Miracle-dz/UniFAR-FTUs huggingface dataset:
A Computational Study of a Recreated G Protein-GEF Reaction Intermediate Competent for Nucleotide Exchange: Fate of the Mg Ion

Small G-proteins of the superfamily Ras function as molecular switches, interacting with different cellular partners according to their activation state. G-protein activation involves the dissociation of bound GDP and its replacement by GTP, in an exchange reaction that is accelerated and regulated in the cell by guanine-nucleotide exchange factors (GEFs). Large conformational changes accompany the exchange reaction, and our understanding of the mechanism is correspondingly incomplete. However, much knowledge has been derived from structural studies of blocked or inactive mutant GEFs, which presumably closely represent intermediates in the exchange reaction and yet which are by design incompetent for carrying out the nucleotide exchange reaction. In this study we have used comparative modelling to recreate an exchangecompetent form of a late, pre-GDP-ejection intermediate species in Arf1, a well-characterized small G-protein. We extensively characterized three distinct models of this intermediate using molecular dynamics simulations, allowing us to address ambiguities related to the mutant structural studies. We observed in particular the unfavorable nature of Mg associated forms of the complex and the establishment of closer Arf1-GEF contacts in its absence. The results of this study shed light on GEF-mediated activation of this small G protein and on predicting the fate of the Mg ion at a critical point in the exchange reaction. The structural models themselves furnish additional targets for interfacial inhibitor design, a promising direction for exploring potentially druggable targets with high biological specificity. Citation: Ben Hamida-Rebaı̈ M, Robert CH (2010) A Computational Study of a Recreated G Protein-GEF Reaction Intermediate Competent for Nucleotide Exchange: Fate of the Mg Ion. PLoS ONE 5(2): e9142. doi:10.1371/journal.pone. 0009142 Editor: Jörg Langowski, German Cancer Research Center, Germany Received September 23, 2009; Accepted January 10, 2010; Published February 18, 2010 Copyright: ! 2010 Ben Hamida-Rebai, Robert. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Funding for this study was provided by the French Centre Nationale de la Recherche Scientifique (CNRS) and the French Ministry of Education. Computational resources were provided by the IDRIS facility of the CNRS and by the Universite Paris Sud 11 (Orsay) Pluriformation Project DEMAIN. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: robert@ibpc.fr ¤ Current address: CNRS Laboratoire de Biochimie Théorique, IBPC, Paris, France
Angiotensin Receptor Blocker is Associated with a Lower Fracture Risk: An Updated Systematic Review and Meta-Analysis

Background Angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) are widely used in the treatment of hypertension. Hypertension is often accompanied by osteoporosis. However, the relationship between ACEI/ARB and fractures remains controversial. The purpose of this meta-analysis was to update the potential relationship between ACEI/ARB and fractures. Methods This meta-analysis was identified through PubMed, EMBASE, Cochrane Library, and Web of Science. Related studies about ACEI/ARB with the risk of fracture were published from inception to June 2022. Results Nine qualified prospective designed studies, involving 3,649,785 subjects, were included in this analysis. Overall, the RRs of ACEI compared with the nonusers were 0.98 (95% CI: 0.88, 1.10; P < 0.001) for composite fractures and 0.96 (95% CI: 0.87, 1.05; P=0.048) for hip fractures; the RRs of ARB compared to the nonusers were 0.82 (95% CI: 0.73, 0.91; P < 0.001) for composite fractures and 0.85 (95% CI: 0.74, 0.97; P=0.028) for hip fractures. Furthermore, in the subgroup analysis, male may benefit from ARB (RR = 0.65, 95% CI: 0.49, 0.89, P=0.028), and the European may also benefit from ARB (RR = 0.86, 95% CI: 0.80, 0.93, P=0.015). Conclusions ACEI usage will not decrease the risk of osteoporosis fracture. On the contrary, ARB usage can decrease the risk of total fracture and hip fracture, especially for males and Europeans. Compared with ACEI, for patients at higher risk of fracture in cardiovascular diseases such as hypertension, the protective effect of ARB should be considered.
A Superconducting Induction Motor with a High Temperature Superconducting Armature: Electromagnetic Theory, Design and Analysis

Large electric superconducting machines are being sought to solve emissions challenges in aircraft and provide a solution to >12 MW wind turbine electricity generation. Superconducting motors with only high temperature superconducting (HTS) armatures can offer advantages of high reliability, high power density, and high efficiency compared with conventional superconducting motors. In this paper, a novel HTS squirrel-cage induction motor is proposed for high speed operation, which adopts the structure of HTS windings with a certain inclination angle in the stator slots. Due to the limitation of curvature radius of superconducting tapes, the pitch of HTS windings can be only set to 1 and adopt the short pitch arrangement structure, which such design details of the HTS motor would ensure the superconducting coils can undertake larger current and reduce AC losses. In order to keep the HTS windings in superconducting state and larger current density, a special fixed cryogenic cooling system below 70 K with the method of gas extraction and decompression, which is made of aramid fiber, has been fabricated and the whole structure of the stator is placed in liquid nitrogen. According to the motor control principles and electromagnetic field theory, the electrical performances of the novel designed stator-HTS motor, which driven by the variable-voltage variable-frequency (VVVF) inverter, are analyzed including the flux density distributions, the torque, the induced electromotive force, losses and efficiency by using the finite element method. Finally, the components of HTS squirrel-cage induction motor have been manufactured according to the designed parameters. Next step, the motor will be assembled and tested.
Tumor Angiogenesis Production in Skeletal Muscle and Promotes Induces Vascular Endothelial Growth Factor Macrophage Colony-Stimulating Factor

Although M-CSF has been used for myelosuppression due to chemotherapy in patients with solid tumors, the effect of exogenous M-CSF on tumor angiogenesis has not been studied. In this study we showed that M-CSF has the ability to accelerate solid tumor growth by enhancing angiogenesis with a novel mechanism. M-CSF accelerated intratumoral vessel density in tumors inoculated into mice, although it did not accelerate the proliferation of malignant cells and cultured endothelial cells in vitro. In both the absence and the presence of tumors, M-CSF signiﬁcantly increased the circulating cells that displayed phenotypic characteristics of endothelial progenitor cells in mice. Moreover, M-CSF treatment induced the systemic elevation of vascular endothelial growth factor (VEGF). VEGFR-2 kinase inhibitor signiﬁcantly impaired the effect of M-CSF on tumor growth. In vivo, M-CSF increased VEGF mRNA expression in skeletal muscles. Even after treatment with carageenan and anti-CD11b mAb in mice, M-CSF increased VEGF production in skeletal muscles, suggesting that systemic VEGF elevation was attributed to skeletal muscle VEGF production. In vitro, M-CSF increased VEGF production and activated the Akt signaling pathway in C2C12 myotubes. These results suggest that M-CSF promotes tumor growth by increasing endothelial progenitor cells and activating angiogenesis, and the effects of M-CSF are largely based on the induction of systemic VEGF from skeletal muscles. The Journal of Immunology, 2005, 174: 7531–7538. One-Step
Primary Infection by Dengue Virus Protein 10 Are Required for Resistance to Both CXCR3 and CXCL10/IFN-Inducible

We examined the extent to which CXCR3 mediates resistance to dengue infection. Following intracerebral infection with dengue virus, CXCR3-deﬁcient (CXCR3 (cid:1) / (cid:1) ) mice showed signiﬁcantly higher mortality rates than wild-type (WT) mice; moreover, surviving CXCR3 (cid:1) / (cid:1) mice, but not WT mice, often developed severe hind-limb paralysis. The brains of CXCR3 (cid:1) / (cid:1) mice showed higher viral loads than those of WT mice, and quantitative analysis using real-time PCR, ﬂow cytometry, and immunohistochemistry revealed fewer T cells, CD8 (cid:2) T cells in particular, in the brains of CXCR3 (cid:1) / (cid:1) mice. This suggests that recruitment of effector T cells to sites of dengue infection was diminished in CXCR3 (cid:1) / (cid:1) mice, which impaired elimination of the virus from the brain and thus increased the likelihood of paralysis and/or death. These results indicate that CXCR3 plays a protective rather than an immunopathological role in dengue virus infection. In studies to identify critical CXCR3 ligands, CXCL10/IFN-inducible protein 10-deﬁcient (CXCL10/IP-10 (cid:1) / (cid:1) ) mice infected with dengue virus showed a higher mortality rate than that of the CXCR3 (cid:1) / (cid:1) mice. Although CXCL10/IP-10, CXCL9/monokine induced by IFN- (cid:3) , and CXCL11/IFN-inducible T cell (cid:4) chemoattractant share a single receptor and all three of these chemokines are induced by dengue virus infection, the latter two could not compensate for the absence of CXCL10/IP-10 in this in vivo model. Our results suggest that both CXCR3 and CXCL10/IP-10 contribute to resistance against primary dengue virus infection and that chemokines that are indistinguishable in in vitro assays differ in their activities in vivo. The Journal of Immunology, 2006, 177: 1855–1863.
COPD_A_206567 1229..1237

1Department of Emergency, Clinical Medical College, Yangzhou University, Northern Jiangsu People’s Hospital, Yangzhou, People’s Republic of China; 2Department of Emergency, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China; 3Department of Emergency, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, People’s Republic of China Background: High-flow nasal cannula (HFNC) oxygen therapy in acute hypoxic respiratory failure is becoming increasingly popular. However, evidence to support the use of HFNC in acute respiratory failure (ARF) with hypercapnia is limited. Methods: Chronic obstructive pulmonary disease (COPD) patients with moderate hypercapnic ARF (arterial blood gas pH 7.25–7.35, PaCO2>50 mmHg) who received HFNC or non-invasive ventilation (NIV) in the intensive care uint from April 2016 to March 2018 were analyzed retrospectively. The endpoint was treatment failure, defined as either invasive ventilation, or a switch to the other study treatment (NIV for patients in the NFNC group, and vice-versa), and 28-day mortality. Results: Eighty-two COPD patients (39 in the HFNC group and 43 in the NIV group) were enrolled in this study. The mean age was 71.8±8.2 and 54 patients (65.9%) were male. The treatment failed in 11 out of 39 patients with HFNC (28.2%) and in 17 of 43 patients with NIV (39.5%) (P=0.268). No significant differences were found for 28-day mortality (15.4% in the HFNC group and 14% in the NIV group, P=0.824). During the first 24 hrs of treatment, the number of nursing airway care interventions in the HFNC group was significantly less than in the NIV group, while the duration of device application was significantly longer in the HFNC group (all P<0.05). Skin breakdown was significantly more common in the NIV group (20.9% vs 5.1%, P<0.05). Conclusion: Among COPD patients with moderate hypercarbic ARF, the use of HFNC compared with NIV did not result in increased rates of treatment failure, while there were fewer nursing interventions and skin breakdown episodes reported in the HFNC group.
Cloning and Characterization of the Lipooligosaccharide Galactosyltransferase II Gene of Haemophilus ducreyi

SHUHUA SUN, BIRGIT SCHILLING, LAURIE TARANTINO, MICHAEL V. TULLIUS, BRADFORD W. GIBSON, AND ROBERT S. MUNSON, JR.* Children’s Research Institute, Department of Pediatrics, and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio 43205-2696, and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-0446
Point of care universal screening for meticillin-resistant Staphylococcus aureus (MRSA) on admission wards with a low prevalence of MRSA has no additional impact on MRSA acquisition on those wards compared with culture screening: a cluster randomised cross-over trial

Citation for published version (APA): Wu, P. J., Jeyaratnam, D. , Tosas, O. , Cooper, B. S. , & French, G. L. (2016). Point of care universal screening for meticillin-resistant Staphylococcus aureus (MRSA) on admission wards with a low prevalence of MRSA has no additional impact on MRSA acquisition on those wards compared with culture screening: a cluster randomised cross-over trial. Journal of Hospital Infection. https://doi.org/10.1016/j.jhin. 2016.08. 017
CエキノSヴWミげゲ ノW;ヴミキミェ aヴラマ ; Smokefree Sports programme: implications for health education

Objective: This paper reports on a qualitative evaluation of the Love Life Smokefree Sports primary school pilot. This eight-week programme delivered sports and physical activity sessions to convey Smokefree messages to 120 children aged ten and eleven in two primary schools in Sheffield in 2018. The ゲデ┌S┞ ;キマWS デラ ┌ミSWヴゲデ;ミS IエキノSヴWミげゲ W┝ヮWヴキWミIWゲ ラa participating in the programme. Its objectives were toぎ W┝ヮノラヴW IエキノSヴWミげゲ ヴWI;ノノ ラa デエW エW;ノデエ promotion mesゲ;ェWゲ ;ゲゲラIキ;デWS ┘キデエ W;Iエ ラa デエW ノW;ヴミキミェ ゲWゲゲキラミゲき W┝ヮノラヴW IエキノSヴWミげゲ perceptions of the meaningfulness of those messages in the context of their everyday lives ;ミSき キSWミデキa┞ ;ミS ┌ミSWヴゲデ;ミS ;ミ┞ IラミデW┝デ┌;ノ a;Iデラヴゲ デエ;デ マキェエデ キマヮ;Iデ ┌ヮラミ IエキノSヴWミげゲ ヴWI;ノノ and/or the meaningfulness of the Smokefree messages. Methods: Qualitative data were generated with 25 children via focus groups after the programme concluded. Data were analysed thematically using cross-sectional, categorical indexing. Results: Learning from the programme was particularly likely to be described as meaningful by children when they could interact with material and visual representations of complex ideas and when sessions involved strongly embodied experiences. However, children did not always find it easy to relate learning to their everyday lives and sometimes struggled to reconcile pre-existing, contextualised understandings with intervention messages. We mobilise the concept of critical health literacy as a theoretical lens through which to interpret these findings. Conclusionぎ HW;ノデエ WS┌I;デキラミ ゲエラ┌ノS HW マW;ミキミェa┌ノ キミ デエW IラミデW┝デ ラa IエキノSヴWミげゲ W┗Wヴ┞S;┞ lives. Starting from the premise that children are active critical health literacy practitioners and working with them to design and evaluate health education initiatives can promote this.
MOL090183 28..41

This communication reports the structural and functional characterization of urotoxin, the first K channel toxin isolated from the venomof the Australian scorpionUrodacus yaschenkoi. It is a basic peptide consisting of 37 amino acids with an amidated C-terminal residue. Urotoxin contains eight cysteines forming four disulfide bridges with sequence similarities resembling the a-potassium channel toxin 6 (a-KTx-6) subfamily of peptides; it was assigned the systematic number of a-KTx-6.21. Urotoxin is a potent blocker of human voltage-gated potassium channel (Kv)1.2 channels, with an IC50 of 160 pM, whereas its affinity for other channels tested was in the nanomolar range (hKv1.1, IC505 253 nM; hKv1.3, IC505 91 nM; and hKCa3.1, IC50 5 70 nM). The toxin had no effect on hKv1.4, hKv1.5, human ether-à-go-go–related gene type 1 (hERG1), or human ether-à-go-go–like (hELK2) channels. Multiple sequence alignments from the venomgland transcriptome showed the existence of four other new peptides similar to urotoxin. Computer modeling of urotoxin’s three-dimensional structure suggests the presence of the a/b-scaffold characteristic of other scorpion toxins, although very likely forming an uncommon disulfide pairing pattern. Using molecular dynamics, a model for the binding of this peptide to human Kv1.2 and hKv1.1 channels is presented, along with the binding of an in silico mutant urotoxin (Lys25Ala) to both channels. Urotoxin enriches our knowledge of K channel toxins and, due to its high affinity for hKv1.2 channels, it may be a good candidate for the development of pharmacologic tools to study the physiologic functions of K channels or related channelopathies and for restoring axonal conduction in demyelinated axons.
Shorter sleep durations in adolescents reduce power density in a wide range of waking electroencephalogram frequencies

Despite sleep’s recognized biological importance, it has been remarkably difficult to demonstrate changes in brain physiology with reduced sleep durations. In a study of adolescents, we varied sleep durations by restricting time in bed for four nights of either 10, 8.5 or 7 h. Shorter sleep durations significantly decreased waking electroencephalogram (EEG) power in a wide range of frequencies with both eyes closed and eyes open in central and occipital leads. These findings suggest new research directions and raise the possibility that waking EEG power density could provide a non-invasive test for biologically sufficient sleep.
WIP: Automating anonymous Processing of peer evaluation comments

De-identifying qualitative datasets is time-consuming and expensive but is a critical step in protecting the confidentiality of study participants. Peer-to-peer comments are an important supplement to peer evaluation ratings in team-based learning courses. Those comments comprise valuable research data for educational study to investigate but they usually contain identifiable information, such as names. In this work in progress, we study and propose a pipeline tool to identify all names appearing in CATME team peer evaluation comments and replacing those names with pseudonyms such as Rater 1 and Rater 2. We explored several natural language processing techniques empowered by machine learning methods and then optimized to the final algorithm. At its core, the algorithm combines the long short-term memory (LSTM) and conditional random field (CRF) approaches most common in the field of named entity recognition. The current algorithm performs well, with a high recall of 0.8 with reasonable precision scores resulting in 76 of 𝐹 " score as we want to put an emphasis on recalls. We also propose this as a tool to make a large amount of data available for research that would otherwise be sensitive due to personally identifiable information.
Towards correlative super-resolution fluorescence

3 4 Georg Wolff, Christoph Hagen, Kay Grünewald, Rainer Kaufmann 5 6 Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, 7 Oxford, United Kingdom 8 Department of Biochemistry, University of Oxford, Oxford, United Kingdom 9 To whom correspondence should be addressed: rainer@strubi.ox. ac.uk 10 11 12 Running Title: Towards super-resolution cryo-CLEM 13
Essential and Partially Overlapping Role of CD3 (cid:103) and CD3 (cid:100) for Development of (cid:97)(cid:98) and (cid:103)(cid:100) T Lymphocytes

(cid:50) / (cid:50) ). In contrast to mice deficient in either CD3 (cid:103) or CD3 (cid:100) chains, early thymic development mediated by pre-TCR is completely blocked, and TCR- (cid:97)(cid:98) (cid:49) or TCR- (cid:103)(cid:100) (cid:49) T cells were absent in the CD3 (cid:103)(cid:100) (cid:50) / (cid:50) mice. Taken together, these studies demonstrated that CD3 (cid:103) and CD3 (cid:100) play an essential, yet partially overlapping, role in the development of both (cid:97)(cid:98) and (cid:103)(cid:100) T cell lineages. for homologous recombination using a 0.8-kb (StuI-XbaI) 5 (cid:57) probe located outside of the construct. Eight clones were identified as targeted clones, which were confirmed by another Southern analysis with a hyg r probe. Four of the targeted clones were injected into the blastocysts of either C57BL/6 or BALB/C origin, and 90– 100% fur color chimerism was observed in 45 founder mice. Test breeding of the chimeras indicated that all of the males ( n (cid:53) 28 from 3 embryonic stem [ES] clones) transmitted the ES cell genome. Four males were mated to C57BL/6 females to generate heterozygous mice, and homozygous CD3 (cid:103)(cid:100) (cid:50) / (cid:50) lines were obtained by sibling breeding. Identical results were obtained from homozygous CD3 (cid:103)(cid:100) (cid:50) / (cid:50) lines of different ES clones. Flow Cytometric Analysis. Single cell suspensions of thymocytes, LN cells, spleen cells, PBL, and small intestine intraepithe-lial lymphocytes (iIEL) were prepared as described (26, 27). Three-color staining of the cells was performed as previously re-ported elsewhere (28).
Automation using Machine Learning and Object Detection

- A major challenge in many of the object detection systems is the dependency on other computer vision techniques for helping the deep learning-based approach, which leads to slow and non-optimal performance. In this paper, a completely deep learning-based approach is used to solve the problem of object detection in an end-to-end fashion. The paper aims to incorporate state-of-the-art technique for detecting the object placed in front of the webcam with the goal of achieving high accuracy with a real-time performance using deep learning. Based on the detected image several preprogrammed robots are used to transport the object in the detected image from the place where humans cannot work flawlessly to the desired location efficiently. This paper comes with the combination of deep learning and robotics which can be used in several areas such as mines, construction sites, steel factories etc where human works in a risky environment. The network is trained on the most publicly available data set, on which an object detection challenge is conducted annually.