Miracle-dz/UniFAR-FTUs huggingface dataset:
OMA Browser - Exploring orthologous relations across 352 complete genomes

MOTIVATION Inference of the evolutionary relation between proteins, in particular the identification of orthologs, is a central problem in comparative genomics. Several large-scale efforts with various methodologies and scope tackle this problem, including OMA (the Orthologous MAtrix project). RESULTS Based on the results of the OMA project, we introduce here the OMA Browser, a web-based tool allowing the exploration of orthologous relations over 352 complete genomes. Orthologs can be viewed as groups across species, but also at the level of sequence pairs, allowing the distinction among one-to-one, one-to-many and many-to-many orthologs. AVAILABILITY http://omabrowser.org.
The utility of sonography for the triage of blunt abdominal trauma patients to exploratory laparotomy.

OBJECTIVE The purpose of this study was to assess the utility of focused abdominal sonography for trauma (FAST) in the triage of hypotensive and normotensive blunt abdominal trauma patients to exploratory laparotomy. MATERIALS AND METHODS Data entered in a trauma registry database were retrospectively reviewed and were correlated with medical records, radiology reports, and surgical laparotomy reports. In the setting of blunt abdominal trauma, hypotensive patients were compared with normotensive patients who underwent FAST. RESULTS During the 6-year study period, 4,029 patients with blunt abdominal trauma underwent sonography, 122 of whom were hypotensive on arrival and underwent FAST. Of 87 hypotensive patients with positive findings on FAST, 69 (79%) were taken directly to exploratory laparotomy without the need for CT. In predicting the need for therapeutic laparotomy in hypotensive patients, the sensitivity of FAST was 85%, specificity was 60%, and accuracy was 77%. Of the 3,907 normotensive patients, 3,584 had negative FAST findings, whereas 323 had positive FAST findings. In normotensive patients, the sensitivity of FAST was 85%, specificity was 96%, and accuracy was 96%. In the combined patient population (all hypotensive and normotensive patients), 4,029 patients with blunt abdominal trauma underwent sonography: 3,619 had negative and 410 had positive FAST findings. In all patients regardless of blood pressure, the sensitivity of FAST was 85%, specificity was 96%, and accuracy was 95%. CONCLUSION Hypotensive patients screened in the emergency department with positive FAST findings may be triaged directly to therapeutic laparotomy, depending on the results of the sonography examination, without the need for CT.
A dual-polarized antenna with pattern diversity

An antenna that is capable of exciting four different kinds of linearly polarized waves by four independent feeding ports across an overlapped frequency band is presented. The four polarizations embrace the x and y polarized waves, which have broadside patterns, and the thetas and phi-polarized waves, which have conical patterns. The antenna can perform as a dual-polarized antenna for pattern diversity (broadside or conical) applications. The x and y polarizations (TM11 mode) and the thetas polarization (TM01 mode) are achieved by exciting a circular patch with four shorting posts and five L-shaped probe fees. The phi polarization is achieved by exciting four slots cut on the patch to produce radial magnetic currents. The performance of the antenna is studied numerically and experimentally. A prototype antenna was built, and the four polarizations overlapped at about 2.1 GHz. The antenna attained a gain of about 4 dBi for the two conical polarizations, and a gain of about 11 dBi for the two broadside polarizations.
Anthrax and the taiga.

Woodbury’s recent review of anthrax emphasized that there is always more than one factor contributing to disease, especially when in outbreak form (1). But the current model for anthrax is based on only one cause that was derived from experiments that demonstrated a dose-dependent relationship between the severity of the disease and the oral dose of spores (2,3). Peracute disease and sudden death, the form normally associated with the disease in the field, requires a large oral dose of spores; at lower doses the animal may recover. Infection through the bites of tabanids caused only a mild, subclinical cutaneous infection (4).
Soluble CD8 levels in the CSF and serum of patients with multiple sclerosis

CD8 is a membrane glycoprotein of 34 kd on cytotoxic/suppressor T lymphocytes and is an endogenous ligand for MHC class I proteins on target cells. CD8 is released in a soluble form upon T-lymphocyte activation. In multiple sclerosis (MS), T lymphocytes exhibit decreased membrane expression of the CD8 molecule and defective suppressor fonction. We measured soluble CD8 (sCD8) levels in the CSF of patients with MS, other inflammatory neurologic diseases (INDs), and noninflammatory neurologic diseases (NINDs). sCD8 levels in the CSF of MS and IND patients were elevated compared with NIND patients. Patients with acute infections of the CNS showed the highest absolute values of sCD8, but the amount of sCD8 per CSF white blood cell was greatest in MS and NIND patients. We found no difference in serum sCD8 levels among the groups. In MS, the combination of increased CSF sCD8 levels and sCD8 per cell may reflect CD8 T-lymphocyte activation within the brain or immunodysregulation confined to the CNS.
Study on the Impact Factors of the Translators’ Post-editing Efficiency in a Collaborative Translation Environment

This paper investigates the factors that influence the translators’ post-editing efficiency in a collaborative translation environment. We developed GE-CCT, a platform that enables hundreds of translators to be organized to complete one large-scale translation task together. On the basis of the platform, this paper made thorough analysis on the post-editing logs of 325 translators within 8 weeks. Results show that some exterior environmental factors and interior personal factors obviously affect the translators’ post-editing speed and quality. Accordingly, we proposed solutions that improved the collaborative translation efficiency.
Once weekly fluconazole for antifungal prophylaxis post-liver transplantation.

BACKGROUND Invasive fungal infections (IFI) remain a significant cause of morbidity and mortality in orthotopic liver transplantation (OLT) recipients. In this retrospective study, the outcomes of a protocol using once weekly fluconazole for 3 months after OLT in low- and high-risk patients were reviewed. METHODS In total, 221 OLTs were evaluated in the 3-year period after institution of the new protocol to determine the incidence of IFI within 6 months post-OLT. RESULTS In this cohort, 11 IFIs developed during the 6-month post-transplant period, with the majority being non-albicans Candida. High-risk patients had a greater rate of IFI (16.7% versus 3.4%, P = 0.038) and a significantly longer intensive unit care (ICU) and hospital lengths of stay compared with low-risk patients. Patient and graft survival were similar between the groups. Our patient population appeared to be at low risk for IFI, with 92% of the entire cohort considered low risk. DISCUSSION Given the low incidence of IFI in the low-risk group and the possibility of such protocol selecting out for fluconazole-resistant fungi, the use of weekly fluconazole for 3 months may not be justifiable in low-risk OLT recipients. Given the increased resource utilization observed with IFI, further examination of a more intensive prophylactic strategy in high-risk patients may be warranted.
Race, class, and environmental health: a review and systematization of the literature.

This paper analyzes and systematizes the race and class differentials in exposure to toxic hazards and actual health outcomes. Research is categorized into the following: Proximity to known hazards includes (1) presence of hazardous waste sites and facilities (landfills, incinerators, Superfund sites), (2) exposure to air pollution, (3) exposure to various environmental hazards, e.g., toxic releases and hazards in pesticides and foods; Regulation, amelioration and cleanup includes (4) record of decisions (RODs) and cleanups at NPL sites, (5) regulatory action, as measured by assessed fines for environmental pollution; Health effects includes (6) specific health outcomes which are related to environmental burden (e.g., blood lead levels). Proximity to prospective hazards includes (7) sitting decisions for incinerators, hazardous waste sites, and nuclear storage sites. The overwhelming bulk of evidence supports the "environmental justice" belief that environmental hazards are inequitably distributed by class, and especially race.
Author ' s response to reviews Title : The effects of treatment with liraglutide on atherothrombotic risk in obese young women with polycystic ovary syndrome and controls : a case control study

Hassan Kahal (hassan.kahal@yahoo.co.uk) Ahmed Aburima (A.Aburima@hull.ac.uk) Tamas Ungvari (drungvaritamas@yahoo.com) Alan S Rigby (asr1960@hotmail.com) Anne M Coady (anne.coady@hey.nhs.uk) Rebecca V Vince (rebecca.vince@hull.ac.uk) Ramzi A Ajjan (R.Ajjan@leeds.ac.uk) Eric S Kilpatrick (Eric.Kilpatrick@hey.nhs.uk) Khalid M Naseem (Khalid.Naseem@hyms.ac.uk) Stephen L Atkin (stephen.atkin@hyms.ac.uk)
X-ray Structure of the Complete ABC Enzyme ABCE1 from Pyrococcus abyssi*

The ATP binding cassette enzyme ABCE1 (also known as RNase-L (ribonuclease L) inhibitor, Pixie, and HP68), one of the evolutionary most sequence-conserved enzymes, functions in translation initiation, ribosome biogenesis, and human immunodeficiency virus capsid assembly. However, its structural mechanism and biochemical role in these processes have not been revealed. We determined the crystal structure of Pyrococcus abyssi ABCE1 in complex with Mg2+ and ADP to 2.8Å resolution. ABCE1 consists of four structural domains. Two nucleotide binding domains are arranged in a head-to-tail orientation by a hinge domain, suggesting that these domains undergo the characteristic tweezers-like powerstroke of ABC enzymes. In contrast to all other known ABC enzymes, ABCE1 has a N-terminal iron-sulfur-cluster (FeS) domain. The FeS domain contains two [4Fe-4S] clusters and is structurally highly related to bacterial-type ferredoxins. However, one cluster is coordinated by an unusual CX4CX3/4C triad. Surprisingly, intimate interactions of the FeS domain with the adenine and ribose binding Y-loop on nucleotide binding domain 1 suggest a linkage between FeS domain function and ATP-induced conformational control of the ABC tandem cassette. The structure substantially expands the functional architecture of ABC enzymes and raises the possibility that ABCE1 is a chemomechanical engine linked to a redox process.
Solar photovoltaic output smoothing: Using battery energy storage system

Battery Energy Storage System (BESS) is widely being implemented along with Solar PV to mitigate the inherent intermittencies of solar power. Solar smoothing is one such application of BESS. In this paper, different techniques for solar power smoothing is compared. An energy compensation based smoothing technique is proposed in this paper. The smoothing method not only ensures an optimal sizing of the battery but also keeps the state of charge of the battery same at the beginning and end of any random day. The different techniques are simulated on a typical moving cloud day output of a 5 MWp solar power-plant.
Robust Backstepping Control of Induction Motor Drives Using Artificial Neural Networks and Sliding Mode Flux Observers

In this paper, using the three-phase induction motor fifth order model in a stationary two axis reference frame with stator current and rotor flux as state variables, a conventional backstepping controller is first designed for speed and rotor flux control of an induction motor drive. Then in order to make the control system stable and robust against all electromechanical parameter uncertainties as well as to the unknown load torque disturbance, the backstepping control is combined with artificial neural networks in order to design a robust nonlinear controller. It will be shown that the composite controller is capable of compensating the parameters variations and rejecting the external load torque disturbance. The overall system stability is proved by the Lyapunov theory. It is also shown that the method of artificial neural network training, guarantees the boundedness of errors and artificial neural network weights. Furthermore, in order to make the drive system free from flux sensor, a sliding- mode rotor flux observer is employed that is also robust to all electrical parameter uncertainties and variations. Finally, the validity and effectiveness of the proposed controller is verified by computer simulation.
Anquilobléfaron filiforme adherente y otras malformaciones

Se realizo un examen fisico a un recien nacido con malformaciones presentadas en el momento del parto, de un embarazo valioso de la raza negra, presento los parpados superior e inferior de ambos ojos unidos por finas bandas en numero variable que impedian la separacion y los movimientos normales. Ademas asociado a labio leporino y hendidura palatina. Luego de descartar otras malformaciones congenitas, fue intervenido para reparar la malformacion. Su estado actual es normal, despues de la recanalizacion de sus otras anomalias
Functional roles of Na,K-ATPase subunits

Purpose of reviewNa,K-ATPase is an oligomeric protein composed of α subunits, β subunits and FXYD proteins. The catalytic α subunit hydrolyzes ATP and transports the cations. Increasing experimental evidence suggest that β subunits and FXYD proteins essentially contribute to the variable physiological needs of Na,K-ATPase function in different tissues. Recent findingsBeta subunits have a crucial role in the structural and functional maturation of Na,K-ATPase and modulate its transport properties. The chaperone function of the β subunit is essential, for example, in the formation of tight junctions and cell polarity. Recent studies suggest that β subunits also have inherent functions, which are independent of Na,K-ATPase activity and which may be involved in cell–cell adhesiveness and in suppression of cell motility. As for FXYD proteins, they modulate Na,K-ATPase activity in a tissue-specific way, in some cases in close cooperation with posttranslational modifications such as phosphorylation. SummaryA better understanding of the multiple functional roles of the accessory subunits of Na,K-ATPase is crucial to appraise their influence on physiological processes and their implication in pathophysiological states.
Kinetic analysis of 2-[carbon-11]thymidine PET imaging studies: compartmental model and mathematical analysis.

UNLABELLED Carbon-11-thymidine is a PET tracer of DNA synthesis and cellular proliferation. Quantitative analysis of [11C]thymidine images is complicated by the presence of significant quantities of labeled metabolites. Estimation of the rate of thymidine incorporation into DNA using [11C]thymidine requires a kinetic model that is capable of describing the behavior of thymidine and labeled metabolites. METHODS Based on previous studies with labeled thymidine, we constructed a five-compartment model describing the kinetic behavior of 2-[11C]thymidine and its labeled metabolites. In addition, we have performed a series of calculations and simulations to calculate the sensitivity and identifiability of model parameters to estimate the extent to which individual parameters can be estimated; to determine appropriate model constraints necessary for reproducible estimates of the constant describing flux of thymidine from the blood into DNA, i.e., thymidine flux constant; and to determine the potential accuracy of model parameter and thymidine flux constant estimates from PET imaging data. RESULTS The underlying assumptions in the thymidine compartmental model lead to a description of the thymidine flux constant for DNA incorporation in terms of model parameters. Sensitivity and identifiability analyses suggest that the model parameters pertaining to labeled metabolites will be difficult to estimate independently of the thymidine parameters. Exact evaluation of the kinetic parameters of the labeled metabolites is not the principal goal of this model. Simulations were performed that suggest that it is preferable to tightly constrain these parameters to preset values near the center of their expected ranges. Although it is difficult to estimate individual thymidine model parameters, the flux constant for incorporation into DNA can be accurately estimated (r > 0.9 for estimated versus true simulated flux constant). Flux constant estimates are not affected by modest levels of local degradation of thymidine that may occur in proliferating tissue. CONCLUSION By using a kinetic model for thymidine and labeled metabolites, it is possible to estimate the flux of thymidine uptake and incorporation into DNA and, thereby, noninvasively estimate regional cellular proliferation using [11C]thymidine and PET.
Newcomers in the process of mitochondrial permeabilization

Under stress conditions, apoptogenic factors normally sequestered in the mitochondrial intermembrane space are released into the cytosol, caspases are activated and cells die by apoptosis. Although the precise mechanism that leads to the permeabilization of mitochondria is still unclear, the activation of multidomain pro-apoptotic proteins of the Bcl-2 family, such as Bax and Bak, is evidently crucial. Regulation of Bax and Bak by other members of the family has been known for a long time, but recent evidence suggests that additional unrelated proteins participate in the process, both as inhibitors and activators. The important rearrangements mitochondrial lipids undergo during apoptosis play a role in the permeabilization process and this role is probably more central than first envisioned.
Europeana Linked Open Data - data.europeana.eu

Europeana is a single access point to millions of books, paintings, films, museum objects and archival records that have been digitized throughout Europe. The data.europeana. eu Linked Open Data pilot dataset contains open metadata on approximately 2.4 million texts, images, videos and sounds gathered by Europeana. All metadata are released under Creative Commons CC0 and therefore dedicated to the public domain. The metadata follow the Europeana Data Model and clients can access data either by dereferencing URIs, downloading data dumps, or executing SPARQL queries against the dataset. They can also follow the links to external linked data sources, such as the Swedish cultural heritage aggregator SOCH, GeoNames, the GEMET thesaurus, or DBPedia.
Challenges of defining reliable clinical surrogate end points in haemophilia trials: a critical review

The success of a treatment in haemophilia patients experiencing a bleeding episode is very difficult to define. A variety of efficacy assessment tools have been developed in an effort to better assess when haemostasis has been achieved. These assessment tools are particularly important for the evaluation of the efficacy of therapeutic agents whose mechanism of action is based on pharmacological activity in haemostasis rather than upon the principle of ‘replacement therapy’. This review focuses on a number of efficacy measures, summarizing their methodology and discussing their validity. In addition, future developments and requirements in order to evaluate the effectiveness of haemostatic treatment are discussed. The majority of end points used for evaluation of haemostasis relate to the relief of symptoms arising from bleeds. The results of this review highlight that several efficacy end points are frequently combined in order to provide a more comprehensive assessment of efficacy. Key limitations of current methodology are the subjectivity of assessment by either the patient or clinician, and the incomparability of results between trials.
Promoting psychosocial competencies in university students: evaluation based on a one-group pre-test/post-test design

Abstract At The Hong Kong Polytechnic University, a two-credit gene\xadral education course entitled “Tomorrow’s Leaders” was developed to promote intra- and interpersonal competencies in university students. The course was piloted in four classes of students in the 2010/11 academic year. Pre-test and post-test data utilizing the Chinese Positive Youth Development Scale (CPYDS) were collected from 50 students taking the course. Positive changes in the program participants based on the total scale and subscale scores were observed. The present study provides pioneering support for the effectiveness of the course in promoting holistic development of Chinese university students in Hong Kong.
An isolated, surface-expressed I domain of the integrin αLβ2 is sufficient for strong adhesive function when locked in the open conformation with a disulfide bond

We introduced disulfide bonds to lock the integrin αLβ2 I domain in predicted open, ligand binding or closed, nonbinding conformations. Transfectants expressing αLβ2 heterodimers containing locked-open but not locked-closed or wild-type I domains constitutively adhered to intercellular adhesion molecule-1 (ICAM-1) substrates. Locking the I domain closed abolished constitutive and activatable adhesion. The isolated locked-open I domain bound as well as the activated αLβ2 heterodimer, and binding was abolished by reduction of the disulfide. Lovastatin, which binds under the conformationally mobile C-terminal α-helix of the I domain, inhibited binding to ICAM-1 by αLβ2 with wild-type, but not locked-open I domains. These data establish the importance of conformational change in the αL I domain for adhesive function and show that this domain is sufficient for full adhesive activity.
Beyond the trustworthy tweet: A deeper understanding of microblogged data use by disaster response and humanitarian relief organizations

In this paper we present findings from interviews conducted with representatives from large international disaster response organizations concerning their use of social media data in crisis response. We present findings in which the barriers to use by responding organizations have gone beyond simple discussions of trustworthiness to that of more operational issues rather than mere data quality. We argue that the landscape of the use of microblogged data in crisis response is varied, with pockets of use and acceptance among organizations. We found that microblogged data is useful to responders in situations where information is limited, such as at the beginning of an emergency response effort, and when the risks of ignoring an accurate response outweigh the risks of acting on an incorrect one. In some situations, such as search and rescue operations, microblogged data may never meet the standards of quality required. In others, such as resource and supply management, microblogging data could be useful as long as it is appropriately verified and classified.
Improving PART algorithm with K-L divergence for imbalanced classification

Rule-learning extracts the knowledge from a dataset and represent it in a form that is easy for people to understand. RIPPER (Repeated Incremental Pruning to Produce Error Reduction) and PART (Partial Decision Trees) are two well-known schemes for rule-learning. However, due to overpruning of RIPPER and skew-sensitivity of PART, it is difficult to use two methods to learn from imbalanced datasets. To bypass these difficulties, we propose a K-L divergence-based PART (KLPART) that use K-L divergence as a splitting criterion to build partial decision trees. An experimental framework is carried out with a wide range of imbalanced datasets over RIPPER, PART, KLPART and the combination of these methods for classification with SMOTE processing. The results obtained, which contrasted through nonparametric statistical tests, show that KLPART is robust in the presence of class imbalance, especially when combined with SMOTE. We thereby recommend the use of KLPART with SMOTE when learning from imbalanced datasets.