Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Plant Glutathione S-Transferase/Peroxidase Suppresses Bax Lethality in Yeast*

The mammalian inducer of apoptosis Bax is lethal when expressed in yeast and plant cells. To identify potential inhibitors of Bax in plants we transformed yeast cells expressing Bax with a tomato cDNA library and we selected for cells surviving after the induction of Bax. This genetic screen allows for the identification of plant genes, which inhibit either directly or indirectly the lethal phenotype of Bax. Using this method a number of cDNA clones were isolated, the more potent of which encodes a protein homologous to the class θ glutathioneS-transferases. This Bax-inhibiting (BI) protein was expressed in Escherichia coli and found to possess glutathione S-transferase (GST) and weak glutathione peroxidase (GPX) activity. Expression of Bax in yeast decreases the intracellular levels of total glutathione, causes a substantial reduction of total cellular phospholipids, diminishes the mitochondrial membrane potential, and alters the intracellular redox potential. Co-expression of the BI-GST/GPX protein brought the total glutathione levels back to normal and re-established the mitochondrial membrane potential but had no effect on the phospholipid alterations. Moreover, expression of BI-GST/GPX in yeast was found to significantly enhance resistance to H2O2-induced stress. These results underline the relationship between oxidative stress and Bax-induced death in yeast cells and demonstrate that the yeast-based genetic strategy described here is a powerful tool for the isolation of novel antioxidant and antiapoptotic genes.
Bacterial Infection and Immune Responses in Lutzomyia longipalpis Sand Fly Larvae Midgut

The midgut microbial community in insect vectors of disease is crucial for an effective immune response against infection with various human and animal pathogens. Depending on the aspects of their development, insects can acquire microbes present in soil, water, and plants. Sand flies are major vectors of leishmaniasis, and shown to harbor a wide variety of Gram-negative and Gram-positive bacteria. Sand fly larval stages acquire microorganisms from the soil, and the abundance and distribution of these microorganisms may vary depending on the sand fly species or the breeding site. Here, we assess the distribution of two bacteria commonly found within the gut of sand flies, Pantoea agglomerans and Bacillus subtilis. We demonstrate that these bacteria are able to differentially infect the larval digestive tract, and regulate the immune response in sand fly larvae. Moreover, bacterial distribution, and likely the ability to colonize the gut, is driven, at least in part, by a gradient of pH present in the gut.
Hybrid Beamforming With Discrete Phase Shifters for Millimeter-Wave Massive MIMO Systems

Hybrid digital and analog beamforming design has been the focus of considerable interest in the context of millimeter-wave massive multiple-input multiple-output systems because such a design can provide a flexible compromise between hardware complexity and system performance. However, most existing hybrid beamforming designs usually assume that infinite resolution phase shifters (PSs) are available to produce analog beamformers. In a practical sense, the employment of such shifters with arbitrary phase is infeasible or, at least, is expensive because of hardware limitations. We propose an iterative hybrid transceiver design algorithm, where PSs can only supply discrete phase adjustments, to facilitate low-cost implementation of the analog beamformers via finite resolution PSs while maximizing spectral efficiency. Simulation results reveal that the performance of the proposed algorithm with low-resolution PSs is close to that of the state-of-the-art algorithm with infinite resolution PSs.
The different ecological niches of enterotoxigenic E scherichia coli

Summary Enterotoxigenic E scherichia coli (ETEC) is a water and food‐borne pathogen that infects the small intestine of the human gut and causes diarrhoea. Enterotoxigenic E. coli adheres to the epithelium by means of colonization factors and secretes two enterotoxins, the heat labile toxin and/or the heat stable toxin that both deregulate ion channels and cause secretory diarrhoea. Enterotoxigenic E. coli as all E. coli, is a versatile organism able to survive and grow in different environments. During transmission and infection, ETEC is exposed to various environmental cues that have an impact on survivability and virulence. The ability to cope with exposure to different stressful habitats is probably shaping the pool of virulent ETEC strains that cause both endemic and epidemic infections. This review will focus on the ecology of ETEC in its different habitats and interactions with other organisms as well as abiotic factors.
The metaphor of "family" in staff communication about dying and death.

OBJECTIVES Caregiving staff need to have a way to make sense out of the death and dying of nursing home residents. A range of cultural and institutional factors (e.g., disenfranchised grief; professional distance) thwart their expression of grief. This research examines the neglected area of staff's social construction of the meaning of their relationship with dying and deceased residents. METHODS As part of a multisite ethnographic study of bereavement in long-term care, we analyzed themes in audiotranscribed in-depth qualitative interviews with 26 hands-on caregiving staff members (over two thirds were nurse's aides) in two religiously and culturally diverse nursing homes. RESULTS A theme of family metaphor emerged as staff members spoke of family-like thoughts, feelings, and behaviors toward long-term residents. Staff members spontaneously told stories of deaths in their own families, and they described how the meanings of resident deaths and family deaths were interrelated. DISCUSSION The family metaphor provides cultural scripts that enable staff to overcome barriers to the expression of grief. The family metaphor structures the meaning for staff of death and bereavement, and it provides a bridge between their work and personal experience.
Prognostic value of metabolic tumor volume measured by 18F-FDG PET/CT in advanced-stage squamous cell carcinoma of the larynx and hypopharynx.

BACKGROUND Metabolic tumor volume (MTV) of (18)F-FDG PET/CT is a volumetric measurement of tumor cells with increased 18F-FDG uptake. We evaluated the prognostic value of MTV in patients with locoregionally advanced laryngeal and hypopharyngeal cancer. PATIENTS AND METHODS We evaluated 81 patients with advanced-stage squamous cell carcinoma of the laryngohypopharynx who underwent 18F-FDG PET/CT between January 2004 and September 2009. Clinicopathologic factors and MTV were analyzed for their association with locoregional control (LRC) and overall survival (OS). RESULTS The 3-year LRC and OS for all patients were 70.9 and 78.7%, respectively, with a median follow-up of 40.4 months (range 24.5-90.1). In univariate analyses, MTV, primary site, and primary treatment strategy were associated with both LRC and OS (P<0.05). On multivariate analysis, MTV was an independent prognostic factor for both LRC [P=0.018; HR=3.141, 95% confidence interval (CI)=1.175-8.399] and OS (P=0.008; HR=3.758, 95% CI=1.415-9.982). Primary site was also a significant prognostic factor for LRC (P=0.047). CONCLUSION Pretreatment MTV is an independent prognostic factor in patients with locoregionally advanced squamous cell carcinoma of the larynx and hypopharynx.
Multi-Criteria-Based Strategy to Stop Active Learning for Data Annotation

In this paper, we address the issue of deciding when to stop active learning for building a labeled training corpus. Firstly, this paper presents a new stopping criterion, classification-change, which considers the potential ability of each unlabeled example on changing decision boundaries. Secondly, a multi-criteria-based combination strategy is proposed to solve the problem of predefining an appropriate threshold for each confidence-based stopping criterion, such as max-confidence, min-error, and overall-uncertainty. Finally, we examine the effectiveness of these stopping criteria on uncertainty sampling and heterogeneous uncertainty sampling for active learning. Experimental results show that these stopping criteria work well on evaluation data sets, and the combination strategies outperform individual criteria.
Number needed to treat and number needed to harm with paliperidone palmitate relative to long-acting haloperidol, bromperidol, and fluphenazine decanoate for treatment of patients with schizophrenia

Background: We analyzed data retrieved through a PubMed search of randomized, placebo-controlled trials of first-generation antipsychotic long-acting injectables (haloperidol decanoate, bromperidol decanoate, and fluphenazine decanoate), and a company database of paliperidone palmitate, to compare the benefit-risk ratio in patients with schizophrenia. Methods: From the eight studies that met our selection criteria, two efficacy and six safety parameters were selected for calculation of number needed to treat (NNT), number needed to harm (NNH), and the likelihood of being helped or harmed (LHH) using comparisons of active drug relative to placebo. NNTs for prevention of relapse ranged from 2 to 5 for paliperidone palmitate, haloperidol decanoate, and fluphenazine decanoate, indicating a moderate to large effect size. Results: Among the selected maintenance studies, NNH varied considerably, but indicated a lower likelihood of encountering extrapyramidal side effects, such as akathisia, tremor, and tardive dyskinesia, with paliperidone palmitate versus placebo than with first-generation antipsychotic depot agents versus placebo. This was further supported by an overall higher NNH for paliperidone palmitate versus placebo with respect to anticholinergic use and Abnormal Involuntary Movement Scale positive score. LHH for preventing relapse versus use of anticholinergics was 15 for paliperidone palmitate and 3 for fluphenazine decanoate, favoring paliperidone palmitate. Conclusion: Overall, paliperidone palmitate had a similar NNT and a more favorable NNH compared with the first-generation long-acting injectables assessed.
Tolerance and dose-volume relationship of intrathoracic stomach irradiation after esophagectomy for patients with thoracic esophageal squamous cell carcinoma

Purpose To identify the tolerance of radiation with a high prescribed dose and predictors for the development of intrathoracic stomach toxicity in patients with thoracic esophageal squamous cell carcinoma (SCC) after esophagectomy followed by gastric conduit reconstruction. Methods and Materials From 2011 to 2013, 105 patients after esophagectomy were treated with postoperative radiotherapy. The intrathoracic stomach was outlined with the calculation of a dose-volume histogram (DVH) for the initial intended treatment of 6020 cGy or 6300 cGy. The volume of the intrathoracic stomach receiving each dose was recorded at 10-Gy intervals between 10 and 40 Gy and at 5-Gy intervals between 40 and 60 Gy. The grade of toxicities was defined by the National Cancer Institute Common Toxicity Criteria version 4.0. Results The mean and maximum doses of the intrathoracic stomach were 2449 ± 986 cGy and 6519 ± 406 cGy, respectively. Sixteen (15.2%) and three (2.9%) experienced Common Toxicity Criteria Grade 2 and Grade 3 acute gastric toxicity. There were no Grade 4 toxicities. Fourteen patients (13.3%) exhibited late gastric complications possibly related to radiation. The volume percent of the intrathoracic stomach receiving at least 50 Gy (V50) was strongly associated with the degree of toxicity (p = 0.024, respectively). Multivariate analysis of patient and treatment-related factors revealed no other significant predictors of severe toxicities. Conclusions The intrathoracic stomach is well tolerated with a high-dose irradiation for patients with esophageal SCC receiving radiotherapy after esophagectomy. A strong dose-volume relationship exists for the development of Grade 2 acute intrathoracic stomach toxicity in our study.
Assessing Advance Directives in the Homebound Elderly

We studied the prevalence of specific barriers that prevent indigent homebound older adults from obtaining advance directives and tested the effectiveness of clinical reminders for lowering the number of clients without advance directives. Case managers interviewed 1569 clients to determine whether they had an advance directive. All 530 clients without advance directives were contacted 3 months later to determine if advance directives had been obtained. Clients who still did not have advance directives were asked to list 1 or more reasons they did not have advance directives. About 57.8% of the barriers identified may reflect reluctance on the part of clients to address their own mortality. Reminders by the case managers were ineffective at lowering the number of homebound older adults without advance directives. Further studies are needed to identify and design strategies for convincing this population of homebound elderly to establish advance directives.
Injections, Cocktails and Diviners: Therapeutic Flexibility in the Context of Malaria Elimination and Drug Resistance in Northeast Cambodia

Background Adherence to effective malaria medication is extremely important in the context of Cambodia’s elimination targets and drug resistance containment. Although the public sector health facilities are accessible to the local ethnic minorities of Ratanakiri province (Northeast Cambodia), their illness itineraries often lead them to private pharmacies selling “cocktails” and artemether injections, or to local diviners prescribing animal sacrifices to appease the spirits. Methods The research design consisted of a mixed methods study, combining qualitative (in-depth interviews and participant observation) and quantitative methods (household and cross-sectional survey). Results Three broad options for malaria treatment were identified: i) the public sector; ii) the private sector; iii) traditional treatment based on divination and ceremonial sacrifice. Treatment choice was influenced by the availability of treatment and provider, perceived side effects and efficacy of treatments, perceived etiology of symptoms, and patient-health provider encounters. Moreover, treatment paths proved to be highly flexible, changing mostly in relation to the perceived efficacy of a chosen treatment. Conclusions Despite good availability of anti-malarial treatment in the public health sector, attendance remained low due to both structural and human behavioral factors. The common use and under-dosage of anti-malaria monotherapy in the private sector (single-dose injections, single-day drug cocktails) represents a threat not only for individual case management, but also for the regional plan of drug resistance containment and malaria elimination.
Knowledge of Native Protein-Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding Candidates

Selection of putative binding poses is a challenging part of virtual screening for protein-protein interactions. Predictive models to filter out binding candidates with the highest binding affinities comprise scoring functions that assign a score to each binding pose. Existing scoring functions are typically deduced by collecting statistical information about interfaces of native conformations of protein complexes along with interfaces of a large generated set of non-native conformations. However, the obtained scoring functions become biased toward the method used to generate the non-native conformations, i.e., they may not recognize near-native interfaces generated with a different method. The present study demonstrates that knowledge of only native protein-protein interfaces is sufficient to construct well-discriminative predictive models for the selection of binding candidates. Here we introduce a new scoring method that comprises a knowledge-based potential called KSENIA deduced from structural information about the native interfaces of 844 crystallographic protein-protein complexes. We derive KSENIA using convex optimization with a training set composed of native protein complexes and their near-native conformations obtained using deformations along the low-frequency normal modes. As a result, our knowledge-based potential has only marginal bias toward a method used to generate putative binding poses. Furthermore, KSENIA is smooth by construction, which allows it to be used along with rigid-body optimization to refine the binding poses. Using several test benchmarks, we demonstrate that our method discriminates well native and near-native conformations of protein complexes from non-native ones. Our methodology can be easily adapted to the recognition of other types of molecular interactions, such as protein-ligand, protein-RNA, etc. KSENIA will be made publicly available as a part of the SAMSON software platform at https://team.inria. fr/nano-d/software .
Experimental warming alters migratory caribou forage quality.

Global declines in caribou and reindeer (Rangifer) populations have drawn attention to the myriad of stressors that these Arctic and boreal forest herbivores currently face. Arctic warming has resulted in increased tundra shrub growth and therefore Rangifer forage quantity. However, its effects on forage quality have not yet been addressed although they may be critical to Rangifer body condition and fecundity. We investigated the impact of 8 yrs of summer warming on the quality of forage available to the Bathurst caribou herd using experimental greenhouses (n = 5) located in mesic birch hummock tundra in the central Canadian Low Arctic. Leaf forage quality and digestibility characteristics associated with nutrients (nitrogen and phosphorus), phenolics, and fiber were measured on the deciduous shrub Betula glandulosa (an important Rangifer diet component) at six time points through the growing season, and on five other very common vascular plant and lichen species in late summer. Experimental warming reduced B. glandulosa leaf nitrogen concentrations by ~10% in both late June and mid-July, but not afterwards. It also reduced late summer forage quality of the graminoid Eriophorum vaginatum by increasing phenolic concentrations 38%. Warming had mixed effects on forage quality of the lichen Cetraria cucullata in that it increased nutrient concentrations and tended to decrease fiber contents, but it also increased phenolics. Altogether, these warming-induced changes in forage quality over the growing season, and response differences among species, highlight the importance of Rangifer adaptability in diet selection. Furthermore, the early season reduction in B. glandulosa nitrogen content is a particular concern given the importance of this time for calf growth. Overall, our demonstration of the potential for significant warming impacts on forage quality at critical times for these animals underscores the importance of effective Rangifer range conservation to ensure sufficient appropriate habitat to support adaptability in forage selection in a rapidly changing environment.
Amistades: The Development of Relationships between Preservice Teachers and Latino Families

Preservice teachers from a Hispanic-serving university and Latino families reflected on their interactions during an after-school children’s tutoring pro gram conducted at an elementary school. This paper focuses on issues that both preservice teachers and families found important to communication and relationship building. These issues were valuing what families bring to the ed ucational process, congruency in the interpretation of teacher roles, and the importance of language to communication and relationship building.
SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model

How to recognize the structural fold of a protein is one of the challenges in protein structure prediction. We have developed a series of single (non-consensus) methods (SPARKS, SP2, SP3, SP4) that are based on weighted matching of two to four sequence and structure-based profiles. There is a robust improvement of the accuracy and sensitivity of fold recognition as the number of matching profiles increases. Here, we introduce a new profile-profile comparison term based on real-value dihedral torsion angles. Together with updated real-value solvent accessibility profile and a new variable gap-penalty model based on fractional power of insertion/deletion profiles, the new method (SP5) leads to a robust improvement over previous SP method. There is a 2% absolute increase (5% relative improvement) in alignment accuracy over SP4 based on two independent benchmarks. Moreover, SP5 makes 7% absolute increase (22% relative improvement) in success rate of recognizing correct structural folds, and 32% relative improvement in model accuracy of models within the same fold in Lindahl benchmark. In addition, modeling accuracy of top-1 ranked models is improved by 12% over SP4 for the difficult targets in CASP 7 test set. These results highlight the importance of harnessing predicted structural properties in challenging remote-homolog recognition. The SP5 server is available at http://sparks.informatics. iupui.edu.
Mobile IP

Mobile IP has been designed within the Internet Engineering Task Force (IETF) to serve the needs of the burgeoning population of mobile computer users who wish to connect to the Internet and maintain communications as they move from place to place. The basic protocol is described, with details given on the three major component protocols: agent advertisement, registration, and tunneling. Then route optimization procedures are outlined, and further topics of current interest are described. The available tunneling mechanisms are shown, which the home agent uses to forward datagrams from the home network to the mobile computer. Having covered the details of the base mobile IP specification, we then describe further protocol messages which help to decrease the inefficiency associated with inserting the home agent in the routing path of data destined for mobile computers. Finally, we summarize and discuss the current problems facing mobile IP, as well as a few areas of active protocol development.
Circulating adiponectin concentrations in patients with congestive heart failure

Objectives: To determine concentrations of adiponectin and its predictive value on outcome in a cohort of patients with congestive heart failure (CHF). Methods: Serum and clinical data were obtained for outpatients with clinically controlled CHF (n = 175). Serum concentrations of adiponectin, C reactive protein, N-terminal pro-brain natriuretic peptide (NT-proBNP), interleukin (IL) -1β, IL-6, IL-8, IL-10, IL-12, tumour necrosis factor α and CD-40 ligand were determined. The association of adiponectin with the clinical severity of CHF was sought as well as the predictive value of this adipokine on mortality, CHF hospitalisations or the occurrence of each of these end points. Results: Concentrations of adiponectin were significantly increased in patients with CHF. Patients with higher New York Heart Association class had significantly higher serum concentrations of adiponectin. Adiponectin serum concentrations were lower in patients with diabetes and CHF as well as in patients with ischaemic cardiomyopathy. Serum adiponectin concentration was positively associated with age and NT-proBNP but was negatively correlated with C reactive protein concentrations. Serum adiponectin above the 75th centile was found to be an independent predictor of total mortality, CHF hospitalisations or a composite of these end points over a two-year prospective follow up. Conclusion: Adiponectin is increased in CHF patients and predicts mortality and morbidity.