Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating signal peptide prediction methods for Gram-positive bacteria

Gram-positive bacteria have been widely investigated for their huge capability to secrete proteins, such as those involved in gene expression, bacterial surface display and bacterial pathogenesis. The N-terminal signal peptide of a secretory protein is responsible for the translocation of polypeptide through the cytoplasmic membrane. Recently, the signal peptide prediction has become a major task in bioinformatics, and many programs with different algorithms were developed to predict signal peptides. In this paper, five prediction programs (SignalP 3.0, PrediSi, Phobius, SOSUIsignal and SIG-Pred) were selected to evaluate their prediction accuracy for signal peptides and cleavage site using 509 unbiased and experimentally verified Gram-positive protein sequences. The results showed that SignalP was the most accurate program in signal peptide (96% accuracy) and cleavage site (83%) prediction. Prediction performance could further be improved by combining multiple methods into consensus prediction, which would increase the accuracy to 98%, and decrease the false positive to zero. When the consensus method was used to predict Bacillus’s extracellular proteins identified by proteomics, more new signal peptides were successfully identified. It could be concluded that the consensus method would be useful to make prediction of signal peptides more reliable.
Metropolis light transport

We present a new Monte Carlo method for solving the light transport problem, inspired by the Metropolis sampling method in computational physics. To render an image, we generate a sequence of light transport paths by randomly mutating a single current path (e.g. adding a new vertex to the path). Each mutation is accepted or rejected with a carefully chosen probability, to ensure that paths are sampled according to the contribution they make to the ideal image. We then estimate this image by sampling many paths, and recording their locations on the image plane. Our algorithm is unbiased, handles general geometric and scattering models, uses little storage, and can be orders of magnitude more efficient than previous unbiased approaches. It performs especially well on problems that are usually considered difficult, e.g. those involving bright indirect light, small geometric holes, or glossy surfaces. Furthermore, it is competitive with previous unbiased algorithms even for relatively simple scenes. The key advantage of the Metropolis approach is that the path space is explored locally, by favoring mutations that make small changes to the current path. This has several consequences. First, the average cost per sample is small (typically only one or two rays). Second, once an important path is found, the nearby paths are explored as well, thus amortizing the expense of finding such paths over many samples. Third, the mutation set is easily extended. By constructing mutations that preserve certain properties of the path (e.g. which light source is used) while changing others, we can exploit various kinds of coherence in the scene. It is often possible to handle difficult lighting problems efficiently by designing a specialized mutation in this way.
Combination of mutations in human immunodeficiency virus type 1 reverse transcriptase required for resistance to the carbocyclic nucleoside 1592U89

The carbocyclic nucleoside 1592U89 is a selective inhibitor of the human immunodeficiency virus (HIV), targeting the reverse transcriptase (RT). In vitro selection studies were undertaken to generate resistant variants with both HIV type 1 (HIV-1) wild-type strain HIV-1(HXB2) and 3'-azido-3'-deoxythymidine (AZT)-resistant strain HIV-1(RTMC). At least two or three mutations in RT were required to produce a 10-fold reduction in susceptibility. The first RT mutation selected was at codon 184, methionine (M) to valine (V), for HIV-1(HXB2) and HIV-1(RTMC), conferring two- and fivefold resistance, respectively. Two additional mutations were selected with HIV-1(HXB2), either leucine (L) 74 to V and lysine (K) 65 to arginine (R) (first-passage series) or L74 to V and tyrosine (Y) 115 to phenylalanine (F) (second-passage series). Cloned variants, obtained from the 1592U89 selection, were either double RT mutants 65R/184V and 74V/184V or triple RT mutant 74V/115Y/184V. Molecular clones were constructed with single, double, and triple combinations of these mutations for resistance analysis with different RT inhibitors. Each individual mutation conferred only low-level resistance (two- to fourfold) to 1592U89 in the HXB2 background. Double mutants containing the 184V mutation and triple mutants showed slightly greater levels of resistance to 1592U89 (7- to 11-fold). Some of the 1592U89-resistant variants were cross-resistant with 2',3'-dideoxycytidine, 2',3'-dideoxyinosine, and (-)-2'-deoxy-3'-thiacytidine, but none were resistant to 2',3'-didehydro-3'-deoxythymidine or AZT.
Bag-Of-Visual-Words Approach based on SURF Features to Polyp Detection in Wireless Capsule Endoscopy Videos

Wireless Capsule Endoscopy (WCE) is a relatively new technology (FDA approved in 2002) allowing doctors to view most of the small intestine. One of the most important goals of WCE is the early detection of colorectal polyps. We introduce “Bag-of-Visual-Words” method which has been successfully used in particular for image classification in non-medical domains. Initially the training image patches are sampled and represented by speeded up robust features (SURF) descriptor, and then the bag of words model is constructed by K-means clustering algorithm. Subsequently the document is represented as the histogram of the visual words which is the feature vector of the image. Finally, a SVM classifier is trained using these feature vectors to distinguish images with polyp regions from ones without them. Our preliminary experiments on our current data set demonstrate that the proposed method achieves promising performances.
Golgi targeting of Drosophila melanogaster β4GalNAcTB requires a DHHC protein family–related protein as a pilot

Drosophila melanogaster β4GalNAcTB mutant flies revealed that this particular N-acetylgalactosaminyltransferase is predominant in the formation of lacdiNAc (GalNAcβ1,4GlcNAc)-modified glycolipids, but enzymatic activity could not be confirmed for the cloned enzyme. Using a heterologous expression cloning approach, we isolated β4GalNAcTB together with β4GalNAcTB pilot (GABPI), a multimembrane-spanning protein related to Asp-His-His-Cys (DHHC) proteins but lacking the DHHC consensus sequence. In the absence of GABPI, inactive β4GalNAcTB is trapped in the endoplasmic reticulum (ER). Coexpression of β4GalNAcTB and GABPI generates the active enzyme that is localized together with GABPI in the Golgi. GABPI associates with β4GalNAcTB and, when expressed with an ER retention signal, holds active β4GalNAcTB in the ER. Importantly, treatment of isolated membrane vesicles with Triton X-100 disturbs β4GalNAcTB activity. This phenomenon occurs with multimembrane-spanning glycosyltransferases but is normally not a property of glycosyltransferases with one membrane anchor. In summary, our data provide evidence that GABPI is required for ER export and activity of β4GalNAcTB.
Organic Molecules in Low-Mass Protostellar Hot Cores: Submillimeter Imaging of IRAS 16293–2422

Arcsecond-resolution spectral observations toward the protobinary system IRAS 16293-2422 at 344 and 354 GHz were conducted using the Submillimeter Array. Several complex organic molecules, such as CH3OH and HCOOCH3, were detected and mapped. Together with the rich organic inventory revealed, it clearly indicates the existence of two, rather than one, compact hot molecular cores (≲400 AU in radius) associated with each of the protobinary components identified by their dust continuum emission in the inner star-forming core.
MCSTL: the multi-core standard template library

Future gain in computing performance will not stem from increased clock rates, but from even more cores in a processor. Since automatic parallelization is still limited to easily parallelizable sections of the code, most applications will soon have to support parallelism explicitly. The Multi-Core Standard Template Library (MCSTL) simplifies parallelization by providing efficient parallel implementations of the algorithms in the C++ Standard Template Library. Thus, simple recompilation will provide partial parallelization of applications that make consistent use of the STL. We present performance measurements on several architectures. For example, our sorter achieves a speedup of 21 on an 8-core 32-thread SUN T1.
Integrating geometric constraints into reactive leg motion generation

This paper proposes a reactive leg motion generation method which integrates geometric constraints into its generation process. In order to react given instructions instantaneously or to keep balance against external disturbances, feasible steps must be generated automatically in real-time for safety. In many cases this feasibility has been realized by using predefined steps or admissible stepping regions. However, these predefinitions are often too conservative or valid only in limited situations. The proposed method considers geometric constraints in addition to joint limits during its generation process and it can utilize the ability of the robot to a maximum extent. It can generate feasible walking pattern in real-time by modifying the swing leg motion and the next landing position at each control cycle. The proposed method is validated by experiments using a humanoid robot HRP-2.
Multilocal feature selection using genetic algorithm for face identification

Face recognition is a biometric authentication method that has become more significant and relevant in recent years. It is becoming a more mature technology that has been employed in many large scale systems such as Visa Information System, surveillance access control and multimedia search engine. Generally, there are three categories of approaches for recognition, namely global facial feature, local facial feature and hybrid feature. Although the global facial-based feature approach is the most researched area, this approach is still plagued with many difficulties and drawbacks due to factors such as face orientation, illumination, and the presence of foreign objects. This paper presents an improved offline face recognition algorithm based on a multi-local feature selection approach for grayscale images. The approach taken in this work consists of five stages, namely face detection, facial feature (eyes, nose and mouth) extraction, moment generation, facial feature classification and face identification. Subsequently, these stages were applied to 3065 images from three distinct facial databases, namely ORL, Yale and AR. The experimental results obtained have shown that recognition rates of more than 89% have been achieved as compared to other global-based features and local facial-based feature approaches. The results also revealed that the technique is robust and invariant to translation, orientation, and scaling
Patient outcomes after treatment with percutaneous cholecystostomy for biliary sepsis.

INTRODUCTION Acute cholecystitis is among the most common general surgical presentations. There is a cohort of patients who develop systemic sepsis and complications of acute cholecystitis. These patients are often elderly and co-morbid. Conservative management with percutaneous cholecystostomy has been shown to be a safe and effective management option in the acute setting. However, there is currently no consensus for the further management of these patients. In particular, there is a paucity of data on readmission rates and subsequent operative or non-operative management. METHODS A retrospective study was carried out of patients treated with a percutaneous cholecystostomy for biliary sepsis over a three-year period in a UK teaching hospital. Outcome measures were subsequent operative or conservative management, conversion rates, operative complications and readmission rates. RESULTS Twenty-five patients had a percutaneous cholecystostomy for the treatment of acute biliary sepsis. The median follow-up duration was 35 months. Thirteen patients (52%) had operative treatment. In the operative group, 6/13 had a laparoscopic cholecystectomy, 2/13 had a planned open cholecystectomy, 2/13 had abandoned procedures and 3/13 had a converted procedure. Complications in the operative group included: postoperative mortality (1/13), common bile duct injury requiring drainage and endoscopic stenting (1/13) and one patient required readmission with recurrent pain. In the non-operative group, 5/12 patients were readmitted with biliary sepsis, 5/12 had no readmissions, 1/12 died in the community and 1/12 was readmitted with biliary colic. CONCLUSIONS Percutaneous cholecystostomy is a recognised treatment modality for elderly, co-morbid patients with biliary sepsis. Nevertheless, the readmission rate in this group is relatively high at 5/12 (42%). Patients who undergo subsequent operative management have a conversion rate of 3/13 (23%) and a significant complication rate of 2/13 (15%). The further management of patients having undergone percutaneous cholecystostomy requires careful consideration on an individual case basis. The P-POSSUM (Portsmouth Physiological and Operative Severity Score for the enUmeration of Mortality and morbidity) may aid decision making.
Fatty acid utilization by L1210 murine leukemia cells.

L1210 murine leukemia cells grow in an ascites plasma that contains lipids, including 0.62 +/- 0.046 (S.E.) MICRONEq free fatty acid per ml. in vitro incubations demonstrated that isolated L1210 cells readily utilize free fatty acid that is added to the incubation medium. When the cells were incubated with albumin-bound [1-14C]palmitate, about 12 times more radioactivity was incorporated into cell lipids than was oxidized to CO2. Triacylglycerols contained 1.5 to 4 times more radioactivity than phospholipids, and from 48 to 69% of the phospholipid radioactivity was recovered in the choline phosphoglycerides. [1-14C]Palmitate utilization increased as the fatty acid concentration of the medium was raised, the largest increase occurring in the triacylglycerol fraction. Palmitate utilization also was increased by the presence of carbohydrates in the medium, their effectiveness (in descending order) being glucose, mannose, galactose, fructose, and glycerol. By contrast, ribose did not produce any stimulatory effect. During a 1-hr incubation, between 82 and 87% of the [1-14C]palmitate that was taken up remained as palmitic acid. From 8 to 15% was elongated to stearate, and only 2 to 3% was desaturated to palmitoleate and oleate. Based upon the lipid content, growth rate, and palmitate utilization rate of the cells, it appears that a major portion of the lipid requirements of the L1210 cell may be supplied by the fatty acid contained in the ascites plasma. In addition, our results suggest that most of the saturated fatty acid taken up is incorporated into cell lipids without structural modification.
Multiplex Identification of Microbes

ABSTRACT We have adapted molecular inversion probe technology to identify microbes in a highly multiplexed procedure. This procedure does not require growth of the microbes. Rather, the technology employs DNA homology twice: once for the molecular probe to hybridize to its homologous DNA and again for the 20-mer oligonucleotide barcode on the molecular probe to hybridize to a commercially available molecular barcode array. As proof of concept, we have designed, tested, and employed 192 molecular probes for 40 microbes. While these particular molecular probes are aimed at our interest in the microbes in the human vagina, this molecular probe method could be employed to identify the microbes in any ecological niche.
Topological Noise Removal

Meshes obtained from laser scanner data often contain topological noise due to inaccuracies in the scanning and merging process. This topological noise complicates subsequent operations such as remeshing, parameterization and smoothing. We introduce an approach that removes unnecessary nontrivial topology from meshes. Using a local wave front traversal, we discover the local topologies of the mesh and identify features such as small tunnels. We then identify non-separating cuts along which we cut and seal the mesh, reducing the genus and thus the topological complexity of the mesh.
of life in subjects with or knee

Please be advised that this information was generated on 2017-04-03 and may be subject to change. This study examines the quality of life (QOL) of community living elderly people aged 55-74 with chronic, episodic or sporadic pain in the hip or knee and of a reference group without pain (total n = 306). Firstly, it was hypothesized that the experienced QOL is lower in people with more chronic pain. Secondly, the potential mediating and moderating roles of disability and of coping with problems in general on the relationship between pain chronicity and QOL were assessed. A Visual Analogue Scale was used to assess global QOL. Physical as well as psychosocial disability was assessed with the Sickness Impact Profile (SIP). Coping with problems in general was assessed with the Utrecht Coping List. As expected, a significantly lower QOL was found in people with more chronic pain (p = 0.045). The difference in QOL between the group with chronic pain and a reference group with­ out pain was 10%. A multivariate regression model showed that physical and especially psychosocial disability are mediators in the relationship between pain chronicity and QOL and that "seeking social support' as a coping style is a more important predictor of the experienced QOL than either pain chronicity or physical disability. No moderating role of the style of coping with problems was found.
Semantic Similarity Measures as Tools for Exploring the Gene Ontology

Many bioinformatics resources hold data in the form of sequences. Often this sequence data is associated with a large amount of annotation. In many cases this data has been hard to model, and has been represented as scientific natural language, which is not readily computationally amenable. The development of the Gene Ontology provides us with a more accessible representation of some of this data. However it is not clear how this data can best be searched, or queried. Recently we have adapted information content based measures for use with the Gene Ontology (GO). In this paper we present detailed investigation of the properties of these measures, and examine various properties of GO, which may have implications for its future design.
Progressive Interval Heuristics for Multi-Item Capacitated Lot-Sizing Problems

We consider a family of N items that are produced in, or obtained from, the same production facility. Demands are deterministic for each item and each period within a given horizon of T periods. If in a given period an order is placed, setup costs are incurred. The aggregate order size is constrained by a capacity limit. The objective is to find a lot-sizing strategy that satisfies the demands for all items over the entire horizon without backlogging, and that minimizes the sum of inventory-carrying costs, fixed-order costs, and variable-order costs. All demands, cost parameters, and capacity limits may be time dependent. In the basic joint setup cost (JS) model, the setup cost of an order does not depend on the composition of the order. The joint and item-dependent setup cost (JIS) model allows for item-dependent setup costs in addition to the joint setup costs. We develop and analyze a class of so-called progressive interval heuristics. A progessive interval heuristic solves a JS or JIS problem over a progressively larger time interval, always starting with period 1, but fixing the setup variables of a progressively larger number of periods at their optimal values in earlier iterations. Different variants in this class of heuristics allow for different degrees of flexibility in adjusting continuous variables determined in earlier iterations of the algorithm. For the JS-model and the two basic implementations of the progressive interval heuristics, we show under some mild parameter conditions that the heuristics can be designed to be e-optimal for any desired value of e > 0 with a running time that is polynomially bounded in the size of the problem. They can also be designed to be simultaneously asymptotically optimal and polynomially bounded. A numerical study covering both the JS and JIS models shows that a progressive interval heuristic generates close-to-optimal solutions with modest computational effort and that it can be effectively used to solve large-scale problems.
Effect of changes in the moisture content due to surrounding relative humidity on the contact stress in traditional mortise and tenon joints III : pull-out strength of compressed sugi komisen joints

This research is focused on evaluating the efficiency and failure mechanism of joints using a komisen (Japanese traditional square key) of compressed sugi (Japanese ceder ;Cryptomeria japonica D. Don), and to evaluate to what extend hozo-komisen (Japanese traditional mortise and tenon) joint strength is being influenced by the recovery of compressed sugi komisen when exposed to long term humidity cycling. Compressed sugi komisen showed a change of yield and rupture mode compared to shirakashi (Quercus myrsinaefolia Blume) komisen, as did the komisen inserting direction into the joint because it has characteristic and anisotropic properties. The compressed sugi komisen joint (C1R), when inserted according to the R-type, yielded by shear of the komisen and reached its maximum strength (Pmax :12.5 kN) just before rupture at 10 mm displacement at the tenon. The failure mode showed a different pattern, compared to the shirakashi komisen joint (S1R) where the central komisen yielded in bending. The strength of the compressed sugi komisen joint (C1RH) exposed to cyclic changes of humidity (40-80%RH) during two years increased in maximum strength, yield strength, and energy absorption. This is in contrast to the shirakashi komisen joint (C1RH) that showed a dramatic and remarkable strength decrease when exposed to the climatic environment.
Effects of various protocols of ischemic preconditioning on rat tram flaps

We used rat transverse rectus abdominis musculocutaneous (TRAM) flaps to investigate whether the ischemic cycle duration and number of cycles influenced the effectiveness of ischemic preconditioning (IPC). First, the animals were divided into one control group and four treatment groups. Controls received no preconditioning; flaps with IPC were treated by two cycles of pedicel clamping and reperfusion for either 5 or 10 min. Then the best of IPC protocols in first part was selected, and flaps were subjected to one or three cycles of IPC before 4 h of normothermic ischemia. The preconditioned flap survival area had improved 2.5–3 times over that of the control area by postoperative day 7. Serum creatine phosphokinase (CPK), water content, and malondialdehyde (MDA) in muscle were significantly decreased in the preconditioned groups after 4 h of reperfusion. Especially, 2 and 3 cycles of the 10/5‐min combination were more effective than other protocols of IPC. © 2007 Wiley‐Liss, Inc. Microsurgery, 2008.