Miracle-dz/UniFAR-FTUs huggingface dataset:
Structures of N‐acetylornithine transcarbamoylase from Xanthomonas campestris complexed with substrates and substrate analogs imply mechanisms for substrate binding and catalysis

N‐acetyl‐L‐ornithine transcarbamoylase (AOTCase) is a new member of the transcarbamoylase superfamily that is essential for arginine biosynthesis in several eubacteria. We report here crystal structures of the binary complexes of AOTCase with its substrates, carbamoyl phosphate (CP) or N‐acetyl‐L‐ornithine (AORN), and the ternary complex with CP and N‐acetyl‐L‐norvaline. Comparison of these structures demonstrates that the substrate‐binding mechanism of this novel transcarbamoylase is different from those of aspartate and ornithine transcarbamoylases, both of which show ordered substrate binding with large domain movements. CP and AORN bind to AOTCase independently, and the main conformational change upon substrate binding is ordering of the 80's loop, with a small domain closure around the active site and little movement of the 240's loop. The structures of the complexes provide insight into the mode of substrate binding and the mechanism of the transcarbamoylation reaction. Proteins 2006. © 2006 Wiley‐Liss, Inc.
TENCKHOFF CATHETER INSERTION BY NEPHROLOGISTS: OPEN DISSECTION TECHNIQUE

♦ Background: The practice of Tenckhoff catheter insertion by nephrologists remains uncommon in most countries. ♦ Methods: We report our single-center experience of Tenckhoff catheter insertion by nephrologists using the open dissection surgical technique in a dedicated ward-based procedure room. ♦ Results: Between November 2005 and September 2008, 250 peritoneal catheters were inserted by 6 nephrologists with varying levels of experience. Surgical dissection followed by exposure of the peritoneum under direct vision was performed under local anesthesia. Primary catheter failure, as defined by catheters that failed to function within 1 month after insertion, occurred in 2.8% of cases. Within 1 month of catheter insertion, 20 patients developed infectious complications: 9 (3.6%) peritonitis, and 11 (4.4%) exit-site infections; none of these complications led to catheter removal. Mean technique survival for the catheters was 41.2 months (95% confidence interval: 39.5 months to 42.9 months). Catheter survival rates at 1 and 2 years were 92.7% and 87.2% respectively. ♦ Conclusions: We reported an encouraging outcome for Tenckhoff catheters inserted by nephrologists in an open surgical manner, with a 2-year catheter survival of 87.2% and a good safety profile.
Large-scale multimedia data mining using MapReduce framework

In this paper, the framework of MapReduce is explored for large-scale multimedia data mining. Firstly, a brief overview of MapReduce and Hadoop is presented to speed up large-scale multimedia data mining. Then, the high-level theory and low-level implementation for several key computer vision technologies involved in this work are introduced, such as 2D/3D interest point detection, clustering, bag of features, and so on. Experimental results on image classification, video event detection and near-duplicate video retrieval are carried out on a five-node Hadoop cluster to demonstrate the efficiency of the proposed MapReduce framework for large-scale multimedia data mining applications.
Exploring the Profiles and Interplays of Pre-service and In-service Teachers' Technological Pedagogical Content Knowledge (TPACK) in China

This research surveyed three hundred and ninety pre-service and three hundred and ninety four in-service teachers with regards to the seven factors of technological pedagogical content knowledge, their beliefs about constructivist oriented teaching (CB) and design disposition (DD). Both exploratory and confirmatory factor analyses showed that the survey based on the nine-factor model had high reliability and validity. Significant differences between pre-service and in-service teachers in the TPACK factors and CB and DD were found and the differences reveal that the pre-service teachers are less knowledgeable and confident with regards to all the factors. In order to identify predictors of TPACK, the research further explores the relationships among TPACK factors, CB and DD through structural equation models. The findings reveal that DD consistently predict both pre-service and in-service teachers’ TPACK and this provide support about the importance of design disposition for TPACK advancement. However, CB does not predict the pre-service teachers’ TPACK. In addition, CB is a significantly negative predictor for the in-service teachers’ TPACK. The findings may imply that while the inservice teachers believe strongly in constructivist oriented teaching, they need further professional development in designing instruction to actualize their desired form of education. Keyword Technological pedagogical content knowledge (TPACK), Teachers’ beliefs, Design disposition, Teacher education
Self-Hardening Calcium Phosphate Composite Scaffold for Bone Tissue Engineering

Calcium phosphate cement (CPC) sets in situ to form solid hydroxyapatite, can conform to complex cavity shapes without machining, has excellent osteoinductivity, and is able to be resorbed and replaced by new bone. Therefore, CPC is promising for craniofacial and orthopaedic repairs. However, its low strength and lack of macroporosity limit its use. This study investigated CPC reinforcement with absorbable fibers, the effects of fiber volume fraction on mechanical properties and macroporosity, and the biocompatibility of CPC-fiber composite. The liquid phase of CPC in this study was the weak acidic solution of chitosan. Chitosan has favourable biocompatibility, which has high viscosity in solution. The incorporation of chitosan could improve the handling properties of CPC. The liquid phase contained citric acid could strongly improve the hydration rate of CPC, which shortened the setting time and increased the compressive strength of CPC. In addition, the weak acidic environment around the biomaterials could accelerate the degradation of CPC, which was important to bone tissue engineering. The rationale was that large-diameter absorbable fibers would initially strengthen the CPC graft, then dissolve to form long cylindrical macropores for colonization by osteoblasts. Compressive strength was measured vs. fiber volume fraction from 0% (CPC Control without fibers) to 70%. Animal experiment showed that the material had osteoinductivity and biodegradability when the material was implanted into the muscle pouches in the thigh of rabbits. Compressive strength (mean ± SD; n=3) of CPC with 70% fibers was 0.8± 0.1 MPa. Long cylindrical macropores 100~300 μm in diameter were created in CPC after fiber dissolution, and the CPC-fiber scaffold reached a total porosity of 75.1±1.2% with 70% fibers. The new CPC-fiber formulation had good potentiality of ectopic bone induction. The method of using large-diameter absorbable fibers in bone graft for mechanical properties and formation of long cylindrical macropores for bone ingrowth may be applicable to other tissue engineering materials.
GENETIC DIVERSITY IN BREONADIA SALICINA BASED ON INTRA-SPECIES SEQUENCE VARIATION OF CHLOROPLAST DNA SPACER SEQUENCE

Assessment and knowledge of the genetic diversity and variation within and between populations of rare and endangered plants is very important for effective conservation. Intergenic spacer sequences variation of psbA-trnH locus of chloroplast genome was assessed within Breonadia salicina (Rubiaceae), a critically endangered and endemic plant species to South western part of Kingdom of Saudi Arabia. The obtained sequence data from 19 individuals in three populations revealed nine haplotypes. The aligned sequences obtained from the overall Saudi accessions extended to 355 bp, revealing nine haplotypes. A high level of haplotype diversity (Hd = 0.842) and low level of nucleotide diversity (Pi = 0.0058) were detected. Consistently, both hierarchical analysis of molecular variance (AMOVA) and constructed neighbor-joining tree indicated null genetic differentiation among populations. This level of differentiation between populations or between regions in psbA-trnH sequences may be due to effects of the abundance of ancestral haplotype sharing and the presence of private haplotypes fixed for each population. Furthermore, the results revealed almost the same level of genetic diversity in comparison with Yemeni accessions, in which Saudi accessions were sharing three haplotypes from the four haplotypes found in Yemeni accessions.
Squamous Cell Carcinoma Antigen for Monitoring Cervical Cancer

The tumour-associated antigen was determined in the plasma of patients with squamous cell carcinoma (SCC) of the uterine cervix by radioimmunoassay. Setting a limit of 2 ng/ml, levels were abnormal in 13.4% of healthy controls, in 14% of patients with carcinoma in situ and in 62% of patients with invasive cervical SCC. The incidence of elevated SCC antigen levels and the absolute antigen plasma concentration were dependent upon the tumour load, increasing significantly with advanced stage disease. Abnormal SCC antigen values in operable cervical cancer declined to normal within one week after radical hysterectomy with pelvic lymphadenectomy. In cases of radiotherapy antigen values took 4-6 weeks after the start of treatment to return to normal. The success of both treatment modalities was announced by an early rise in the SCC antigen in the initial phase of therapy, followed by normalisation. After successful primary treatment and a complete remission during further follow-up SCC antigen in plasma was only increased in 3.8% of the cases. Retrospective evaluations in ten patients with progressive disease showed the reappearance of abnormal SCC titers and further increase preceeding the clinically detectable relapse or progression, with a median interval of 8 weeks. The present study indicates that SCC antigen determination is not useful for the early diagnosis of cervical cancer, but it is a potential means for monitoring the efficacy of individual anticancer therapy of SCC of the uterine cervix and for detecting recurrent disease.
Material Removal Rate, Electrode Wear Rate, and Surface Roughness Evaluation in Die Sinking EDM with Hollow Tool through Response Surface Methodology

Electrical discharge machining is one of the earliest nontraditional machining, extensively used in industry for processing of parts having unusual profiles with reasonable precision. In the present work, an attempt has been made to model material removal rate, electrode wear rate, and surface roughness through response surface methodology in a die sinking EDM process. The optimization was performed in two steps using one factor at a time for preliminary evaluation and a Box-Behnken design involving three variables with three levels for determination of the critical experimental conditions. Pulse on time, pulse off time, and peak current were changed during the tests, while a copper electrode having tubular cross section was employed to machine through holes on EN 353 steel alloy workpiece. The results of analysis of variance indicated that the proposed mathematical models obtained can adequately describe the performances within the limits of factors being studied. The experimental and predicted values were in a good agreement. Surface topography is revealed with the help of scanning electron microscope micrographs.
Evaluation of the Length and Isometric Pattern of the Anterolateral Ligament With Serial Computer Tomography

Background: Recent anatomical studies have identified the anterolateral ligament (ALL). Injury to this structure may lead to the presence of residual pivot shift in some reconstructions of the anterior cruciate ligament. The behavior of the length of this structure and its tension during range of motion has not been established and is essential when planning reconstruction. Purpose: To establish differences in the ALL length during range of knee motion. Study Design: Descriptive laboratory study. Methods: Ten unpaired cadavers were dissected. The attachments of the ALL were isolated. Its origin and insertion were marked with a 2 mm–diameter metallic sphere. Computed tomography scans were performed on the dissected parts under extension and 30°, 60°, and 90° of flexion; measurements of the distance between the 2 markers were taken at all mentioned degrees of flexion. The distances between the points were compared. Results: The mean ALL length increased with knee flexion. Its mean length at full extension and at 30°, 60°, and 90° of flexion was 37.9 ± 5.3, 39.3 ± 5.4, 40.9 ± 5.4, and 44.1 ± 6.4 mm, respectively. The mean increase in length from 0° to 30° was 3.99% ± 4.7%, from 30° to 60° was 4.20% ± 3.2%, and from 60° to 90° was 7.45% ± 4.8%. From full extension to 90° of flexion, the ligament length increased on average 16.7% ± 12.1%. From 60° to 90° of flexion, there was a significantly higher increase in the mean distance between the points compared with the flexion from 0° to 30° and from 30° to 60°. Conclusion: The ALL shows no isometric behavior during the range of motion of the knee. The ALL increases in length from full extension to 90° of flexion by 16.7%, on average. The increase in length was greater from 60° to 90° than from 0° to 30° and from 30° to 60°. The increase in length at higher degrees of flexion suggests greater tension with increasing flexion. Clinical Relevance: Knowledge of ALL behavior during the range of motion of the knee will allow for fixation (during its reconstruction) to be performed with a higher or lower tension, depending on the chosen degree of flexion.
Shared Axiomatizations and Virtual Datatypes

In the form of a literate Haskell program, we provide a “shared axiomatization” of Peano arithmetics, a bit-stack representation of bijective base-2 arithmetics, hereditarily finite sets (ZF-set theory with the negation of the axiom of infinity and -induction) and a few other equivalent constructs, that turn out to express basic programming language concepts ranging from lists, sets and multisets, to trees, graphs and hypergraphs. The “axiomatization” is described as a progressive refinement of Haskell type classes with examples of instances converging to an efficient implementation in terms of arbitrary length integers and bit operations. The resulting framework, extended with combinators providing isomorphisms between equivalent data representations, virtualizes data types as isomorphisms to a common representation supporting safe transfer of operations in the presence of polymorphic types. The self-contained source code of the paper is available at http://logic.cse. unt.edu/tarau/research/2009/sharedAxioms.hs .
Heavy Metal Isotopic Anomalies in Supernovae Presolar Grains

Savina, W. F. Calaway, C. E. Tripa, J. G. Barzyk, A. M. Davis, F. Gyngard, S. Amari, E. Zinner, R. S. Lewis, R. N. Clayton. Materials Science Division, Argonne National Laboratory, Argonne, IL 60439, Chicago Center for Cosmochemistry, Chicago, IL 60637, Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, Enrico Fermi Institute, University of Chicago, Chicago, IL 60637, Laboratory for Space Sciences, Washington University, St. Louis, MO 63130, Department of Chemistry, University of Chicago, Chicago, IL 60637
Identification of differences in the specificity‐determining residues of antibodies that recognize antigens of different size: implications for the rational design of antibody repertoires

Studies of antibodies of known three‐dimensional structure have revealed that insertion and deletion of amino acids at the hypervariable loops change the canonical structures, thus generating differences in the antigen‐binding site topography. Such differences determine the size of the antigen with which the antibody interacts. Here, 59 unique antibodies determined at a resolution of 3.0 Å or below, including 19 in complex with proteins, 18 with peptides and 22 with haptens, were analyzed to identify and characterize differences in the residues that are directly involved in the interaction with antigen, so‐called specificity‐determining residues (SDRs). It was found that antibodies use a similar number of SDRs to recognize proteins and peptides but contact haptens with five SDRs less. By using a score of SDR usage, differences in the location of the SDRs, depending on the type of antigen recognized, were then identified with precision. An analysis of the surface generated by the SDRs usage indicates that the differences found correlate well with the size of the antigen. Anti‐protein antibodies have the largest SDR surface, with SDRs of high usage located in the edge of the surface. The SDR surface of anti‐hapten antibodies is the smallest, with hot spots of contacts in the interior of the binding surface and buried in the VL:VH interface. The SDR surface of anti‐peptide antibodies has a size in between anti‐protein and anti‐hapten antibodies, with the SDRs of high usage located in the interior of the antigen‐binding site but do not buried as in anti‐hapten antibodies. These findings led to a fine‐tuning of the model correlating differences in the antigen‐binding site topography with its preference to recognize antigens of different size. Therefore, it is discussed how this knowledge should help to design antibody repertoires biased toward the recognition of antigens of predefined size. Copyright © 2004 John Wiley & Sons, Ltd.
Extracting Databases from Dark Data with DeepDive

DeepDive is a system for extracting relational databases from dark data: the mass of text, tables, and images that are widely collected and stored but which cannot be exploited by standard relational tools. If the information in dark data --- scientific papers, Web classified ads, customer service notes, and so on --- were instead in a relational database, it would give analysts access to a massive and highly-valuable new set of "big data" to exploit. DeepDive is distinctive when compared to previous information extraction systems in its ability to obtain very high precision and recall at reasonable engineering cost; in a number of applications, we have used DeepDive to create databases with accuracy that meets that of human annotators. To date we have successfully deployed DeepDive to create data-centric applications for insurance, materials science, genomics, paleontologists, law enforcement, and others. The data unlocked by DeepDive represents a massive opportunity for industry, government, and scientific researchers. DeepDive is enabled by an unusual design that combines large-scale probabilistic inference with a novel developer interaction cycle. This design is enabled by several core innovations around probabilistic training and inference.
A Sub-μ W Fully Tunable CMOS DPS for Uncooled Infrared Fast Imaging

This paper presents a very low-power and fully programmable CMOS digital active pixel sensor for uncooled IR fast imaging. The proposed circuit topology includes selfbiasing, built-in input capacitance compensation, predictive A/D conversion and a truly digital I/O interface, all at pixel level. Furthermore, full FPN cancellation is also supplied by the external digital tuning of both offset and gain for each individual pixel at no speed costs. Two DPS circuit implementations for IR PbSe sensors have been integrated in standard 0. 35μm 2-polySi 4metal CMOS technology. Finally, exhaustive experimental results from their electrical tests are reported to validate the proposed DPS design techniques.
Amygdalohippocampal involvement in tinnitus and auditory memory

Conclusion: The preliminary results suggest that in chronic unilateral tinnitus the contralateral amygdalohippocampal complex does seem to be involved in tinnitus perception of pure tones. Objectives: Functional neuroimaging studies have revealed that the hippocampus and amygdala are involved in tinnitus perception. The amygdala and hippocampus are supplied by the anterior choroidal artery. Selective amobarbital injections in the anterior choroidal artery result in a non-functional amygdalohippocampal area for 10 min. The aim of this study was to assess the influence of this procedure on tinnitus perception. Patients and methods: Amobarbital (80 mg in total) was injected selectively in two sessions in the left and right anterior choroidal artery in six male patients with tinnitus: four with unilateral tinnitus, two with bilateral tinnitus. Of the patients with unilateral tinnitus, three had right-sided tinnitus and one had left-sided tinnitus. The average age was 57.3 years (range 43–69). Average tinnitus duration was 5.3 years (range 1–10). The differences in visual analogue scale (VAS) scores before and after the amytal tests were analysed. Results: Amytal injection ipsilateral to the side where the tinnitus was perceived resulted in a maximum of 30% tinnitus suppression, whereas amytal injection contralateral to the tinnitus side yielded a 60–70% tinnitus suppression in three patients with unilateral chronic tinnitus (>4 years). Only pure tone tinnitus was suppressed, white noise was not. Two patients with bilateral tinnitus had no suppression, irrespective of the tinnitus type. A third patient without clinical tinnitus suppression had tinnitus of more recent origin (1.5 years).
Right ventriculo-arterial coupling in pulmonary hypertension: a magnetic resonance study

Objective To quantify right ventriculo-arterial coupling in pulmonary hypertension by combining standard right heart catheterisation (RHC) and cardiac magnetic resonance (CMR) and to estimate it non-invasively with CMR alone. Design Cross-sectional analysis in a retrospective cohort of consecutive patients. Setting Tertiary care centre. Patients 139 adults referred for pulmonary hypertension evaluation. Interventions CMR and RHC within 2 days (n=151 test pairs). Main outcome measures Right ventriculo-arterial coupling was quantified as the ratio of pulmonary artery (PA) effective elastance (Ea, index of arterial load) to right ventricular maximal end-systolic elastance (Emax, index of contractility). Right ventricular end-systolic volume (ESV) and stroke volume (SV) were obtained from CMR and adjusted to body surface area. RHC provided mean PA pressure (mPAP) as a surrogate of right ventricular end-systolic pressure, pulmonary capillary wedge pressure (PCWP) and pulmonary vascular resistance index (PVRI). Ea was calculated as (mPAP − PCWP)/SV and Emax as mPAP/ESV. Results Ea increased linearly with advancing severity as defined by PVRI quartiles (0.19, 0.50, 0.93 and 1.63 mm Hg/ml/m2, respectively; p<0.001 for trend) whereas Emax increased initially and subsequently tended to decrease (0.52, 0.67, 0.54 and 0.56 mm Hg/ml/m2; p=0.7). Ea/Emax was maintained early but increased markedly with severe hypertension (0.35, 0.72, 1.76 and 2.85; p<0.001), indicating uncoupling. Ea/Emax approximated non-invasively with CMR as ESV/SV was 0.75, 1.17, 2.28 and 3.51, respectively (p<0.001). Conclusions Right ventriculo-arterial coupling in pulmonary hypertension can be studied with standard RHC and CMR. Arterial load increases with disease severity whereas contractility cannot progress in parallel, leading to severe uncoupling.
AUTOMATIC TERM EXTRACTION AND DOCUMENT SIMILARITY IN SPECIAL TEXT CORPORA

This paper confirms that the performance of a state-of-the-art automatic term extraction method on a computer science corpus is similar to previously published performance data on a medical corpus. The extracted terms are then used to estimate the similarity of papers in the computer science corpus using the standard Vector Space Model. The precision of retrieval using a term-based representation is compared with that of a word-based representation, and a link-based similarity metric based on the overlap of the local neighborhoods of the papers in the citation graph. The term-based approach offers comparable performance to the word-based approach, but potentially with a much smaller vocabulary size.