Miracle-dz/UniFAR-FTUs huggingface dataset:
Transmitter release in the neuromuscular synapse of the protein kinase C theta‐deficient adult mouse

We studied structural and functional features of the neuromuscular junction in adult mice (P30) genetically deficient in the protein kinase C (PKC) theta isoform. Confocal and electron microscopy shows that there are no differences in the general morphology of the endplates between PKC theta‐deficient and wild‐type (WT) mice. Specifically, there is no difference in the density of the synaptic vesicles. However, the myelin sheath is not as thick in the intramuscular nerve fibers of the PKC theta‐deficient mice. We found a significant reduction in the size of evoked endplate potentials and in the frequency of spontaneous, asynchronous, miniature endplate potentials in the PKC theta‐deficient neuromuscular preparations in comparison with the WT, but the mean amplitude of the spontaneous potentials is not different. These changes indicate that PKC theta has a presynaptic role in the function of adult neuromuscular synapses. J. Comp. Neurol. 519:849–855, 2011. © 2010 Wiley‐Liss, Inc.
On the Adaptivity Gap in Two-Stage Robust Linear Optimization under Uncertain Constraints

In this paper, we study the performance of static solutions in two-stage adjustable robust packing linear optimization problem with uncertain constraint coefficients. Such problems arise in many important applications such as revenue management and resource allocation problems where demand requests have uncertain resource requirements. The goal is to find a two-stage solution that maximizes the worst case objective value over all possible realizations of the secondstage constraints from a given uncertainty set. We consider the case where the uncertainty set is column-wise and constraint-wise (any constraint describing the set involve entries of only a single column or a single row). This is a fairly general class of uncertainty sets to model constraint coefficient uncertainty. We show that the two-stage adjustable robust problem is Ω(log n)hard to approximate. On the positive side, we show that a static solution is an O ( log n · min(log Γ, log(m + n)) ) -approximation for the two-stage adjustable robust problem where m and n denote the numbers of rows and columns of the constraint matrix and Γ is the maximum possible ratio of upper bounds of the uncertain constraint coefficients. Therefore, for constant Γ, surprisingly the performance bound for static solutions matches the hardness of approximation for the adjustable problem. Furthermore, in general the static solution provides nearly the best efficient approximation for the two-stage adjustable robust problem.
Prescott tests of equality in binary data under a three-treatment three-period crossover design

ABSTRACT Three test procedures accounting for patients with tied responses based on Prescott’s ideas are developed for comparing three treatments under a three-period crossover trial in binary data. Monte Carlo simulation is employed to evaluate the performance of these test procedures in a variety of situations. The test procedures proposed here are noted to have power larger than those procedures, which utilize only those patients with un-tied responses. The data taken from a three-period crossover trial comparing two different doses of an analgesic with placebo for the relief of primary dysmenorrhea are used to illustrate the use of the test procedures developed here.
Feeding-induced rearrangement of green leaf volatiles reduces moth oviposition

The ability to decrypt volatile plant signals is essential if herbivorous insects are to optimize their choice of host plants for their offspring. Green leaf volatiles (GLVs) constitute a widespread group of defensive plant volatiles that convey a herbivory-specific message via their isomeric composition: feeding of the tobacco hornworm Manduca sexta converts (Z)-3- to (E)-2-GLVs thereby attracting predatory insects. Here we show that this isomer-coded message is monitored by ovipositing M. sexta females. We detected the isomeric shift in the host plant Datura wrightii and performed functional imaging in the primary olfactory center of M. sexta females with GLV structural isomers. We identified two isomer-specific regions responding to either (Z)-3- or (E)-2-hexenyl acetate. Field experiments demonstrated that ovipositing Manduca moths preferred (Z)-3-perfumed D. wrightii over (E)-2-perfumed plants. These results show that (E)-2-GLVs and/or specific (Z)-3/(E)-2-ratios provide information regarding host plant attack by conspecifics that ovipositing hawkmoths use for host plant selection. DOI: http://dx.doi. org/10.7554/eLife.00421. 001
Endoscopic Transnasal Surgery as a Replacement for Maxillotomy Techniques to Approach the Central Skull Base: Fewer Complications and More Acceptable to Patients?

Abstract Objectives To compare the complication rates of endoscopic transnasal and open maxillotomy approaches for the central skull base. Design Retrospective review. Setting Single-center study, London, United Kingdom. Participants From 1992 to 2012, 81 patients underwent surgery for skull base lesions, 59 by maxillotomy and 22 by endoscopy. Main Outcome Measures Total time of surgical anesthesia, blood loss, complications, duration of tracheal intubation, duration of hospital stay, myelopathy score, and mortality rate. Results The surgical time, blood loss, and duration of the postoperative intubation period were significantly less with endoscopy (p < 0.001). Requirements for intensive care, ward stay, and total hospital stay were also significantly less in the endoscopic group (p = 0.01, p < 0.001, and p < 0.001, respectively). The complication rate was lower with transnasal endoscopic surgery. Conclusion In patients for whom open maxillotomy or endoscopic surgery are both feasible, the preference should be to perform endoscopic surgery, with better visualization and fewer complications.
Large-scale experiment of co-allocation strategies for Peer-to-Peer supercomputing in P2P-MPI

High Performance computing generally involves some parallel applications to be deployed on the multiples resources used for the computation. The problem of scheduling the application across distributed resources is termed as co-allocation. In a grid context, co-allocation is difficult since the grid middleware must face a dynamic environment. Middleware architecture on a peer-to-peer (P2P) basis have been proposed to tackle most limitations of centralized systems. Some of the issues addressed by P2P systems are fault tolerance, ease of maintenance, and scalability in resource discovery. However, the lack of global knowledge makes scheduling difficult in P2P systems. In this paper, we present the new developments concerning locality awareness as well as co-allocation strategies available in the latest release of P2P-MPI. i) The spread strategy tries to map processes on hosts so as to maximize the total amount of available memory while maintaining locality of processes as a secondary objective, ii) The concentrate strategy tries to maximize locality between processes by using as many cores as hosts offer. The co-allocation scheme has been devised to be simple for the user and meets the main high performance computing requirement which is locality. Extensive experiments have been conducted on Grid5000 with up to 600 processes on 6 sites throughout France. Results show that we achieved the targeted goals in these real conditions.
Determinants of Optimizing the Role of Bhabinkamtibmas in Building Public Trust

Determinants as supporters or obstacles to optimizing the role of Bhabinkamtibmas in building public trust are analogous to two sides of one coin which revolves around the implementation of the main tasks, authority, and functions of the institution that accommodate it. These organizational factors have a sustainable impact on service effectiveness and strengthening relations between government institutions and the community. The article resulting from this research explains the determinants of optimizing the role of Bhabinkamtibmas in building public trust in certain loci. Data, information, and knowledge regarding the research focus were obtained through observations, interviews, and focus group discussions with informants as members of Bhabinkamtibmas (police, army, sub-district officials), community leaders, religious leaders, non-governmental organizations (NGOs), and academics. The data is analyzed using an interactive model which includes data collection, data condensation, and verification using the Important Performance Analysis (IPA) technique which is presented through a spider curve, and drawing conclusions. The research results found that there are several aspects as determinants that support or hinder efforts to build public trust in the demarcation of duties of the Makassar Indonesian Big City Resort Police (Polrestabes). Determinants as supporters or obstacles to optimizing the role of Bhabinkamtibmas in building public trust include the quality of public services, actor leadership style, transparency and accountability, public participation, effective communication, justice and equality in public policies and services, competency and integrity of the apparatus. The glue that unites the sustainability of these determinants is the leadership style and learning of the Bhabinkamtibmas organization as a representation of the Indonesian National Police (Polri).
The impact of wrapping on sidechain-mainchain hydrogen bonds

We investigate the frequencies of hydrogen bonds in protein secondary structure, including ones involving sidechains. We study the effect of wrapping on the frequency of these bonds. We show that hydrogen bonds between the mainchain and sidechains occur most frequently when there are nearby structural defects due to a lack of wrapping. It is remarkable that there are more mainchain-mainchain hydrogen bonds than ones involving sidechains [9] in protein structure as represented in the Protein Data Bank (PDB). To investiage this, and to assess the effect of wrapping [1, 2, 3, 4] on formation of hydrogen bonds involving sidechains, we experimented with a prototype code developed by an intern from École Polytechnique, Thuong Van Du Tran, who visited the University of Chicago in the summer of 2006. This code was a precursor to the code Wrappa [5, 6]. Since wrapping for hydrogen bonds involving sidechains has not yet been extensively studied, we simply followed norms for mainchain-mainchain hydrogen bonds [6]. We used a subset of the PDB called PDBSelect [7], generated in 2006, consisting of 1547 proteins complexes (PDB files). This data set has only 68,917 hydrogen bonds between sidechains and mainchains, contrasted with 233,879 mainchain-mainchain hydrogen bonds. All data was restricted to intramolecular hydrogen bonds within a single chain for simplicity, since the basic PDBSelect unit is a chain. Thus it would be difficult to know what to do to limit bias if a neighboring chain might have a structure redundant with another chain in the data set. In addition, there are 33,021 sidechain-sidechain hydrogen bonds, 152 of which involve terminal oxygens. If we classify bonds according to whether the sidechain is the donor (S-M) or acceptor (M-S), then we find that 30,640 of the total hydrogen bonds between sidechains and mainchains have the sidechain as acceptor (M-S), not including another 75 which involve terminal oxygens. Correspondingly, the remainder (38,277) are S-M bonds. The rotameric diversity of most sidechains [8] indicates a torsional flexibility that is considerably greater than that allowed by the backbone rotational degrees of freedom. Thus one might expect that sidechain hydrogen bonds would play a dominant role in protein structure. However, the above data shows that the opposite is true. This may be due to the higher entropic cost associated with freezing the position of the sidechain in order to form a hydrogen bond. To be sure
Distributed Flow Monitoring Tool Using Network Processor

There is an emerging requirement for real-time flow-based traffic monitoring, which is vital for quality of service (QoS) monitoring, anomaly monitoring, and traffic engineering in Internet service provider networks. In this report, we discuss a distributed architecture for real-time and scalable flow monitoring tools and implement a prototype tool using network processor (NP). The contributions of the present paper are two-folds. First, we clarify the elemental functions that are required and commonly used by passive flow monitoring tools, and refine a distribution-processing architecture for combining these functions based on our previous work in order to cope with heavy-load input traffic. Second, we implement the packet distribution component, which plays a core role and might be bottleneck in the proposed architecture, by using pipeline-mode NP hardware, and experimentally prove its applicability to 10 Gbit/s-class input traffic
Purification and characterization of a cephalosporin esterase from Rhodosporidium toruloides

A novel cephalosporin esterase (EC 3.1.1.41) from Rhodosporidium toruloides was purified to gel electrophoretic homogeneity. The enzyme is a glycoprotein with a molecular mass of 80 kDa. Upon deglycosylation, several forms of the enzyme were observed with a molecular mass range between 60 and 66 kDa. The isoelectric point of the enzyme is approximately 5.6, with the pH optimum for activity occurring at 6.0. The optimal activity of the enzyme occurred at 25 degrees C, with the enzyme rapidly losing activity at temperatures above 25 degrees C. The enzyme deacetylated a variety of cephalosporin derivatives, including cephalosporin C; the Km for this substrate is 51.8 mM, and the Vmax is 7.9 mumol/min/mg. In addition to cephalosporins, the enzyme hydrolyzed short-chain p-nitrophenyl esters, with the activity decreasing with increasing ester chain length. The enzyme also has the ability to acetylate desacetyl cephalosporins in high yields under mild conditions in the presence of various acetyl donors. A comparison of the physical properties of the esterase with those of other well-characterized cephalosporin esterases indicates that the enzyme is unique in this class.
Assessing the Value of DNA Barcodes for Molecular Phylogenetics: Effect of Increased Taxon Sampling in Lepidoptera

Background A common perception is that DNA barcode datamatrices have limited phylogenetic signal due to the small number of characters available per taxon. However, another school of thought suggests that the massively increased taxon sampling afforded through the use of DNA barcodes may considerably increase the phylogenetic signal present in a datamatrix. Here I test this hypothesis using a large dataset of macrolepidopteran DNA barcodes. Methodology/Principal Findings Taxon sampling was systematically increased in datamatrices containing macrolepidopteran DNA barcodes. Sixteen family groups were designated as concordance groups and two quantitative measures; the taxon consistency index and the taxon retention index, were used to assess any changes in phylogenetic signal as a result of the increase in taxon sampling. DNA barcodes alone, even with maximal taxon sampling (500 species per family), were not sufficient to reconstruct monophyly of families and increased taxon sampling generally increased the number of clades formed per family. However, the scores indicated a similar level of taxon retention (species from a family clustering together) in the cladograms as the number of species included in the datamatrix was increased, suggesting substantial phylogenetic signal below the ‘family’ branch. Conclusions/Significance The development of supermatrix, supertree or constrained tree approaches could enable the exploitation of the massive taxon sampling afforded through DNA barcodes for phylogenetics, connecting the twigs resolved by barcodes to the deep branches resolved through phylogenomics.
Technical efficiency of organic tea smallholders: Evidence from Uva region of Sri Lanka

Today the society is moving towards sustainable agriculture, as a sustainable farming system, where cultivation is carried out without using chemically synthesized products such as urea, ammonium sulphate, pesticides, herbicides, hormones, activators, etc. With the introduction of organic agriculture to the world, organic tea also became important. Farmer productivity is one of the most important concerns in this regard. In the short run, the farmer productivity can be raised by improvement in technical efficiency. However, there is dearth of empirical evidence on technical efficiency of tea cultivation in Sri Lanka. Hence this article contributes to the pertinent literature by providing estimates of a stochastic frontier production model in a sample of organic tea smallholders in Diyathalawa region of Badulla district in Sri Lanka where the highest number of smallholders cultivate organic tea. The results reveal that the mean technical efficiency of organic tea smallholders is 24.7% implying that there is a scope of further increasing the output by 75.3%. Furthermore, livelihood diversification and crop diversification activities of smallholders contribute to decrease the efficiency.
Distinct roles for distal‐less genes Dlx3 and Dlx5 in regulating ectodermal development in Xenopus

In vertebrates, there are six or more copies of genes related to the Drosophila pattern formation homeodomain gene Distal‐less. Among this family, Dlx3 and Dlx5 share extensive sequence homology and have similar, but distinctive, expression patterns, suggesting that these two factors may have substantially redundant developmental functions. Here we show that at the earliest phases of embryogenesis in Xenopus, there are significant differences between Dlx3 and Dlx5 expression and that this correlates with different functions in the restriction of neural crest and neural plate boundaries, respectively. Mol. Reprod. Dev. 60: 331–337, 2001. © 2001 Wiley‐Liss, Inc.
Tell Me What You See and I Will Show You Where It Is

We tackle the problem of weakly labeled semantic segmentation, where the only source of annotation are image tags encoding which classes are present in the scene. This is an extremely difficult problem as no pixel-wise labelings are available, not even at training time. In this paper, we show that this problem can be formalized as an instance of learning in a latent structured prediction framework, where the graphical model encodes the presence and absence of a class as well as the assignments of semantic labels to superpixels. As a consequence, we are able to leverage standard algorithms with good theoretical properties. We demonstrate the effectiveness of our approach using the challenging SIFT-flow dataset and show average per-class accuracy improvements of 7% over the state-of-the-art.
The structure of claw-free graphs

A graph is claw-free if no vertex has three pairwise nonadjacent neighbours. At first sight, there seem to be a great variety of types of claw-free graphs. For instance, there are line graphs, the graph of the icosahedron, complements of triangle-free graphs, and the Schläfli graph (an amazingly highly-symmetric graph with 27 vertices), and more; for instance, if we arrange vertices in a circle, choose some intervals from the circle, and make the vertices in each interval adjacent to each other, the graph we produce is claw-free. There are several other such examples, which we regard as “basic” claw-free graphs. Nevertheless, it is possible to prove a complete structure theorem for clawfree graphs. We have shown that every connected claw-free graph can be obtained from one of the basic claw-free graphs by simple expansion operations. In this paper we explain the precise statement of the theorem, sketch the proof, and give a few applications.
Learning Spatiotemporal Graphical Models From Incomplete Observations

This paper investigates the problem of learning a graphical model from incomplete spatio-temporal measurements. Our purpose is to analyze a time-varying graph signal represented by an incomplete data matrix, the rows and columns of which correspond to spatial and temporal features/measurements of the signal, respectively. In contrast to the conventional approaches which utilize either a directed or an undirected graphical model for data analysis, we propose a compound multi-relational model exploiting both directed and undirected structures. Our approach is based on statistical inference in which a spatio-temporal signal is considered as a random graph process to which we can apply maximum-a-posteriori estimation methods for model identification. We incorporate the Gaussian-Markov random field (GMRF) and the vector auto-regressive (VAR) models to capture both the (undirected) spatial correlations and the (directed) temporal dependencies. We propose an algorithm for joint estimation of the signal and the graphical models, from incomplete measurements. For this purpose, we formulate an optimization problem that we solve using the block successive upperbound minimization (BSUM) method. Our simulation results confirm the efficiency of the proposed method for signal recovery and graph learning.
A Review on Preprocessing Techniques for Digital Mammography Images

Mammograms are the soft X-rays kind of imaging technique used for the detection of any lesions or cysts in breasts. Digital mammograms have many kinds of artifacts that affect the accuracy of the detection of tumor tissues in the automated Computer Aided Detection (CAD) system for mammograms. Preprocessing helps to remove such artifacts is an important step. Image preprocessing is used to maintain image efficiency in mammogram images there are many artifacts need to be removed like labels, patient name, muscle part, etc. and enhance the region of interest which helps for efficient segmentation and detection of tumor. The basic objective of this study is to evaluate and discuss different techniques and approaches proposed in order to enhance the breast cancer images and an efficient preprocessing technique for mammography. It aims to find the existing preprocessing techniques for mammography images and discuss the techniques used and their advantages. General Terms Digital Image Processing, Preprocessing of Mammography and Image Enhancement.
Transcriptomics of Besnoitia besnoiti-Infected Fibroblasts Reveals Hallmarks of Early Fibrosis and Cancer Progression

Endothelial injury, inflammatory infiltrate and fibrosis are the predominant lesions in the testis of bulls with besnoitiosis that may result in sterility. Moreover, fibroblasts, which are key players in fibrosis, are parasite target cells in a Besnoitia besnoiti chronic infection. This study aimed to decipher the molecular basis that underlies a drift toward fibrosis during the disease progression. Transcriptomic analysis was developed at two times post-infection (p.i.), representative of invasion (12 h p.i.) and intracellular proliferation (32 h p.i.), in primary bovine aorta fibroblasts infected with B. besnoiti tachyzoites. Once the enriched host pathways were identified, we studied the expression of selected differentially expressed genes (DEGs) in the scrotal skin of sterile infected bulls. Functional enrichment analyses of DEGs revealed shared hallmarks of cancer and early fibrosis. Biomarkers of inflammation, angiogenesis, cancer, and MAPK signaling stood out at 12 h p.i. At 32 h p.i. , again MAPK and cancer pathways were enriched together with the PI3K–AKT pathway related to cell proliferation. Some DEGs were also regulated in the skin samples of naturally infected bulls (PLAUR, TGFβ1, FOSB). We have identified potential biomarkers and host pathways regulated during fibrosis that may hold prognostic significance and could emerge as potential therapeutic targets.