Miracle-dz/UniFAR-FTUs huggingface dataset:
Code Summarization with Structure-induced Transformer

Code summarization (CS) is becoming a promising area in recent language understanding, which aims to generate sensible human language automatically for programming language in the format of source code, serving in the most convenience of programmer developing. It is well known that programming languages are highly structured. Thus previous works attempt to apply structure-based traversal (SBT) or non-sequential models like Tree-LSTM and graph neural network (GNN) to learn structural program semantics. However, it is surprising that incorporating SBT into advanced encoder like Transformer instead of LSTM has been shown no performance gain, which lets GNN become the only rest means modeling such necessary structural clue in source code. To release such inconvenience, we propose structure-induced Transformer, which encodes sequential code inputs with multi-view structural clues in terms of a newly-proposed structure-induced self-attention mechanism. Extensive experiments show that our proposed structure-induced Transformer helps achieve new state-of-the-art results on benchmarks.
Testing for unit roots based on sample autocovariances

We propose a new unit root test for a stationary null hypothesis H0 against a unit root alternative H1. Our approach is nonparametric as H0 only assumes that the process concerned is I(0) without specifying any parametric forms. The new test is based on the fact that the sample autocovariance function converges to the finite population autocovariance function for an I(0) process while it diverges to infinity for a process with unit roots. Therefore the new test rejects H0 for the large values of the sample autocovariance function. To address the technical challenge of how large is large, we split the sample and establish an appropriate normal approximation for the null-distribution of the test statistic. The substantial discriminative power of the new test statistic is rooted from the fact that it takes a finite value under H0 and diverges to infinity under H1. This allows us to truncate the critical values of the test so that it has asymptotic power one. It also alleviates the loss of power due to the sample-splitting. The test is implemented in a user-friendly R function.
Perceived Pain Responses to Foam Rolling Associate with Basal Heart Rate Variability

Background Foam rolling (FR) is a self-myofascial release technique with unclear effects on autonomic functioning, indexed by heart rate variability (HRV). FR can be perceived as painful or relaxing, which may explain interindividual HRV responses. Purpose To determine if acute FR alters resting HRV. A secondary aim was to determine if perceived pain during FR would predict HRV responses. Setting Academic institution. Methods In a randomized, crossover design, healthy adults (50% female) performed total body FR or control on separate days. Perceived pain ratings were obtained following FR of each muscle group and summed to generate an overall perceived pain rating. Seated measures of the mean RR interval and the natural logarithm of the root-mean square of successive RR interval differences (LnRMSSD, a parasympathetic HRV index) were obtained at 5–10 min pre-, 5–10 min post-, and 25–30 min post-FR. Results No effects were observed for RR interval (p = .105–.561) or LnRMSSD (p = .110–.129). All effect sizes ranged from trivial–small (0.00–0.26). Changes in RR interval (r = 0.220–0.228, p = .433–.488) and LnRMSSD (r = 0.013–0.256, p = .376–.964) were not associated with pain scale sum. Baseline LnRMSSD was associated with pain scale sum (r = −0.663; p = .001). Conclusion FR did not systematically alter HRV, nor did perceived pain ratings predict HRV responses. Those with lower pre-FR HRV reported higher perceived pain during FR. Basal cardiac autonomic activity may, therefore, influence pain sensitivity to FR in healthy adults.
H1N1 exposure during the convalescent stage of SARS-CoV-2 infection results in enhanced lung pathologic damage in hACE2 transgenic mice

ABSTRACT The risk of secondary infection with SARS-CoV-2 and influenza A virus is becoming a practical problem that must be addressed as the flu season merges with the COVID-19 pandemic. As SARS-CoV-2 and influenza A virus have been found in patients, understanding the in vivo characteristics of the secondary infection between these two viruses is a high priority. Here, hACE2 transgenic mice were challenged with the H1N1 virus at a nonlethal dose during the convalescent stage on 7 and 14 days post SARS-CoV-2 infection, and importantly, subsequent H1N1 infection showed enhanced viral shedding and virus tissue distribution. Histopathological observation revealed an extensive pathological change in the lungs related to H1N1 infection in mice recovered from SARS-CoV-2 infection, with severe inflammation infiltration and bronchiole disruption. Moreover, upon H1N1 exposure on 7 and 14 dpi of SARS-CoV-2 infection, the lymphocyte population activated at a lower level with T cell suppressed in both PBMC and lung. These findings will be valuable for evaluating antiviral therapeutics and vaccines as well as guiding public health work.
Corrigendum to Laura M. Pompano and Erick Boy. Effects of Dose and Duration of Zinc Interventions on Risk Factors for Type 2 Diabetes and Cardiovascular Disease: A Systematic Review and Meta-Analysis. Adv Nutr 2021;12(1):141-60.

Corrigendum to Laura M. Pompano and Erick Boy. Effects of Dose and Duration of Zinc Interventions on Risk Factors for Type 2 Diabetes and Cardiovascular Disease: A Systematic Review and Meta-Analysis. Adv Nutr 2021;12(1):141–60. This study was made possible with support from the UK Government and donors to the CGIAR Research Program on Agriculture for Nutrition and Health (A4NH). Funding sources were excluded from the acknowledgements section by mistake of the authors. The authors apologize for this error.
Staphylococcal Protein A Induces Leukocyte Necrosis by Complexing with Human Immunoglobulins

Staphylococcus aureus is one of the largest health care threats faced by humankind, with a reported mortality rate within the United States greater than that of HIV/AIDS, tuberculosis, and viral hepatitis combined. One of the defining features of S. aureus as a human pathogen is its ability to evade and impair the human immune response through expression of staphylococcal protein A. ABSTRACT One of the defining features of Staphylococcus aureus is its ability to evade and impair the human immune response through expression of staphylococcal protein A (SpA). Herein, we describe a previously unknown mechanism by which SpA can form toxic immune complexes when in the presence of human serum, which leads to the loss of human leukocytes. Further, we demonstrate that these toxic complexes are formed specifically through SpA’s interaction with intact human IgG and that, in the presence of purified IgG Fab and Fc fragments, SpA shows no such toxicity. The mechanism of action of this toxicity appears to be one mediated by necrosis and not by apoptosis, as previously hypothesized, with up to 90% of human B cells rapidly becoming necrotic following stimulation with SpA-IgG complexes. This phenomenon depends on the immunoglobulin binding capacity of SpA, as a nonbinding mutant of SpA did not induce necrosis. Importantly, immune sera raised against SpA had the capacity to significantly reduce the observed toxicity. An unprecedented toxic effect of SpA-IgG complexes on monocytes was also observed, suggesting the existence of a novel mechanism independent from the interaction of SpA with the B cell receptor. Together, these data implicate SpA in inducing indiscriminate leukocyte toxicity upon formation of complexes with IgG and highlight the requirement for vaccination strategies to inhibit this mechanism. IMPORTANCE Staphylococcus aureus is one of the largest health care threats faced by humankind, with a reported mortality rate within the United States greater than that of HIV/AIDS, tuberculosis, and viral hepatitis combined. One of the defining features of S. aureus as a human pathogen is its ability to evade and impair the human immune response through expression of staphylococcal protein A. Herein, we show that SpA induces necrosis in various immune cells by complexing with human immunoglobulins. Vaccination of mice with a nontoxigenic SpA mutant induced sera capable of inhibiting this mechanism. These observations shed new light on the toxic mechanisms of this key staphylococcal virulence factor and on protective modalities of SpA-based vaccination.
A case of tripterygium glycosides‐associated AGEP‐like drug reaction combined with bullous pemphigoid

Acute generalized exanthematous pustulosis (AGEP) is a severe cutaneous drug reaction. Bullous pemphigoid (BP) is an acquired autoimmune disease that might be associated with drugs. There is currently no report of tripterygium glycosides (TG)‐induced AGEP‐like lesions combined with BP. A 66‐year‐old male with a 20‐year history of psoriasis was prescribed oral TG at 1 mg/kg, three times a day, due to aggravated psoriasis. Seven days later, erythemas, and blisters appeared. After another 3 days, there were two types of blisters: (1) numerous small tension blisters with a lot of neutrophils on the top similar to AGEP combined with BP; (2) a BP. After intravenous injection of methylprednisolone and gamma globulin, the lesions were controlled. This patient developed two types of lesions, including one similar to AGEP combined BP (AGEP‐like) and a BP. It is a rare drug reaction induced by TG.
Effects of Spaceflight on Human Skin

During both short- and long-duration spaceflight, several health problems can occur, including those of the skin. Astronauts in space and after returning to earth experience erythematous, burning, itchy, dry, sensitive, and thinning skin. Other skin problems, such as infections, abrasions, lacerations, delayed wound healing, and accelerated skin aging, are also common. Human skin is an ecosystem composed of a wide range of habitats for bacteria, fungi, and viruses called microbiome, which not only show a strong skin site-specific preference but also serve as microbial fingerprints that are highly unique to individuals. These human skin-associated microorganisms make a substantial contribution to the microbial ecosystems that inhabit the closed environments in space. On the other hand, human skin microbiome is also subject to change during spaceflight, which may lead to skin infections or the flare up of skin diseases. This review highlights some of the interactions between the space environment and the skin.
The influence of stress on distractor-response bindings

Abstract Stimuli and responses that occur in close temporal contiguity are bound to each other and stored in short-term episodic traces or event files. A repetition of any of the features within an event file results in the retrieval of the entire event file and can influence responding. Along with task-relevant features, event files also contain task-irrelevant features, which are also bound to responses – distractor-response binding. In the present study, the distractor-response binding effect was examined under stress. Stress was induced via a Cold Pressor Test (CPT) and was manipulated between subjects. Distractor-response binding effects were measures at pre- and post-intervention. The CPT produced reliable effects on cortisol measurements and subjective ratings, however, no difference in the distractor-response binding effects between the groups was observed. Results are discussed against the background of the inconsistent results in the literature with respect to stimulus-response binding and stress.
Effect of Water Deficit and Plant Growth Regulators on Leaf Chlorophyll, Proline and Total Soluble Sugar Content of Two Durum Wheat Cultivars (Triticum turgidum L. var. durum)

Two greenhouse studies were conducted at the University of Jordan campus during 2000/2001 growing season to examine the influence of mepiquat chloride (1,1-dimethyl piperidinium chloride) and ethephon (2-chloroethyl-phosphonic acid) on leaf chlorophyll, soluble sugars, and proline contents of two wheat cultivars (Triticum turgidum L. var durum; Hourani and Petra) grown under various soil moisture levels. In the first experiment, seeds of the two cultivars were soaked within the second experiment, mepiquat chloride solution at the rate of 0, 250, 500, and 750 mg kg–1 for 12 hours before sowing, while in the second experiment, ethephone was foliary applied at the rate of 0, 150, 300 g ha–1 at seedling and tillering stages. Plants were subjected to water deficit stress (soil water maintained around 1/3 of available water) initiated at various growth stages as compared to well water conditions (soil water maintained around 60 to 100% of available water). Leaf proline and total soluble sugar contents were increased with mepiquat chloride treatment up to 750 mg.kg-1 while chlorophyll content was decreased. Total chlorophyll, total soluble sugar, and proline content of both cultivars were not affected by ethephon treatment. Water stress was found to reduce total chlorophyll and to increase proline contents as well as total soluble sugar of the two cultivars. Cultivar variation was observed where Petra cultivar had the highest content of proline and total chlorophyll and chlorophyll a compared to Hourani cultivar, while Hourani was higher in total soluble sugar than Petra. A significant interaction between cultivars and water levels were observed on both total soluble sugar and proline contents and between water levels and sampling stage only for proline content. This indicates variation between the two cultivars at various stages in some of their biochemical constituents and this could be altered by both water deficit and growth regulators such as mepiquat chloride.
Defining an Orbitofrontal Compass: Functional and Anatomical Heterogeneity Across Anterior–Posterior and Medial–Lateral Axes

The orbitofrontal cortex (OFC) plays a critical role in the flexible control of behaviors and has been the focus of increasing research interest. However, there have been a number of controversies around the exact theoretical role of the OFC. One potential source of these issues is the comparison of evidence from different studies, particularly across species, which focus on different specific sub-regions within the OFC. Furthermore, there is emerging evidence that there may be functional diversity across the OFC which may account for these theoretical differences. Therefore, in this review we consider evidence supporting functional heterogeneity within the OFC and how it relates to underlying anatomical heterogeneity. We highlight the importance of anatomical and functional distinctions within the traditionally defined OFC subregions across the medial–lateral axis, which are often not differentiated for practical and historical reasons. We then consider emerging evidence of even finer-grained distinctions within these defined subregions along the anterior–posterior axis. These fine-grained anatomical considerations reveal a pattern of dissociable, but often complementary functions within the OFC.
Secondary hyperparathyroidism, weight loss, and longer term mortality in haemodialysis patients: results from the DOPPS

Wasting is a common complication of kidney failure that leads to weight loss and poor outcomes. Recent experimental data identified parathyroid hormone (PTH) as a driver of adipose tissue browning and wasting, but little is known about the relations among secondary hyperparathyroidism, weight loss, and risk of mortality in dialysis patients.
Dalbergione — Wirkstoffe der Dalbergia-Arten

creased as the moisture content of the wood drops below the fiber saturation point (below about 30%) if a resonable rate of drying is to be maintained. The experiments with small wood samples raised the question of whether or not it is advantageous to use polar rather than non-polar solvents. The small samples dried in ethyl acetate under vacuum and at low temperatures showed lesser volumetric shrinkage than samples dried in toluene at atmospheric pressure and at higher temperatures immediately after distillation but before stripping. Similar trends were observed for large wood samples. The swelling of wood in nonaqueous solvents is usually less than in water. There also are differences between these solvents, e. g. , ethyl acetate a polar solvent swells wood significantly more than toluene a non-polar solvent. Ethyl acetate by its swelling action on the wood retarded the formation of defects. Thus it was possible to carry out the azeotropic drying in ethyl acetate at atmospheric pressure (70.4° C) and thereby simplify the process for the following species: black walnut, yellow poplar, sugar maple, red oak, and shagbark hickory. With toluene, which swells wood to a very limited degree, we could not start drying these species at 70.4° C but at a much lower temperature. Hence, it is clear that some wood species could best be dried in ethyl acetate, whereas another species can most advantageously be dried in toluene. Of the solvents suitable for azeotropic drying, polar solvents generally have lower boiling points than the non-polar solvents used in past experiments, and consequently impart slower maximum drying rates. This behavior was very much evident in our work with ethyl acetate and toluene. However, ethyl acetate can be removed from wood easier at lower temperatures than toluene. The experiments with small wood samples indicate the advantage of including "soaking periods" when attempting to dry wood at low temperatures with polar solvents (Eckelman / Galezewski I97ob). These samples dried during the periodically interrupted process faster than if the drying process were continuous. This trend was not ovserved in case of large samples possibly because the system was allowed cooling — heating cycles that were too short to reach the optimum equilibrium conditions. The interrupted drying process may be of practical value if it will decrease the consumption of electricity for heating and vacuum while still maintaining reasonable drying schedules. Laboratory results show that azeotropic drying of wood is indeed feasible, but its ultimate usefulness will depend on whether it can be used to dry, or pre-dry, without defects, commercial size lumber at a rate and cost competitive with presently used methods.
Removal of N-Linked Glycosylation Enhances PD-L1 Detection in Colon Cancer: Validation Research Based on Immunohistochemistry Analysis

In recent years, immunotherapies have emerged as effective therapeutic strategies for treating human cancers. However, accumulating evidence has revealed an inconsistency between the response to immune checkpoint inhibitors and programmed death ligand 1 (PD-L1) expression status detected by immunohistochemistry staining. Recent research has revealed that the removal of N-Linked glycosylation significantly enhanced PD-L1 detection, resulting in both more accurate PD-L1 quantification and clinical outcome prediction. In the present study, we evaluated natural and deglycosylated PD-L1 expression in colon cancer using the PD-L1 28–8 antibody. The results of the present study validated the hypothesis that PD-L1 had a higher expression in colon cancer tissues compared with normal tissues. Additionally, colon tumors with defective mismatch repair tended to express higher PD-L1 than those without. Most importantly, the results of the present study indicated that the removal of N-linked glycosylation remarkably enhanced PD-L1 detection. Moreover, the PD-L1 signal intensity of samples with a low natural PD-L1 signal was enhanced more remarkably than that of samples with high signal intensity. Overall, our research provides an improved strategy for patient stratification for anti-PD-1/PD-L1 therapy, which deepens the clinical significance of this established strategy for treatment of colon cancer.
The protective effect of α7‐nACh receptor and its interaction with 5‐HT1B/1D receptors in acute intestinal ischemia‐reperfusion injury in rats

Over the past decades, great attention has been given to the nervous system modulating effects on the immune response in inflammation‐associated injuries, such as acute intestinal ischemia‐reperfusion (IR). Recently, we proved the anti‐inflammatory and antioxidant effects of 5‐hydroxytryptamine (5‐HT)1B/1D receptors in intestinal IR injury in rats. Also, the alpha7 nicotinic acetylcholine (α7‐nACh) receptor has anti‐inflammatory effects in different inflammation‐associated injuries. Starting from these premises, we aimed to examine the function of the α7‐nACh receptors and the functional interactions between the anti‐inflammatory and antioxidant effects of α7‐nACh and 5‐HT1B/1D receptors in acute intestinal IR injury. To confirm the expression and localization of α7‐nACh receptors on the ileum nerves, an immunofluorescence‐based method was applied. Then, intestinal IR injury was induced by 30‐min occlusion of superior mesenteric artery and reperfusion for 2 h in rats. Acute systemic administration of α7‐nACh receptor agonist PNU‐282987 and antagonist methyllycaconitine, and 5‐HT1B/1D receptors agonist (sumatriptan) and antagonist (GR127, 935) were used in the model of intestinal IR injury. Finally, biochemical and histological parameters were assessed. Α7‐nACh receptors were expressed by 9% on the ileum nerves. Likewise, activation of the α7‐nACh receptor showed anti‐inflammatory and antioxidant effects in intestinal IR injury but not as well as 5‐HT1B/1D receptors. Interestingly, 5‐HT1B/1D receptors via attenuation of glutamate (Glu) release indirectly activated the α7‐nACh receptor and its protective effects against inflammation and oxidative stress. The protective effect of the α7‐nACh receptor on intestinal IR injury was activated indirectly through the 5‐HT1B/1D receptors’ modulatory impact on Glu release.
Diversity in Starvation Survival Strategies and Outcomes among Heterotrophic Proteobacteria

Heterotrophic Proteobacteria are versatile opportunists that have been extensively studied as model organisms in the laboratory, as both pathogens and beneficial symbionts of plants and animals, and as ubiquitous organisms found free-living in many environments. Succeeding in these niches requires an ability to persist for potentially long periods of time in growth-arrested states when essential nutrients become limiting. The tendency of these bacteria to grow in dense biofilm communities frequently leads to the development of steep nutrient gradients and deprivation of interior cells even when the environment is nutrient rich. Surviving within host environments also likely requires tolerating growth arrest due to the host limiting access to nutrients and transitioning between hosts may require a period of survival in a nutrient-poor environment. Interventions to maximise plant-beneficial activities and minimise infections by bacteria will require a better understanding of metabolic and regulatory networks that contribute to starvation survival, and how these networks function in diverse organisms. Here we focus on carbon starvation as a growth-arresting condition that limits availability not only of substrates for biosynthesis but also of energy for ongoing maintenance of the electrochemical gradient across the cell envelope and cellular integrity. We first review models for studying bacterial starvation and known strategies that contribute to starvation survival. We then present the results of a survey of carbon starvation survival strategies and outcomes in ten bacterial strains, including representatives from the orders Enterobacterales and Pseudomonadales (both Gammaproteobacteria) and Burkholderiales (Betaproteobacteria). Finally, we examine differences in gene content between the highest and lowest survivors to identify metabolic and regulatory adaptations that may contribute to differences in starvation survival.