females. The mechanisms underlying metabolic and nutritional effects on reproductive functions have been established based on a large body of clinical and experimental data. From the 1980s to 1990s, it was revealed that disrupted gonadotropin-releasing hormone (GnRH) secretion is the main cause of reproductive impairments in metabolic and nutritional disorders. From the late 1990s to early 2000s, it was demonstrated that, in addition to their primary functions, some appetite- or metabolism-regulating factors affect GnRH secretion. Furthermore, in the early 2000s, kisspeptin, which is a potent positive regulator of GnRH secretion, was newly discovered, and it has been revealed that kisspeptin integrates the effects of metabolic status on GnRH neurons. Recent studies have shown that kisspeptin mediates at least some of the effects of appetite- and metabolism-regulating factors on GnRH neurons. Thus, kisspeptin might be a useful clinical target for treatments aimed at restoring reproductive functions in individuals with metabolic or nutritional disturbances, such as those who exercise excessively, experience marked weight loss, or suffer from eating disorders. This paper presents a review of what is currently known about the effects of metabolic status on reproductive functions and their underlying mechanisms by summarizing the available evidence.
Complete Genome Sequence of the Bacterium Serratia marcescens SGAir0764, Isolated from Singapore Air

Serratia marcescens strain SGAir0764 was isolated from a tropical air sample collected in Singapore. The complete genome, sequenced on the PacBio RS II platform, consists of one chromosome with 5.1 Mb and one plasmid with 76.4 kb. ABSTRACT Serratia marcescens strain SGAir0764 was isolated from a tropical air sample collected in Singapore. The complete genome, sequenced on the PacBio RS II platform, consists of one chromosome with 5.1 Mb and one plasmid with 76.4 kb. Genome annotation predicts 4,723 protein-coding genes, 89 tRNAs, and 22 rRNAs.
Association of High-Risk Drinking with Metabolic Syndrome and Its Components in Elderly Korean Men: The Korean National Health and Nutrition Examination Survey 2010–2012

Background Previous studies have examined the association between alcohol consumption and metabolic syndrome (MetS) in adults, but studies in the elderly are lacking. We examined the relationship between high-risk alcohol consumption and MetS in elderly Korean men using the Alcohol Use Disorders Identification Test (AUDIT) questionnaire from the 2010–2012 Korean National Health and Nutrition Examination Survey. Methods Among 25,534 subjects, 2,807 were men >60 years of age; after exclusions, we included 2,088 men in the final analysis. We categorized the study participants into three groups according to AUDIT score: low risk (0–7), intermediate risk (8–14), and high risk (≥15 points). Results Among the study population, 17.0% of the men were high-risk drinkers, who had the highest mean waist circumference, systolic and diastolic blood pressure (BP), fasting plasma glucose (FPG), and triglyceride (TG) levels. The overall prevalence of MetS was 41.9% in the elderly men, and it was significantly higher in the group with high (48.3%) versus low (31.9%) AUDIT scores. The prevalence of MetS components (elevated BP, high FPG, high TG, and low high-density lipoprotein cholesterol) was associated with a high AUDIT score. The odds ratios (95%confidence interval) of the high-risk group for MetS, elevated BP, and high TG were 1.40 (1.03–1.89), 1.82 (1.28– 2.60), and 1.77 (1.30–2.41) after adjustment for confounding variables. Conclusion AUDIT score was correlated with most MetS components in elderly Korean men.
Environmental stress does not increase the mean strength of selection

A common intuition among evolutionary biologists and ecologists is that environmental stress will increase the strength of selection against deleterious alleles and among alternate genotypes. However, the strength of selection is determined by the relative fitness differences among genotypes, and there is no theoretical reason why these differences should be exaggerated as mean fitness decreases. We update a recent review of the empirical results pertaining to environmental stress and the strength of selection and find that there is no overall trend towards increased selection under stress, in agreement with other recent analyses of existing data. The majority of past studies measure the strength of selection by quantifying the decrease in fitness imposed by single or multiple mutations in different environments. However, selection rarely acts on one locus independently, and the strength of selection will be determined by variation across the whole genome. We used 20 inbred lines of Drosophila melanogaster to make repeated fitness measurements of the same genotypes in four different environments. This framework allowed us to determine the variation in fitness attributable to genotype across stressful environments and to calculate the opportunity for selection among these genotypes in each stress. Although we found significant decreases in mean fitness in our stressful environments, we did not find any significant differences in the strength of selection among any of the four measured environments. Therefore, in agreement with our updated review, we find no evidence for the oft‐cited verbal model that stress increases the strength of selection.
The role of the chronic care model in promoting the management of the patient with rare liver disease

ABSTRACT Introduction: The chronic care model (CCM) provides a holistic approach for managing chronic illnesses. Patients with rare liver diseases (RLD) have complex needs, impaired quality of life and often life-threatening complications. Most RLD meet the criteria for a long-term chronic condition and should be viewed through the prism of CCM. We aimed to ascertain whether the CCM has been considered for the frequently-encountered RLD. Methods: MEDLINE®/PubMed®/Cochrane/EMBASE were searched to identify publications relating to the use of the CCM for the management of six RLD. We identified 33 articles eligible for inclusion. Results: Six, eleven, one, thirteen, two and zero studies, discussed individual components of the CCM for autoimmune hepatitis (AIH), primary biliary cholangitis (PBC), primary sclerosing cirrhosis (PSC), Wilsons disease (WD), alpha-1 antitrypsin deficiency (A1AD) and lysosomal acid lipase deficiency (LALd) respectively. We have not identified studies using the full CCM for any of the aforementioned RLD. Discussion: Unlike in common chronic conditions e.g. diabetes, there has been limited consideration of the use of CCM (or its components) for the management of RLD. This may reflect a reluctance of the clinical community to view these diseases as chronic or lack of healthcare policy investment in rare diseases in general.
Longitudinal analysis of statistical and clinically significant psychosocial change following mental health rehabilitation

Abstract Purpose: With appropriate mental health rehabilitation, schizophrenia is increasingly associated with reports of recovery and stability. However, there is little empirical evidence evaluating the efficacy of services delivering this care. This study evaluated the effectiveness of rehabilitation for improving psychosocial function in consumers with schizophrenia. Methods: An electronic database of standardized assessment instruments mandated and maintained by the health service was retrospectively reviewed to extract ratings of psychosocial function, daily living skills, and mood state from consecutive admissions to an inpatient rehabilitation service. Outcomes were compared at admission, discharge, and one-year follow-up to identify statistically significant change. Individual reliable and clinically significant change was also assessed by comparison with a normative group of clients functioning independently in the community. Results: From admission to discharge the rehabilitation group made statistically significant gains in psychosocial function and daily living skills. Improvements were reliable and clinically significant in one-quarter to one-third of individual consumers. Approximately half sustained their improvements at follow-up, although this represented only a small fraction of the overall cohort. Consumers not demonstrating gains exhibited psychometric floor effects at admission. Conclusions: Rehabilitation can produce statistically and clinically significant immediate improvement in psychosocial function for a sub-set of consumers with elevated scores at admission. The durability of any gains is less clear, and strategies promoting longer-term maintenance are encouraged. Furthermore, currently mandated outcome measures are confounded by issues of sensitivity and reporting compliance, and exploration of alternative instruments for assessing recovery is recommended. Implications for Rehabilitation Routinely collected standardized outcome measures can be used to investigate the effectiveness of mental health rehabilitation In addition to statistical significance, the clinical significance of outcomes should be evaluated to identify change that is individually meaningful Currently mandated outcomes instruments do not adequately evaluate many individuals’ recovery journey Mental health service evaluation and quality improvement processes would likely benefit from adoption of recovery-oriented measures
Virological and Immunological Outcomes of Coinfections

Coinfections involving viruses are being recognized to influence the disease pattern that occurs relative to that with single infection. Classically, we usually think of a clinical syndrome as the consequence of infection by a single virus that is isolated from clinical specimens. SUMMARY Coinfections involving viruses are being recognized to influence the disease pattern that occurs relative to that with single infection. Classically, we usually think of a clinical syndrome as the consequence of infection by a single virus that is isolated from clinical specimens. However, this biased laboratory approach omits detection of additional agents that could be contributing to the clinical outcome, including novel agents not usually considered pathogens. The presence of an additional agent may also interfere with the targeted isolation of a known virus. Viral interference, a phenomenon where one virus competitively suppresses replication of other coinfecting viruses, is the most common outcome of viral coinfections. In addition, coinfections can modulate virus virulence and cell death, thereby altering disease severity and epidemiology. Immunity to primary virus infection can also modulate immune responses to subsequent secondary infections. In this review, various virological mechanisms that determine viral persistence/exclusion during coinfections are discussed, and insights into the isolation/detection of multiple viruses are provided. We also discuss features of heterologous infections that impact the pattern of immune responsiveness that develops.
Critical and Challenging Issues in the Surgical Management of Low-Lying Rectal Cancer

Despite innovative advancements, the management of distally located rectal cancer (RC) remains a formidable endeavor. The critical location of the tumor predisposes it to a circumferential resection margin that tends to involve the sphincters and surrounding organs, pelvic lymph node metastasis, and anastomotic complications. In this regard, colorectal surgeons should be aware of issues beyond the performance of total mesorectal excision (TME). For decades, abdominoperineal resection had been the standard of care for low-lying RC; however, its association with high rates of tumor recurrence, tumor perforation, and poorer survival has stimulated the development of novel surgical techniques and modifications, such as extralevator abdominoperineal excision. Similarly, difficult dissections and poor visualization, especially in obese patients with low-lying tumors, have led to the development of transanal TME or the “bottom-to-up” approach. Additionally, while neoadjuvant chemoradiotherapy has allowed for the execution of more sphincter-saving procedures without oncologic compromise, functional outcomes remain an issue. Nevertheless, neoadjuvant treatment can lead to significant tumor regression and complete pathological response, permitting the utilization of organ-preserving strategies. At present, an East and West dualism pervades the management of lateral lymph node metastasis, thereby calling for a more global and united approach. Moreover, with the increasing importance of quality of life, a tailored, individualized treatment approach is of utmost importance when taking into account oncologic and anticipated functional outcomes.
The Apical Region of the Herpes Simplex Virus Major Capsid Protein Promotes Capsid Maturation

Herpesviruses assemble capsids and encapsidate their genomes by a process that is unlike those of other mammalian viruses but is similar to those of some bacteriophage. Many important aspects of herpesvirus morphogenesis remain enigmatic, including how the capsid shell matures into a stable angularized configuration. Capsid maturation is triggered by activation of a protease that cleaves an internal protein scaffold. We report on the fortuitous discovery that a region of the major capsid protein that is exposed on the outer surface of the capsid also contributes to capsid maturation, demonstrating that the morphogenesis of the capsid shell from its procapsid precursor to the mature angularized form is dependent upon internal and external components of the megastructure. ABSTRACT The herpesvirus capsid assembles in the nucleus as an immature procapsid precursor built around viral scaffold proteins. The event that initiates procapsid maturation is unknown, but it is dependent upon activation of the VP24 internal protease. Scaffold cleavage triggers angularization of the shell and its decoration with the VP26 and pUL25 capsid-surface proteins. In both the procapsid and mature angularized capsid, the apical region of the major capsid protein (VP5) is surface exposed. We investigated whether the VP5 apical region contributes to intracellular transport dynamics following entry into primary sensory neurons and also tested the hypothesis that conserved negatively charged amino acids in the apical region contribute to VP26 acquisition. To our surprise, neither hypothesis proved true. Instead, mutation of glutamic acid residues in the apical region delayed viral propagation and induced focal capsid accumulations in nuclei. Examination of capsid morphogenesis based on epitope unmasking, capsid composition, and ultrastructural analysis indicated that these clusters consisted of procapsids. The results demonstrate that, in addition to established events that occur inside the capsid, the exterior capsid shell promotes capsid morphogenesis and maturation. IMPORTANCE Herpesviruses assemble capsids and encapsidate their genomes by a process that is unlike those of other mammalian viruses but is similar to those of some bacteriophage. Many important aspects of herpesvirus morphogenesis remain enigmatic, including how the capsid shell matures into a stable angularized configuration. Capsid maturation is triggered by activation of a protease that cleaves an internal protein scaffold. We report on the fortuitous discovery that a region of the major capsid protein that is exposed on the outer surface of the capsid also contributes to capsid maturation, demonstrating that the morphogenesis of the capsid shell from its procapsid precursor to the mature angularized form is dependent upon internal and external components of the megastructure.
Effect of Squat Exercises on Lung Function in Elderly Women with Sarcopenia

We explored whether a mechanically-assisted squat exercise improved muscle mass, muscle function, and pulmonary function in elderly women with or without sarcopenia. In total, 76 community-dwelling elderly subjects (>60 years of age) were screened. We ultimately included 30 subjects who completed more than 80% of the six-week course of mechanically-assisted squat exercises (three days per week, 30 min per day). We measured body composition, lung function, knee extensor strength, hand grip strength, and the 3-min walk distance (3MWD) before and after the exercise program. Subjects with sarcopenia had poor hand grip strength and knee extensor strength, and a slow walking speed. Their lung function parameters, including forced vital capacity (FVC), was lower than those of the controls. After six weeks of squat exercises, the hand grip strength, knee extensor strength, and 3MWD increased significantly in both groups. Appendicular skeletal muscle mass and leg lean mass were increased in subjects without sarcopenia. The FVC (L) increased significantly only in the sarcopenia group (p = 0.019). The mechanically-assisted squat exercise program increased muscle function and lung function, including FVC, in patients with sarcopenia. Muscle mass increased in subjects without sarcopenia.