Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical outcome of gallstone ileus; a single-centre experience of case series and review of the literature

Abstract Background Gallstone ileus (GI) is a rare entity which is seen in 0.5% of patients with cholelithiasis. In this study, we aimed to share our clinical approach to GI, to present our long-term results and to draw clinicians' attention to this rare entity. Materials and methods This study included 11 patients with GI whose medical records were evaluated retrospectively. Results Majority of the 11 patients were female (63.7%, n:7) and the mean age was 71.9 ± 14.10 (range: 50–91). Most common presenting complaints were vomiting (n: 9) and abdominal pain (n: 9). The mean interval from the onset of symptoms to the hospital admission was 3.8 ± 0.75 (range 3–5) days. Rigler triad in abdominal computed tomography (CT) was detected in all cases. Enterolithotomy, one-step procedure and conservative treatment were performed in five (45.4%), four (36.3%) and two (18.1%) patients, respectively. Enterolithotomy group was found to have higher risk according to American Society of Anesthesiologists (ASA) classification, shorter operation time and less intraoperative blood loss. Conclusion Although enterolithotomy is the first choice for patients with GI, one-step procedure should be kept in mind as a more advantageous technique in low-risk patients.
The Effects of Adding Transcutaneous Spinal Cord Stimulation (tSCS) to Sit-To-Stand Training in People with Spinal Cord Injury: A Pilot Study

Spinal cord stimulation may enable recovery of volitional motor control in people with chronic Spinal Cord Injury (SCI). In this study we explored the effects of adding SCS, applied transcutaneously (tSCS) at vertebral levels T10/11, to a sit-to-stand training intervention in people with motor complete and incomplete SCI. Nine people with chronic SCI (six motor complete; three motor incomplete) participated in an 8-week intervention, incorporating three training sessions per week. Participants received either tSCS combined with sit-to-stand training (STIM) or sit-to-stand training alone (NON-STIM). Outcome measures were carried out before and after the intervention. Seven participants completed the intervention (STIM N = 5; NON-STIM N = 2). Post training, improvements in International Standards for Neurological Classification of Spinal Cord Injury (ISNCSCI) motor scores were noted in three STIM participants (range 1.0–7.0), with no change in NON-STIM participants. Recovery of volitional lower limb muscle activity and/or movement (with tSCS off) was noted in three STIM participants. Unassisted standing was not achieved in any participant, although standing with minimal assistance was achieved in one STIM participant. This pilot study has shown that the recruitment of participants, intervention and outcome measures were all feasible in this study design. However, some modifications are recommended for a larger trial.
Pinhead signaling regulates mesoderm heterogeneity via the FGF receptor-dependent pathway

ABSTRACT Among the three embryonic germ layers, the mesoderm plays a central role in the establishment of the vertebrate body plan. The mesoderm is specified by secreted signaling proteins from the FGF, Nodal, BMP and Wnt families. No new classes of extracellular mesoderm-inducing factors have been identified in more than two decades. Here, we show that the pinhead (pnhd) gene encodes a secreted protein that is essential for the activation of a subset of mesodermal markers in the Xenopus embryo. RNA sequencing revealed that many transcriptional targets of Pnhd are shared with those of the FGF pathway. Pnhd activity was accompanied by Erk phosphorylation and required FGF and Nodal but not Wnt signaling. We propose that during gastrulation Pnhd acts in the marginal zone to contribute to mesoderm heterogeneity via an FGF receptor-dependent positive feedback mechanism. Summary: Xenopus Pinhead is a secreted cystine-knot protein that functions in a positive feedback loop with FGF to activate Erk signaling and induce mesoderm.
Assessing open-book examination in medical education: The time is now

Abstract As a result of the coronavirus pandemic, the feasibility of holding secure closed-book examinations in medical education is compromised. In this Personal View, we compare the underlying reasoning for using open-book and closed-book exams. We rethink the role of open-book assessment and offer ways in which we believe they can complement closed-book exams. We highlight the gap in research, highlight future directions, and call on medical educators to seize our current golden opportunity to explore the impact of open-book exams – on their own or combined to closed-book tests, as a blended approach – on learners, educators, and licensing bodies.
QUALIDADE DO INHAME (Dioscorea sp.) MINIMAMENTE PROCESSADO CONSERVADO EM DUAS TEMPERATURAS

O objetivo deste trabalho foi estudar as alteracoes fisico-quimicas, bioquimicas e incidencia de Pseudomonas sp. em inhame minimamente processado conservado em duas temperaturas. O delineamento experimental utilizado foi o inteiramente casualizado em esquema fatorial 2x8, referente as temperaturas (5 e 10 °C) e tempos de conservacao refrigerada (0, 2, 4, 6, 8, 10, 12 e 14 dias), com tres repeticoes. O inhame foi selecionado, descascado e cortado em rodelas de aproximadamente 3 cm de espessura. Essas rodelas foram enxaguadas em agua, sanitizadas e drenadas em escorredores de cozinha. Aproximadamente 300 g do produto processado foram embalados em Nylon multicamadas de 15 µm de espessura, com 15 cm de largura por 20 cm de comprimento. As embalagens foram seladas, pesadas e mantidas a 5 e 10 ± 2 °C por 14 dias. Avaliou-se a perda de massa, tempo de coccao, atividade enzimatica das polifenoloxidases e peroxidases, conteudo de fenois soluveis totais, capacidade antioxidante, analise visual e incidencia de Pseudomonas sp. As medias entre as temperaturas foram comparadas pelo teste de Tukey a 5 % de significância. A temperatura de 5 °C reduziu a perda de massa fresca e da qualidade visual, o tempo de coccao e a atividade das enzimas polifenoloxidases e peroxidases. Por outro lado, proporcionou maior conteudo de fenois soluveis totais e capacidade antioxidante. Ao longo da conservacao, nao foi observada incidencia de Pseudomonas sp. O inhame minimamente processado, sob temperatura de 10 °C, pode ser comercializado por ate 6 dias. A 5o C, por ate 14 dias.
Immunohistochemical Characterization of Sudden Death While Bathing:Evaluating the Expression of SP-A, HSP70 and c-Fos Following Drowningand Thermal Stress

Sudden death while bathing is a major issue in elderly Japanese individuals. Despite its growing incidence, the exact processes underlying sudden death while bathing remain unknown. This study was designed to establish reliable diagnostic markers for drowning while bathing, as well as to assess the pathological conditions associated with sudden death while bathing, by analyzing the immunohistochemical intensity and localization of surfactant protein-A (SP-A), heat shock protein 70 (HSP70) and c-Fos protein in the lungs and central nervous system, including the cerebral cortex and hippocampus. We found that a distinct pattern of immunohistochemical expression of SP-A, HSP70 and c-Fos in the lung can be utilized to diagnose drowning. In most of these individuals, c-Fos protein was absent from the central nervous system, providing insight into patterns of ischemia in the central nervous system, or a loss in consciousness while bathing. We also found that rapid hypothermia or a cold stimulus increased c-Fos expression in the hippocampus (CA4). Furthermore, our results suggest that HSP70 expression in the hippocampus (CA4) can be used to estimate the length of time between the initial occurrence of stress and death.
Creation of glyphosate-resistant Brassica napus L. plants expressing DesC desaturase of cyanobacterium Synechococcus vulcanus

Aim. Creation of glyphosate-resistant canola plants expressing bifunctional hybrid desC::licBM3 gene. In the hybrid gene the sequence of DesC desaturase of cyanobacterium S. vulcanus without plastid targeting was fused with the sequence of thermostable lichenase reporter LicBM3 gene. Methods. Agrobacterium tumefaciensmediated transformation, PCR, quantitative and qualitative determination of lichenase activity, genetic analysis. Results. Transgenic canola plants, carring the enolpyruvat shikimat phosphate syntase gene (epsps), conferring on plants resistance to phosphonomethyl glycine herbicides (Roundup), as well as the desC::licBM3 gene, were selected. The presence of transgenes was confimed by multiplex PCR. The epsps gene expression in canola was shown at the transcription level, during in vitro growth and after greenhouse herbicide treatment. Activity of the licBM3 gene product as a part of hybrid protein allowed quantitative and qualiative estimation of the desaturase gene expression. Inheritance of heterologous genes and their expression in the first generation were investigated. Conclusions. Transgenic canola plants were obtained, the presence of trangenes in plant genome was proved and expression of the target genes was detected.
Pre-Planned Cranioplasty Using Computer-Assisted Designed Temporalis Muscle Augmentation in Patients With Decompressive Craniectomy Involving Resection of the Temporalis Muscle

Background: Decompressive craniectomy (DC) is the last-resort surgical procedure to reduce intracranial pressure and prevent secondary brain injury. Additional resection of the temporalis muscle and fascia can achieve a higher extracranial herniation volume compared to the standard DC technique at the expense of cosmetic problems for the patients. Various methods have been used to augment temporal fossa hollowing. Methods: To improve the cosmetic outcome, the authors report a patient who had a skull defect restored using a precisely shaped implant engineered via a computer using the opposite temporalis muscle as a mirror image. Polyether-ether-ketone cranioplasty was performed for the 52-year-old man with temporal hollowing after DC with resection of the temporalis muscle and fascia, due to a ruptured cerebral arteriovenous fistula. Results: The shape of the patient's surgical side was restored and not asymmetrical. The patient was very satisfied Conclusion: In the case of cranioplasty (CP) in patients with DC with resection of the temporalis muscle, CP with implants that include the opposite muscle may increase patient satisfaction without the risk of additional complications.
Inactivation of AdeABC and AdeIJK efflux pumps elicits specific nonoverlapping transcriptional and phenotypic responses in Acinetobacter baumannii

Multidrug resistant (MDR) strains of Acinetobacter baumannii present a serious clinical challenge. The development of antibiotic resistance in this species is enabled by efflux pumps of the Resistance‐Nodulation‐Division (RND) superfamily of proteins creating an efficient permeability barrier for antibiotics. At least three RND pumps, AdeABC, AdeIJK, and AdeFGH are encoded in the A. baumannii genome and are reported to contribute to antibiotic resistance in clinical isolates. In this study, we analyzed the contributions of AdeABC and AdeIJK in antibiotic resistance and growth physiology of the two MDR strains, AYE and AB5075. We found that not only the two pumps have nonoverlapping substrate specificities, their inactivation leads to specific nonoverlapping changes in gene expression as determined by RNA sequencing and confirmed by gene knockouts and growth phenotypes. Our results suggest that inactivation of AdeIJK elicits broader changes in the abundances of mRNAs and this response is modified in the absence of AdeB. In contrast, inactivation of AdeB leads to a focused cellular response, which is not sensitive to the activity of AdeIJK. We identified additional efflux pumps and transcriptional regulators that contribute to MDR phenotype of clinical A. baumannii isolates.
Characteristics of a Series of Three Bacteriophages Infecting Salmonella enterica Strains

Molecular and functional characterization of a series of three bacteriophages, vB_SenM-1, vB_SenM-2, and vB_SenS-3, infecting various Salmonella enterica serovars and strains is presented. All these phages were able to develop lytically while not forming prophages. Moreover, they were able to survive at pH 3. The phages revealed different host ranges within serovars and strains of S. enterica, different adsorption rates on host cells, and different lytic growth kinetics at various temperatures (in the range of 25 to 42 °C). They efficiently reduced the number of cells in the bacterial biofilm and decreased the biofilm mass. Whole genome sequences of these phages have been determined and analyzed, including their phylogenetic relationships. In conclusion, we have demonstrated detailed characterization of a series of three bacteriophages, vB_SenM-1, vB_SenM-2, and vB_SenS-3, which reveal favorable features in light of their potential use in phage therapy of humans and animals, as well as for food protection purposes.
Characterization of Fibroblasts in Iatrogenic Laryngotracheal Stenosis and Type II Diabetes Mellitus

Iatrogenic laryngotracheal stenosis (iLTS) is the pathological narrowing of the glottis, subglottis, and/or trachea due to scar tissue. Patients with type 2 diabetes mellitus (T2DM) are over 8 times more likely to develop iLTS and represent 26% to 53% of all iLTS patients. In this investigation, we compared iLTS scar‐derived fibroblasts in patients with and without T2DM.
Socioeconomic Position, Multimorbidity and Mortality in a Population Cohort: The HUNT Study

Multimorbidity and socioeconomic position are independently associated with mortality. We investigated the association of occupational position and several multimorbidity measures with all-cause mortality. A cohort of people aged 35 to 75 years who participated in the Trøndelag Health Study in 2006–2008 and had occupational data was linked to the Norwegian National Population Registry for all-cause mortality from study entry until 1 February 2019. Logistic regression models for each occupational group were used to analyze associations between the number of conditions and 10-year risk of death. Cox regression models were used to examine associations between combinations of multimorbidity, occupational position, and mortality. Analyses were conducted for men and women. Included were 31,132 adults (16,950 women (54.4%)); occupational groups: high, 7501 (24.1%); low, 15,261 (49.0%)). Increased mortality was associated with lower occupational group, more chronic conditions, and all multimorbidity measures. The joint impact of occupational group and multimorbidity on mortality was greater in men than women. All multimorbidity measures are strongly associated with mortality, with varying occupational gradients. Social differences in multimorbidity are a public health challenge and necessitate consideration in health care. Men in lower occupational groups seem to be a particularly vulnerable group.
Role of prohibitins for proteolysis in yeast and murine mitochondria

Prohibitins, Phb1 and Phb2, are evolutionary conserved proteins with diverse cellular localization and different functions. In yeast, prohibitins form a high molecular weight complex in the inner mitochondrial membrane which physically interacts with the mAAA protease and affects the stability of non assembled proteolytic substrates. In the present work, I examined two possible roles of prohibitins in proteolysis: i) role as negative regulators of the mAAA protease (Steglich et al., 1999) and/or ii) function as molecular chaperones for the assembly of newly synthesized mitochondrial proteins (Nijtmans et al., 2000). To discriminate between both possibilities, the stability of proteolytic substrates of the mAAA protease was examined in cells harboring different levels of prohibitins. While overexpression of prohibitins did not stabilize non-native inner membrane proteins absence of prohibitins resulted in their rapid proteolysis. The results presented in this work suggest that prohibitins do not play a role as chaperones for the stabilization of mitochondrial proteins. Rather, prohibitins function by binding to the mAAA protease in a nucleotide independent manner and presumably modulating the accessibility of substrate to the protease or the activity of the protease. The mAAA protease is recognized as a crucial component of the mitochondrial quality control system in yeast and in human (Arlt et al., 1996; Arlt et al., 1998; Nolden et al., 2005). In human, the mAAA protease is built up of paraplegin and Afg3l2 which are homologous to the yeast Yta10 and Yta12 proteins (Atorino et al., 2003). In mice, a third AAA subunit called Afg3l1 is expressed (Kremmidiotis et al., 2001) and, therefore, the subunit composition of the murine mAAA protease is unknown. Here, the complexes between paraplegin, Afg3l1 and Afg3l2 were examined in mitochondria from wild type and in SPG7-/- mouse strains. Immunoprecipitation experiments showed that paraplegin, Afg3l1 and Afg3l2 physically interact and are contained in a high molecular weight complex with prohibitins suggesting a conserved role of Phb1 and Phb2 for proteolysis in murine mitochondria. Co-immunoprecipitation and immunodepletion experiments using liver mitochondria from a SPG7-/- mouse strain showed that Afg3l1 and Afg3l2 can also form high molecular weight complexes in the absence of paraplegin. These complexes were additionally able to interact with prohibitins suggesting that paraplegin is not essential for this interaction. Since paraplegin-specific antibodies are able to precipitate Phb1 and Phb2, it is conceivable that also paraplegin-Afg3l1 and paraplegin-Afg3l2 complexes will be able to bind prohibitins. Thus, mAAA proteases with different subunit composition appear to exist in the inner membrane of murine mitochondria. The physiological relevance of mAAA proteases with different subunit composition is discussed in view of differences in their substrate specificities and/or different tissue distribution.
An apoplastic fluid extraction method for the characterization of grapevine leaves proteome and metabolome from a single sample.

The analysis of complex biological systems keeps challenging researchers. The main goal of systems biology is to decipher interactions within cells, by integrating datasets from large scale analytical approaches including transcriptomics, proteomics and metabolomics and more specialized 'OMICS' such as epigenomics and lipidomics. Studying different cellular compartments allows a broader understanding of cell dynamics. Plant apoplast, the cellular compartment external to the plasma membrane including the cell wall, is particularly demanding to analyse. Despite our knowledge on apoplast involvement on several processes from cell growth to stress responses, its dynamics is still poorly known due to the lack of efficient extraction processes adequate to each plant system. Analysing woody plants such as grapevine raises even more challenges. Grapevine is among the most important fruit crops worldwide and a wider characterization of its apoplast is essential for a deeper understanding of its physiology and cellular mechanisms. Here, we describe, for the first time, a vacuum-infiltration-centrifugation method that allows a simultaneous extraction of grapevine apoplastic proteins and metabolites from leaves on a single sample, compatible with high-throughput mass spectrometry analyses. The extracted apoplast from two grapevine cultivars, Vitis vinifera cv 'Trincadeira' and 'Regent', was directly used for proteomics and metabolomics analysis. The proteome was analysed by nanoLC-MS/MS and more than 700 common proteins were identified, with highly diverse biological functions. The metabolome profile through FT-ICR-MS allowed the identification of 514 unique putative compounds revealing a broad spectrum of molecular classes. This article is protected by copyright. All rights reserved.
Proteomic and Transcriptomic Analyses Indicate Metabolic Changes and Reduced Defense Responses in Mycorrhizal Roots of Oeceoclades maculata (Orchidaceae) Collected in Nature

Orchids form endomycorrhizal associations with fungi mainly belonging to basidiomycetes. The molecular events taking place in orchid mycorrhiza are poorly understood, although the cellular changes necessary to accommodate the fungus and to control nutrient exchanges imply a modulation of gene expression. Here, we used proteomics and transcriptomics to identify changes in the steady-state levels of proteins and transcripts in the roots of the green terrestrial orchid Oeceoclades maculata. When mycorrhizal and non-mycorrhizal roots from the same individuals were compared, 94 proteins showed differential accumulation using the label-free protein quantitation approach, 86 using isobaric tagging and 60 using 2D-differential electrophoresis. After de novo assembly of transcriptomic data, 11,179 plant transcripts were found to be differentially expressed, and 2175 were successfully annotated. The annotated plant transcripts allowed the identification of up- and down-regulated metabolic pathways. Overall, proteomics and transcriptomics revealed, in mycorrhizal roots, increased levels of transcription factors and nutrient transporters, as well as ethylene-related proteins. The expression pattern of proteins and transcripts involved in plant defense responses suggested that plant defense was reduced in O. maculata mycorrhizal roots sampled in nature. These results expand our current knowledge towards a better understanding of the orchid mycorrhizal symbiosis in adult plants under natural conditions.
How sure can we be that a student really failed? On the measurement precision of individual pass-fail decisions from the perspective of Item Response Theory

Abstract Background In high-stakes assessments in medical education, the decision to let a particular participant pass or fail has far-reaching consequences. Reliability coefficients are usually used to support the trustworthiness of assessments and their accompanying decisions. However, coefficients such as Cronbach’s Alpha do not indicate the precision with which an individual’s performance was measured. Objective Since estimates of precision need to be aligned with the level on which inferences are made, we illustrate how to adequately report the precision of pass-fail decisions for single individuals. Method We show how to calculate the precision of individual pass-fail decisions using Item Response Theory and illustrate that approach using a real exam. In total, 70 students sat this exam (110 items). Reliability coefficients were above recommendations for high stakes test (> 0.80). At the same time, pass-fail decisions around the cut score were expected to show low accuracy. Conclusions Our results illustrate that the most important decisions–i.e. those based on scores near the pass-fail cut-score–are often ambiguous, and that reporting a traditional reliability coefficient is not an adequate description of the uncertainty encountered on an individual level.