Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome‐based identification and characterization of a putative mucin‐binding protein from the surface of Streptococcus pneumoniae

Streptococcus pneumoniae open reading frame SP1492 encodes a surface protein that contains a novel conserved domain similar to the repeated fragments of mucin‐binding proteins from lactobacilli and lactococci. To investigate the functional role(s) of this protein and its potential adhesive properties, the surface‐exposed region of SP1492 was expressed in Escherichia coli, purified to homogeneity, and partially characterized by biophysical and immunological methods. Circular dichroism and sedimentation measurements confirmed that SP1492 is an all‐β protein that exists in solution as a monomer. The SP1492 protein has been shown to be expressed by S. pneumoniae and was experimentally localized to its surface. The protein functional domain binds to mucins II and III from porcine stomach and to purified submaxillary bovine gland mucin. It appears to be one of the very few unambiguous pneumococcal adhesin molecules known to date. A hypothetical model constructed by ab initio techniques predicts a novel β‐sandwich protein structure. Proteins 2007. © 2006 Wiley‐Liss, Inc.
A Novel Bioinformatics Approach Identifies Candidate Genes for the Synthesis and Feruloylation of Arabinoxylan1[W][OA]

Arabinoxylans (AXs) are major components of graminaceous plant cell walls, including those in the grain and straw of economically important cereals. Despite some recent advances in identifying the genes encoding biosynthetic enzymes for a number of other plant cell wall polysaccharides, the genes encoding enzymes of the final stages of AX synthesis have not been identified. We have therefore adopted a novel bioinformatics approach based on estimation of differential expression of orthologous genes between taxonomic divisions of species. Over 3 million public domain cereal and dicot expressed sequence tags were mapped onto the complete sets of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genes, respectively. It was assumed that genes in cereals involved in AX biosynthesis would be expressed at high levels and that their orthologs in dicotyledonous plants would be expressed at much lower levels. Considering all rice genes encoding putative glycosyl transferases (GTs) predicted to be integral membrane proteins, genes in the GT43, GT47, and GT61 families emerged as much the strongest candidates. When the search was widened to all other rice or Arabidopsis genes predicted to encode integral membrane proteins, cereal genes in Pfam family PF02458 emerged as candidates for the feruloylation of AX. Our analysis, known activities, and recent findings elsewhere are most consistent with genes in the GT43 families encoding β-1,4-xylan synthases, genes in the GT47 family encoding xylan α-1,2- or α-1,3-arabinosyl transferases, and genes in the GT61 family encoding feruloyl-AX β-1,2-xylosyl transferases.
Evaluation of Systematic Position of Helicoprorodontids and Chaeneids (Ciliophora, Litostomatea): An Attempt to Break Long Branches in 18S rRNA Gene Phylogenies

Phylogenetic position of some free‐living litostomatean taxa has not been correctly determined because of long‐branch artifacts in 18S rRNA gene trees. The main aim of this study was to test the effectiveness of various masking algorithms, tree‐building techniques, binarization of DNA data as well as combining morphological and molecular data to eliminate long‐branch attraction of two problematic groups, helicoprorodontids and chaeneids. Guidance and SlowFaster masking in a combination with PhyloBayesian tree construction erased the artifactual positions of helicoprorodontids and chaeneids. On the other hand, binarization of DNA sequences and the strategy of combining morphological and molecular data eliminated only the artifactual position of chaeneids but not that of helicoprorodontids which were still being attracted by out‐group taxa. According to statistical tree topology tests and comparative morphological studies, helicoprorodontids are classified as a distinct order while chaeneids are considered to be fast evolving members of the order Lacrymariida. The high body contractility, “cephalization” of the anterior body end, and helicalization of the anterior portion of some or all somatic ciliary rows indicate relatedness of helicoprorodontids, chaeneids, and lacrymariids. On the other hand, the dorsal brush separated from the circumoral kinety by dense ciliary files supports kinships of chaeneids, lacrymariids, and didiniids.
Angular Radii of Stars via Microlensing

We outline a method by which the angular radii of giant and main-sequence stars located in the Galactic bulge can be measured to a few percent accuracy. The method combines comprehensive ground-based photometry of caustic-crossing bulge microlensing events, with a handful of precise (~10 μas) astrometric measurements of the lensed star during the event, to measure the angular radius of the source, θ*. Dense photometric coverage of one caustic crossing yields the crossing timescale Δt. Less frequent coverage of the entire event yields the Einstein timescale tE and the angle ϕ of source trajectory with respect to the caustic. The photometric light-curve solution predicts the motion of the source centroid up to an orientation on the sky and overall scale. A few precise astrometric measurements therefore yield θE, the angular Einstein ring radius. Then the angular radius of the source is obtained by θ* = θE(Δt/tE) sin ϕ. We argue that the parameters tE, Δt, ϕ, and θE, and therefore θ*, should all be measurable to a few percent accuracy for Galactic bulge giant stars using ground-based photometry from a network of small (1 m class) telescopes, combined with astrometric observations with a precision of ~10 μas to measure θE. We find that a factor of ~50 times fewer photons are required to measure θE to a given precision for binary lens events than for single-lens events. Adopting parameters appropriate to the Space Interferometry Mission (SIM), we find that ~7 minutes of SIM time is required to measure θE to ~5% accuracy for giant sources in the bulge. For main-sequence sources, θE can be measured to ~15% accuracy in ~1.4 hr. Thus, with access to a network of 1 m class telescopes, combined with 10 hr of SIM time, it should be possible to measure θ* to 5% for ~80 giant stars, or to 15% for roughly seven main-sequence stars. We also discuss methods by which the distances and spectral types of the source stars can be measured. A by-product of such a campaign is a significant sample of precise binary lens mass measurements.
Incremental Model-Based Clustering for Large Datasets With Small Clusters

Clustering is often useful for analyzing and summarizing information within large datasets. Model-based clustering methods have been found to be effective for determining the number of clusters, dealing with outliers, and selecting the best clustering method in datasets that are small to moderate in size. For large datasets, current model-based clustering methods tend to be limited by memory and time requirements and the increasing difficulty of maximum likelihood estimation. They may fit too many clusters in some portions of the data and/or miss clusters containing relatively few observations. We propose an incremental approach for data that can be processed as a whole in memory, which is relatively efficient computationally and has the ability to find small clusters in large datasets. The method starts by drawing a random sample of the data, selecting and fitting a clustering model to the sample, and extending the model to the full dataset by additional EM iterations. New clusters are then added incrementally, initialized with the observations that are poorly fit by the current model. We demonstrate the effectiveness of this method by applying it to simulated data, and to image data where its performance can be assessed visually.
Dimensionality Reduction Using Semantic Analysis

An efficient method to compress and reduce the dimensionality of Arabic texts using semantic model-based representation of text is introduced. The proposed system creates equivalence classes, where similar words, generated according to the rich productive morphology of the language and based on the stemroot-pattern paradigm, are grouped together and represented by a class identifier. In addition, synonyms and similarly named entities are regrouped in order to improve the representation and reduce its size. The reduced representation of the text is accessible to most machine learning algorithms and natural language processing applications that require heavy computational complexity. Distributional similarity measures were used to create equivalence classes of similar words. These measures were applied to the word-context matrix associated with the document in order to identify similar words based on a text's context. The results confirmed that the proposed method shows that incorporation of sematic information in vector representation is superior to classical bag-of-words representation, in terms of size reduction and results quality of applications. The best results are achieved for the clustering of words that are semantically similar, based on their stems. In addition, regrouping differently named entities representing the same concepts improved the reduction amount by 5%. Key-Words: Semantic vector space model, word-context matrix, Arabic natural language processing, text dimension reduction, semantic feature extraction
N for the Price of 1: Bundling Web Objects for More Eecient Content Delivery 1

Persistent connections address ine ciencies associated with multiple concurrent connections. They can improve response time when successfully used with pipelining to retrieve a set of objects from a Web server. In practice, however, there is inconsistent support for persistent connections, particularly with pipelining, from Web servers, user agents, and intermediaries. Web browsers continue to open multiple concurrent TCP connections to the same server. This paper proposes a new idea of packaging the set of objects embedded on a Web page into a single bundle object for retrieval by clients. Our analysis indicates that if embedded objects on a Web page are delivered to clients as a single bundle, the response time experienced by the clients is as good as or better than that provided by currently deployed mechanisms. We also show that, relative to the currently used retrieval methods, our approach reduces the load on the network and servers. The key contribution of our work is a mechanism that gives Web servers control over the number and duration of TCP connections they support. Implementation of the mechanism requires no changes to the HTTP protocol.
Selenium in poultry nutrition: a review

Selenium has been known for two centuries and its biological activities have been studied for nearly a hundred years, however the problem of Se deficit has still been persisting both in humans and animals. The cause of Se deficit in animals may be low Se level in soil. This mainly applies to cattle and sheep with their direct link to soil via roughage. The risk of Se deficit in pigs and poultry is lower due to lower dependence on soil Se level in the region and Se fortification in feed mixes. The present research focuses on the effects of Se on meat and egg quality, antioxidant activity of Se, effects on fatty acid levels, activity of glutathione-peroxidase, or the effect of Se on the immune system. Ensuring natural Se supply in human nutrition by food of animal origin, mainly poultry meat and eggs (the "functional foods"), is another area to which extensive attention has recently been paid.
The Five-Factor Model Describes the Structure of Social Perceptions

My graduate school cohort was the first admitted into a newly merged social and personality psychology program. That merger, and the combination of perspectives that I was exposed to, turned out to be an important part of my intellectual identity and professional development. And along the way, it produced a number of enlightening exchanges when the formerly separate areas were compelled to make serious efforts to figure each other out. I vividly remember one particular exchange that happened in our weekly graduate student brownbag.1 Two graduate students who had entered the merger from the social psychology side stood up to present an ambitious idea for a research project. In their reading of the social perception literature, they had become dissatisfied with studies that examined dimensions of social perception on an ad hoc basis. They wanted to embark on a project to identify the fundamental dimensions of social perception used by lay perceivers. A hand came up from somebody who’d come from the personality side. Could you just have people make ratings on the Big Five? No, no, they replied. We aren’t trying to study personality, we’re interested in social perception. As the meeting progressed, they presented a broad agenda for achieving their goal. They needed to come up with some way to get a representative sample of the terms and concepts ordinary people use to describe each other in everyday social perception. Then they would ask subjects to use those concepts to make ratings of various target persons, and they would factor the results. More hands came up. More suggestions (actually the same ones) were offered and dismissed (for the same reasons). Frustration built on both sides of the podium, as everyone became convinced that the other side wasn’t listening to them. If you think I am a personality psychologist sharing this anecdote as a reason to point and laugh at the silly social psychologists, you’ve got me exactly wrong. I held these two classmates in very high esteem and still do today, and both are now highly accomplished scholars. Rather, to me this is an illustration of what has gone awry with the way we study and talk about personality structure.
From Fatherhood to Fathering: Transmission and Change among British Fathers in Four-generation Families

Drawing upon biographical-narrative research involving case studies of British families in which four generations were alive at the same time, the article examines change and continuity among fathers and sons, focusing in detail upon one family.The article examines the scheduling of fatherhood in the life course of three generations; the ways in which they talked about ‘fathering’ and fatherhood when their children were young; and the transmission of fathering within families. The particular case, a family of low-skilled men, demonstrates how structural changes and cultural resources combine in the negotiation of a model of ‘hands-on fathering’ in the current father generation. The article draws out some theoretical aspects of the analysis; in particular, how structural and cultural changes and gender intersect differently for different social classes.The theoretical insights depend upon a biographical approach which emphasized the changing context and the ways in which each generation acted upon that context.
Western Perspectives in Applied Linguistics in Africa.

The aim of this article is to analyze the nature of the historical and contemporary social contexts within which applied linguistics in Africa emerged, and is currently practiced. The article examines the challenges ‘local’ applied Linguistics in Africa is confronted with as it tries to amplify applied linguistic programs emanating from Europe and North America. The article argues that seemingly progressive applied linguistic projects interconnect in consolidating a western view of Africa in postcolonial Africa. In this way these projects end up mirroring the very theories which they seek to challenge.
Definition Extraction Using a Sequential Combination of Baseline Grammars and Machine Learning Classifiers

The paper deals with the task of definition extraction from a small and noisy corpus of instructive texts. Three approaches are presented: Partial Parsing, Machine Learning and a sequential combination of both. We show that applying ML methods with the support of a trivial grammar gives results better than a relatively complicated partial grammar, and much better than pure ML approach.
Collagen sutures in cataract surgery: clinical and experimental observations.

SINCE HUGHES IN 1943 advised the use of absorbable sutures in ocular surgery great efforts have been made to develop new absorbable suture materials.1"2 Larmi and Vannas, Trautmann, Vorosmarthy and Scheid, and other Europeans have investigated biosutures formed from rator nutria-tail tendons and have used them successfully in both cataract and corneal surgery.3-1" In this country similar studies have been made with extruded collagen sutures. McPherson and Young, and Kreshon and coworkers reported their use in keratoplasty and in cataract extraction; Truhlsen and Fitzpatrick have used collagen sutures in experimental strabismus surgery.12-'4 Although there have been other histologic studies we felt it worthwhile to report the tissue reactions produced when extruded 6-0 plain collagen sutures are used to close experimental cataract incisions.1"'15"16 These findings are compared with those from earlier investigations of silk and surgical gut (catgut) sutures.17"l8
The Effects of Pair Programming on Learning Efficiency in Short Programming Assignments

Pair programming is one of the important practices of a lightweight development methodology namely eXtreme Programming (XP). It emphasizes the practice of two persons work- ing together at a single computer terminal, to design, code and test computer programs. The effects of pair programming on software development in industrial organizations were studied and it was found that pair programming increases the productivity by 15%. This evidence created an interest in amongst community of computer science educators to apply pair programming in educational settings. We have conducted an experiment with the students of computer science courses to compare the learning efficiency of students when they adopt pair programming with that of students using tradi- tional method to do laboratory exercises of short duration. The learning efficiency was measured by evaluating design documents, completion time, and marks obtained in a written test that was con- ducted after every exercise. Our research confirms that the adoption of pair programming improves the design ability, reduces time taken to do a laboratory exercise and increases the knowledge and programming skill.
A slight improvement to Garaev’s sum product estimate

max(\A + A\,\AA\)>Ce\A\? -*. In the finite field setting this situation is much more complicated because the main tool, the Szemer? di-Trotter incidence theorem, does not hold in the same generality. It is known, via the work in [BKT], that if A is a subset of Fp, the field of p elements with p prime, and if p6 0, then one has the sum product estimate max(|? + A|,|AA|)>|,4|1+ for some e > 0. This result has found many applications in combinatorial problems and exponential sum estimates (see e.g. [BKT], [BGK], [G2]). Recently, Garaev [Gl] showed that when \A\ < pz, one has the estimate
Force and Motion: Pre-service and Practising Secondary Science Teachers' Language and Understanding

Abstract The words used by pre‐sewice and practising secondary science teachers to denote various forces and their possible misconceptions about force and motion were investigated. Many teachers, particularly biology and chemistry specialists, were found to hold misconceptions about forces and to use inappropriate terminology. This problem was especially evident in the pre‐service biology and chemistry specialists.
Phosphorylation of the RNA Polymerase II Carboxyl-Terminal Domain by CDK9 Is Directly Responsible for Human Immunodeficiency Virus Type 1 Tat-Activated Transcriptional Elongation

ABSTRACT Stimulation of transcriptional elongation by the human immunodeficiency virus type 1 Tat protein is mediated by CDK9, a kinase that phosphorylates the RNA polymerase II carboxyl-terminal domain (CTD). In order to obtain direct evidence that this phosphorylation event can alter RNA polymerase processivity, we prepared transcription elongation complexes that were arrested by the lac repressor. The CTD was then dephosphorylated by treatment with protein phosphatase 1. The dephosphorylated transcription complexes were able to resume the transcription elongation when IPTG (isopropyl-β-d-thiogalactopyranoside) and nucleotides were added to the reaction. Under these chase conditions, efficient rephosphorylation of the CTD was observed in complexes containing the Tat protein but not in transcription complexes prepared in the absence of Tat protein. Immunoblots and kinase assays with synthetic peptides showed that Tat activated CDK9 directly since the enzyme and its cyclin partner, cyclin T1, were present at equivalent levels in transcription complexes prepared in the presence or absence of Tat. Chase experiments with the dephosphorylated elongation transcription complexes were performed in the presence of the CDK9 kinase inhibitor DRB (5,6-dichloro-1-β-d-ribofuranosyl-benzimidazole). Under these conditions there was no rephosphorylation of the CTD during elongation, and transcription through either a stem-loop terminator or bent DNA arrest sequence was strongly inhibited. In experiments in which the CTD was phosphorylated prior to elongation, the amount of readthrough of the terminator sequences was proportional to the extent of the CTD modification. The change in processivity is due to CTD phosphorylation alone, since even after the removal of Spt5, the second substrate for CDK9, RNA polymerase elongation is enhanced by Tat-activated CDK9 activity. We conclude that phosphorylation of the RNA polymerase II CTD by CDK9 enhances transcription elongation directly.
Dyslipidemia and lipid peroxidation of Saudi type 2 diabetics with proliferative retinopathy.

OBJECTIVES To assess lipid profile and lipid peroxidation in type 2 diabetics with proliferative retinopathy (PDR), and investigate the association between these biochemical parameters and PDR. METHODS This study was conducted between June 2011 and February 2012 in the Research Laboratory, College of Applied Medical Sciences, Qassim University, Qasssim, Kingdom of Saudi Arabia. The study included 54 patients with type 2 diabetes (21 with PDR and 33 controls) and 30 healthy subjects. The biochemical parameters were measured using standard laboratory procedures. RESULTS Patients with PDR characterized by significantly (p<0.05) increased levels of serum cholesterol, triglyceride, low density lipoprotein (LDL-C), plasma malondialdehyde; decreased levels of serum high density lipoprotein (HDL-C) and apolipoprotein A1 (Apo A1); positive correlation of malondialdehyde with triglyceride, but negative with HDL-C, Apo A1. In logistic regression, malondialdehyde, LDL-C, and Apo A1 were not associated with PDR. However, triglyceride (OR = 1.745; p=0.000), total cholesterol (OR = 0.079; p=0.000), and HDL-C (OR = 10.676; p=0.000) were independent risk factors for developing PDR. CONCLUSION Dyslipidemia and lipid peroxidation may play a role in pathogenesis of diabetic retinopathy. Patients with PDR displayed marked lipid abnormalities and increased lipid peroxidation. The control of lipid alterations through glycemic control and/or lipid lowering medication is required for type 2 diabetics at least to postpone or prevent loss of vision from retinopathy.