Miracle-dz/UniFAR-FTUs huggingface dataset:
Determining r-Robustness of Arbitrary Digraphs Using Zero-One Linear Integer Programming

There has been an increase in the use of resilient control algorithms based on the graph theoretic properties of $r$- and $(r,s)$-robustness. These algorithms guarantee consensus of normally behaving agents in the presence of a bounded number of arbitrarily misbehaving agents if the values of the integers $r$ and $s$ are sufficiently high. However, determining the largest integer $r$ for which an arbitrary digraph is $r$-robust is highly nontrivial. This paper introduces a novel method for calculating this value using zero-one integer programming. The method only requires knowledge of the graph Laplacian matrix, and can be formulated with affine objective and constraints, except for the integer constraint. Integer programming methods such as branch-and-bound can allow both lower and upper bounds on $r$ to be iteratively tightened. Simulations suggest the proposed method demonstrates greater efficiency than prior algorithms.
Into the breach: how cells cope with wounds

Repair of wounds to individual cells is crucial for organisms to survive daily physiological or environmental stresses, as well as pathogen assaults, which disrupt the plasma membrane. Sensing wounds, resealing membranes, closing wounds and remodelling plasma membrane/cortical cytoskeleton are four major steps that are essential to return cells to their pre-wounded states. This process relies on dynamic changes of the membrane/cytoskeleton that are indispensable for carrying out the repairs within tens of minutes. Studies from different cell wound repair models over the last two decades have revealed that the molecular mechanisms of single cell wound repair are very diverse and dependent on wound type, size, and/or species. Interestingly, different repair models have been shown to use similar proteins to achieve the same end result, albeit sometimes by distinctive mechanisms. Recent studies using cutting edge microscopy and molecular techniques are shedding new light on the molecular mechanisms during cellular wound repair. Here, we describe what is currently known about the mechanisms underlying this repair process. In addition, we discuss how the study of cellular wound repair—a powerful and inducible model—can contribute to our understanding of other fundamental biological processes such as cytokinesis, cell migration, cancer metastasis and human diseases.
A Deep Learning Architecture for De-identification of Patient Notes: Implementation and Evaluation

De-identification is the process of removing 18 protected health information (PHI) from clinical notes in order for the text to be considered not individually identifiable. Recent advances in natural language processing (NLP) has allowed for the use of deep learning techniques for the task of de-identification. In this paper, we present a deep learning architecture that builds on the latest NLP advances by incorporating deep contextualized word embeddings and variational drop out Bi-LSTMs. We test this architecture on two gold standard datasets and show that the architecture achieves state-of-the-art performance on both data sets while also converging faster than other systems without the use of dictionaries or other knowledge sources.
Abscisic acid-independent stomatal CO2 signal transduction pathway and convergence of CO2 and ABA signaling downstream of OST1 kinase

Significance Elevated CO2 and abscisic acid (ABA) induce rapid stomatal closure, but the underlying signal transduction mechanisms of CO2/ABA interaction remain unclear. Here we show that elevated CO2-induced stomatal closure is not abolished but is slowed in higher-order ABA biosynthesis and receptor mutants. Physiological CO2 elevations activate anion channels in these mutants. In vivo time-resolved ABA nanoreporter imaging indicates that CO2 elevation does not change ABA concentrations in guard cells. Unexpectedly, CO2 signaling proceeds without direct OST1/SnRK2 kinase activation in guard cells. This study points to a model that elevated CO2 triggers stomatal closure through an ABA-independent pathway downstream of OST1/SnRK2 kinases and that basal ABA signaling and OST1/SnRK2 activity enhance stomatal closure in response to CO2 elevation. Stomatal pore apertures are narrowing globally due to the continuing rise in atmospheric [CO2]. CO2 elevation and the plant hormone abscisic acid (ABA) both induce rapid stomatal closure. However, the underlying signal transduction mechanisms for CO2/ABA interaction remain unclear. Two models have been considered: (i) CO2 elevation enhances ABA concentrations and/or early ABA signaling in guard cells to induce stomatal closure and (ii) CO2 signaling merges with ABA at OST1/SnRK2.6 protein kinase activation. Here we use genetics, ABA-reporter imaging, stomatal conductance, patch clamp, and biochemical analyses to investigate these models. The strong ABA biosynthesis mutants nced3/nced5 and aba2-1 remain responsive to CO2 elevation. Rapid CO2-triggered stomatal closure in PYR/RCAR ABA receptor quadruple and hextuple mutants is not disrupted but delayed. Time-resolved ABA concentration monitoring in guard cells using a FRET-based ABA-reporter, ABAleon2.15, and ABA reporter gene assays suggest that CO2 elevation does not trigger [ABA] increases in guard cells, in contrast to control ABA exposures. Moreover, CO2 activates guard cell S-type anion channels in nced3/nced5 and ABA receptor hextuple mutants. Unexpectedly, in-gel protein kinase assays show that unlike ABA, elevated CO2 does not activate OST1/SnRK2 kinases in guard cells. The present study points to a model in which rapid CO2 signal transduction leading to stomatal closure occurs via an ABA-independent pathway downstream of OST1/SnRK2.6. Basal ABA signaling and OST1/SnRK2 activity are required to facilitate the stomatal response to elevated CO2. These findings provide insights into the interaction between CO2/ABA signal transduction in light of the continuing rise in atmospheric [CO2].
Consultant psychiatrists' experience of workplace violence – a national survey

Abstract Objectives: In recent years there have been a number of high profile cases in Irish psychiatry where consultant psychiatrists have been subjected to serious physical assaults. The last survey of assaults on consultant psychiatrists in Ireland was carried out in 1998. Therefore we sought to update the data on this topic. Method: An anonymous questionnaire was sent out by post to all consultant psychiatrists (n = 330) identified as currently working in the Republic of Ireland. Results: The response rate was 48.2%. Sixty per cent of respondents were working in general adult psychiatry and respondents were evenly spread throughout the country. Ninety per cent of respondents had been the victim of verbal aggression/intimidation/threatening behaviour while 55% had been physically assaulted. The majority of incidents involved male patients aged between 21-40 years with a diagnosis of paranoid schizophrenia. Nearly 66% of incidents of physical violence occurred during a relapse of illness. The perpetrator had a history of violence in approximately half of all reported incidents. Physical assaults tended to occur more commonly in inpatient settings (63.7%). Incident reporting occurred more often in physical assaults with 66% reported informally to colleagues and 20% reported to An Garda Siochana (police force of Ireland). Eighty-nine (56%) consultants described feeling ‘safe’ at work. Less than 50% reported the provision of standard safety equipment in the workplace and nearly half ofrespondents had not attended any safety training courses since their appointment. Longer experience working as a consultant psychiatrist did not appear to have an impact on reducing the rate of assaults. In addition, those who attended safety training courses did not report a reduced rate of physical assaults. Conclusions: These findings highlight the need for both organisational and personal changes in practice in order to reduce the assault rate. Organisational changes include the provision of appropriate safety equipment, safety training for consultants, enhancing multidisciplinary teams and utilising risk assessment. Consultants' personal practices to improve their safety may offer useful information for inclusion in safety training courses. This is an area which merits further research.
Promising vaccines for treating glioblastoma

ABSTRACT Introduction: Conventional therapies for glioblastoma (GBM) typically fail to provide lasting antitumor benefits, owing to their inability to specifically eliminate all malignant cells. Cancer vaccines are currently being evaluated as a means to direct the adaptive immune system to target residual GBM cells that remain following standard-of-care treatment. Areas covered: In this review, we provide an overview of the more noteworthy cancer vaccines that are under investigation for the treatment of GBM, as well as potential future directions that may enhance GBM-vaccine effectiveness. Expert opinion: To date, no cancer vaccines have been proven effective against GBM; however, only a few have reached phase III clinical testing. Clinical immunological monitoring data suggest that GBM vaccines are capable of stimulating immune responses reactive to GBM antigens, but whether these responses have an appreciable antitumor effect on GBM is still uncertain. Nevertheless, there have been several promising outcomes in early phase clinical trials, which lend encouragement to this area of study. Further studies with GBM vaccines are, therefore, warranted.
Prelamin A causes aberrant myonuclear arrangement and results in muscle fiber weakness

Physiological and premature aging are frequently associated with an accumulation of prelamin A, a precursor of lamin A, in the nuclear envelope of various cell types. Here, we aimed to underpin the hitherto unknown mechanisms by which prelamin A alters myonuclear organization and muscle fiber function. By experimentally studying membrane-permeabilized myofibers from various transgenic mouse lines, our results indicate that, in the presence of prelamin A, the abundance of nuclei and myosin content is markedly reduced within muscle fibers. This leads to a concept by which the remaining myonuclei are very distant from each other and are pushed to function beyond their maximum cytoplasmic capacity, ultimately inducing muscle fiber weakness.
Endoplasmic reticulum stress affected chondrocyte apoptosis in femoral head necrosis induced by glucocorticoid in broilers

ABSTRACT In our previous study, chondrocyte apoptosis in femoral head necrosis (FHN)‐affected broilers was found to be associated with the endoplasmic reticulum stress (ERS) signaling pathway. In the present study, we further explored the role of ERS‐induced chondrocyte apoptosis in FHN‐affected broilers and the parallel test was carried out with articular chondrocytes cultivated in vitro. The broilers and chondrocytes were treated with methylprednisolone (MP). The main pathological changes in FHN‐affected broilers included the proximal femoral head separated from its articular cartilage and growth plate lesions. MP‐treated chondrocytes demonstrated morphology changes, cell viability reduction, secretory capacity dysfunction, and apoptosis. The mRNA expressions of pro‐apoptotic genes controlled by ERS signaling pathway were up‐regulated both in vivo and in vitro experiments. It showed that MP induced FHN in broilers, activated apoptosis‐related genes on ERS signaling pathway, and affected the survival and apoptosis of chondrocytes, and bone growth.
Predicting Factuality of Reporting and Bias of News Media Sources

We present a study on predicting the factuality of reporting and bias of news media. While previous work has focused on studying the veracity of claims or documents, here we are interested in characterizing entire news media. This is an under-studied, but arguably important research problem, both in its own right and as a prior for fact-checking systems. We experiment with a large list of news websites and with a rich set of features derived from (i) a sample of articles from the target news media, (ii) its Wikipedia page, (iii) its Twitter account, (iv) the structure of its URL, and (v) information about the Web traffic it attracts. The experimental results show sizable performance gains over the baseline, and reveal the importance of each feature type.
Bioactive Compounds and Antioxidant Capacity of Rosa rugosa Depending on Degree of Ripeness

Maturity stage affects the bioactive compounds as well as the antioxidant capacity in the fruit. This study was designed to identify and quantify carotenoids, as well as to evaluate vitamin E, vitamin C, antioxidant capacity and total phenolic compounds of Rosa rugosa hips at different degrees of ripeness. HPLC (high performance liquid chromatography) analysis showed different types of carotenoids at different stages of maturity of R. rugosa hips with significant differences (p ˂ 0.05), where the maximum concentration was observed at late harvesting. In the hips investigated, only α-tocopherol was detected, the maximum concentration of both vitamin E and vitamin C was obtained in the orange hips with significant difference (p ˂ 0.05). On the other hand, the highest hydrophilic and lipophilic TEAC (Trolox equivalent antioxidant capacity) values, as well as total phenolic contents, were determined in the mature hips (red colour) with significant difference (p < 0.0001) and (p < 0.001) respectively, whereas ORAC (oxygen radical absorbance capacity) showed lower activity in the mature hips with significant difference (p ˂ 0.05). Late harvesting is recommended if a high content of carotenoids is desired, while harvesting should be carried out earlier if a higher vitamin E and vitamin C content is desired, which in turn affects the antioxidants capacity.
Heterogeneous Domain Adaptation Through Progressive Alignment

In real-world transfer learning tasks, especially in cross-modal applications, the source domain and the target domain often have different features and distributions, which are well known as the heterogeneous domain adaptation (HDA) problem. Yet, existing HDA methods focus on either alleviating the feature discrepancy or mitigating the distribution divergence due to the challenges of HDA. In fact, optimizing one of them can reinforce the other. In this paper, we propose a novel HDA method that can optimize both feature discrepancy and distribution divergence in a unified objective function. Specifically, we present progressive alignment, which first learns a new transferable feature space by dictionary-sharing coding, and then aligns the distribution gaps on the new space. Different from previous HDA methods that are limited to specific scenarios, our approach can handle diverse features with arbitrary dimensions. Extensive experiments on various transfer learning tasks, such as image classification, text categorization, and text-to-image recognition, verify the superiority of our method against several state-of-the-art approaches.
Nonpathogenic Heterologous Prions Can Interfere with Prion Infection in a Strain-Dependent Manner

As a general conclusion, the outcome of prion coinfection is strongly dependent on the strain combination and the model utilized and is therefore difficult to predict. The coexistence of several prion strains may remain undetected if one of the strains has more favorable conditions to replicate in the host. The use of several models (such as a transgenic mouse expressing PrP from different species) to analyze field prion isolates is recommended to avoid this situation. The inference effect exerted by nonreplicative prion strains should be considered an interesting tool to advance in new therapeutic strategies for treating prion diseases; it may even be a proper therapeutic strategy. ABSTRACT Co-occurrence of different prion strains into the same host has been recognized as a natural phenomenon for several sporadic Creutzfeldt-Jakob disease (sCJD) patients and natural scrapie cases. The final outcome of prion coinfection is not easily predictable. In addition to the usual factors that influence prion conversion, the replication of one strain may entail positive or negative consequences to the other. The main aim of this study was to gain insights into the prion coinfection and interference concepts and their potential therapeutic implications. Here, different mouse models were challenged with several combinations of prion strains coupled on the basis of the lengths of their incubation periods and the existence/absence of a species barrier in the tested animal model. We found that nontransmissible strains can interfere the replication of fully transmissible strains when there is a species transmission barrier involved, as happened with the combination of a mouse (22L) and a human (sCJD) strain. However, this phenomenon seems to be strain dependent, since no interference was observed when the human strain coinoculated was vCJD. For the other combinations tested in this study, the results suggest that both strains replicate independently without effect on the replication of one over the other. It is common that the strain with more favorable conditions (e.g., a higher speed of disease development or the absence of a species barrier) ends being the only one detectable at the terminal stage of the disease. However, this does not exclude the replication of the least favored strain, leading to situations of the coexistence of prion strains. IMPORTANCE As a general conclusion, the outcome of prion coinfection is strongly dependent on the strain combination and the model utilized and is therefore difficult to predict. The coexistence of several prion strains may remain undetected if one of the strains has more favorable conditions to replicate in the host. The use of several models (such as a transgenic mouse expressing PrP from different species) to analyze field prion isolates is recommended to avoid this situation. The inference effect exerted by nonreplicative prion strains should be considered an interesting tool to advance in new therapeutic strategies for treating prion diseases; it may even be a proper therapeutic strategy.
Preemptive Analgesia with Parecoxib in Total Hip Arthroplasty: A Randomized, Double-Blind, Placebo-Controlled Trial.

BACKGROUND Total hip arthroplasty (THA) is a well-accepted surgical treatment for terminal hip diseases. OBJECTIVE To evaluate the effect of preemptive analgesia with parecoxib in patients undergoing primary unilateral THA. STUDY DESIGN A randomized, double-blind, placebo-controlled study. SETTING This study was conducted at Peking Union Medical College Hospital and Beijing Jishuitan Hospital in Beijing, China. METHODS A total of 94 patients scheduled for primary unilateral THA in 2 centers (Peking Union Medical College Hospital and Beijing Jishuitan Hospital) were randomly assigned to receive 40 mg parecoxib (n = 48) or 0.9% normal saline solution (n = 46) 30 minutes before incision. All patients received standardized intravenous patient-controlled analgesia (PCA) postoperatively. Preoperative baseline data, surgery-related conditions, postoperative Visual Analog Scale (VAS) pain score, cumulative narcotic consumption of PCA, and complications were compared between the parecoxib group and the placebo group. RESULTS There were no significant differences in postoperative VAS pain score, cumulative narcotic consumption of PCA, proportion of analgesic remedy, and complications between the 2 groups. LIMITATIONS Only a single dose of parecoxib was used without including a dose-dependent control group. CONCLUSION A single dose of parecoxib 30 minutes before incision did not provide effective preemptive analgesia for the management of postoperative pain after primary unilateral THA. The possible effect of preemptive analgesia with parecoxib needs further investigation. KEY WORDS Total hip arthroplasty, pain, parecoxib, COX-2 selective inhibitor, preemptive analgesia, clinical trial, patient-controlled analgesia, analgesics.
Micronuclei frequency in urothelial cells of bladder cancer patients, as a biomarker of prognosis

It has been suggested that the frequency of micronuclei (MN) in defoliated urothelial cells could be used as a biomarker for both the potential risk of bladder cancer (BC) and its progression. To prove this we have carried out a large study evaluating the MN frequency in a group of 383 hospital patients submitted to cystoscopy. From them, 77 were negative in their first cystoscopy, and were considered as a reference group; 79 were positive and were classified as patients with tumor; and 227 with previous bladder cancer submitted to follow‐up monitoring were negative and classified as BC patients without tumor. Vesical washes were processed and the obtained cells were placed onto microscope slides for further scoring. To minimize scoring misinterpretations, cells were stained with DAPI, and observed in a fluorescence microscope. Results indicated that patients with BC presented higher incidence of MN than controls (18.29 ± 10.04 vs. 14.40 ± 8.49, P = 0.010, respectively). When individuals with BC were classified depending on whether the BC was a primary or a recidivated tumor, those patients with recurrent BC presented a higher frequency of MN than those where BC was detected for the first time (19.22 ± 9.59 vs. 16.60 ± 10.78, respectively); nevertheless, this increase did not reach statistical significance. Finally, a positive and significant correlation was observed between MN frequency and the degree of the tumor (P = 0.038). All this together would confirm the potentiality of the MN frequency in urothelial defoliated cells assay to be used, at least, in the follow‐up and surveillance of BC patients. Environ. Mol. Mutagen. 60: 168–173, 2019. © 2018 Wiley Periodicals, Inc.
Has the Mental Health Act 2001 altered the clinical profile of involuntary admissions?

Abstract Objectives: To assess whether transition from the Mental Treatment Act (MTA), 1945 to the Mental Health Act (MHA), 2001 has had any impact on the clinical profile of patients in the West Galway Mental Health Services who are admitted on an involuntary basis. Methods: Data were collected from clinical records in relation to all those individuals residing in the West Galway Mental Health Services who were admitted involuntarily in the 12 months prior to and subsequent to the introduction of the MHA 2001. Results: A total of 175 individuals were included in this study (n = 91 - MTA 1945; and n = 84 - MHA 2001). No significant differences were found between the two groups in relation to demographic data, rates of involuntary detention or duration of involuntary detention. The applicant was less likely to be a family member under the MHA 2001 (54%) than the MTA 1945 (85%). Conclusions: Transition from the MTA 1945 to the MHA 2001 has had minimal impact on the admission rates, clinical profile or duration of detention of patients admitted involuntarily in the West Galway Mental Health Services.
Dynamically Weighted Optimal Switching Vector Model Predictive Control of Power Converters

In this paper, new techniques are presented to improve the performance of the optimal switching vector model predictive control. A well-defined analytic technique is proposed for the real-time adjustment of dynamic weighting factors, as well as a new objective function formulation. These techniques provide a dynamic controller behavior, automatically adapted to distinct operating points. This ensures better steady-state performance in different conditions while improving simultaneously the dynamic response. The proposed controller presents a lower computational load than the conventional formulation and its design requires less extensive testing. General guidelines are presented to guide the user in the controller design. Simulation and experimental results are presented, demonstrating the advantages and superior performance of the proposed controller.