Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the usability of the central library websites of medical sciences universities

This research aims to determine the usability of the central library websites of medical sciences universities in Iran. This was a descriptive, cross-sectional study which employed a heuristic evaluation method to evaluate the usability of the websites. Three trained evaluators independently examined the 12 library websites from 11 July to 10 September 2013 using Nielsen’s usability heuristics. A list of usability problems was obtained and the severity of identified problems was determined. We identified 668 usability problems. The highest number of problems concerned ‘aesthetic and minimalist design’ (27.1%) and the lowest number concerned the ‘help and documentation’ heuristic (1%). Since the importance of libraries’ websites cannot be understated, the websites should consider the identified problems and attempt to address them.
Improving load balancing for MapReduce-based entity matching

The effectiveness and scalability of MapReduce-based implementations for data-intensive tasks depends on the data assignment made from map to reduce tasks. The robustness of this assignment strategy is crucial to achieve skewed data handling and balanced workload distribution among all reduce tasks. For the entity matching problem in the Big Data context, we propose BlockSlicer, a MapReduce-based approach that supports blocking techniques to reduce the entity matching search space. The approach utilizes a preprocessing MapReduce job to analyze the data distribution and provides an improved load balancing by applying an efficient block slice strategy as well as a well-known optimization algorithm to assign the generated match tasks. We evaluate the approach against an existing one that addresses the same problem on a real cloud infrastructure. The results show that our approach increases significantly the performance of distributed entity matching task by reducing the amount of data generated from the map phase and diminishing the overall execution time.
Next-generation sequencing and the expanding domain of phylogeography

Abstract. Phylogeography is experiencing a revolution brought on by next-generation sequencing methods. A historical survey of the phylogeographic literature suggests that phylogeography typically incorporates new questions, expanding on its classical domain, when new technologies offer novel or increased numbers of molecular markers. A variety of methods for subsampling genomic variation, including restriction site associated DNA sequencing (Rad-seq) and other next generation approaches, are proving exceptionally useful in helping to define major phylogeographic lineages within species as well as details of historical demography. Next-generation methods are also blurring the edges of phylogeography and related fields such as association mapping of loci under selection, and the emerging paradigm is one of simultaneously inferring both population history across geography and genomic targets of selection. However, recent examples, including some from our lab on Anolis lizards and songbirds, suggest that genome subsampling methods, while extremely powerful for the classical goals of phylogeography, may fail to allow phylogeography to fully achieve the goals of this new, expanded domain. Specifically, if genome-wide linkage disequilibrium is low, as is the case in many species with large population sizes, most genome subsampling methods will not sample densely enough to detect selected variants, or variants closely linked to them. We suggest that whole-genome resequencing methods will be essential for allowing phylogeographers to robustly identify loci involved in phenotypic divergence and speciation, while at the same time allowing free choice of molecular markers and further resolution of the demographic history of species.
Making and using antibodies : a practical handbook

Antibodies Matthew R. Kaser and Gary C. Howard Antigens and Adjuvants Paul Algate, Jory Baldridge, and Sally P. Mossman Production of Polyclonal Antibodies Lon V. Kendall Purification and Characterization of Antibodies Joseph P. Chandler Production of Monoclonal Antibodies Kathleen C. F. Sheehan Quantitative Production of Monoclonal Antibodies David A. Fox and Elizabeth M. Smith Making Antibodies in Bacteria Frederic A. Fellouse and Sachdev S. Sidhu In Vitro Selection of Aptamers Tianjiao Wang, Xiangyu Cong, and Marit Nilsen-Hamilton Chemical and Proteolytic Modification of Antibodies George P. Smith Western Blots and Other Applications Lee Bendickson and Marit Nilsen-Hamilton Immunohistochemical Methods Jose A. Ramos-Vara Immunoelectron Microscopy Sara E. Miller and David N. Howell Flow Cytometry Steven B. McClellan ELISAs John Chen and Gary C. Howard Humanization of Antibodies Juan Carlos Almagro, Sreekumar Kodangattil, and Jian Li Antibodies in the Future: Challenges and Opportunities Gary C. Howard and Matthew R. Kaser Index
Bradykinin and changes in microvascular permeability in the hamster cheek pouch: role of nitric oxide

1 The objective of this study in the hamster cheek pouch was to investigate the role of nitric oxide in bradykinin‐induced microvascular leakage. The cheek pouch microcirculatory bed of the anaesthetized hamster was directly observed under microscope and vascular leakage was evidenced by dextran‐fluorescein isothiocyanate (FITC‐dextran) extravasation. 2 Bradykinin superfusion (but not [des‐Arg9]‐bradykinin up to 3 × 10−6 m) induced an increase in microvascular permeability (log EC50: −6.5 ± 0.4) which was exclusively located on the post‐capillary venule. Plasma extravasation was blocked by intravenous pretreatment with Hoe 140, a bradykinin B2 receptor antagonist (estimated log ID50: −9.5 ± 0.2). 3 The effects of bradykinin (3 × 10−7 m) superfusion were partially but significantly inhibited by indomethacin (10−5 m, P < 0.05) and abolished by pretreatment with L‐nitro‐arginine (L‐NOARG; 10−5 m). 4 Acetylcholine (10−6 m, which releases endothelial nitric oxide (NO)) and sodium nitroprusside (10−6 m, a nitrovasodilator) superfusion did not induce any changes in permeability, per se. Cromakalim (10−5 m, a potassium channel opener) superfusion induced a moderate but significant plasma extravasation. 5 The effects of bradykinin, blocked by L‐NOARG pretreatment, were restored by the co‐perfusion of either sodium nitroprusside or cromakalim. Conversely vasoconstriction, produced by a stable analogue of thromboxane A2 (U46619, 3 × 10−7 m), inhibited the increase in permeability produced by bradykinin. 6 The measurement of arteriolar diameter showed that bradykinin induced a vasodilatation which was blocked by L‐NOARG. L‐NOARG in itself was a powerful vasoconstrictor. Sodium nitroprusside and cromakalim, in the presence of L‐NOARG, were able to restore the inhibited vasodilator response to bradykinin. 7 These results suggest: (1) bradykinin‐induced microvascular leakage is mediated by bradykinin B2 receptor activation; (2) the increase in permeability is due to two different independent phenomena, i.e. post‐capillary venular endothelial gap formation and arteriolar vasodilatation which increases the post‐capillary venular transmural pressure; (3) NO is only involved in the arteriolar dilatation component of the bradykinin‐induced increase in microvascular permeability.
Gaussian Lower Bound for the Information Bottleneck Limit

The Information Bottleneck (IB) is a conceptual method for extracting the most compact, yet informative, representation of a set of variables, with respect to the target. It generalizes the notion of minimal sufficient statistics from classical parametric statistics to a broader information-theoretic sense. The IB curve defines the optimal trade-off between representation complexity and its predictive power. Specifically, it is achieved by minimizing the level of mutual information (MI) between the representation and the original variables, subject to a minimal level of MI between the representation and the target. This problem is shown to be in general NP hard. One important exception is the multivariate Gaussian case, for which the Gaussian IB (GIB) is known to obtain an analytical closed form solution, similar to Canonical Correlation Analysis (CCA). In this work we introduce a Gaussian lower bound to the IB curve; we find an embedding of the data which maximizes its "Gaussian part", on which we apply the GIB. This embedding provides an efficient (and practical) representation of any arbitrary data-set (in the IB sense), which in addition holds the favorable properties of a Gaussian distribution. Importantly, we show that the optimal Gaussian embedding is bounded from above by non-linear CCA. This allows a fundamental limit for our ability to Gaussianize arbitrary data-sets and solve complex problems by linear methods.
Expression of the p16 and Ki-67 in relation to the grade of cervical intraepithelial neoplasia and high-risk human papillomavirus infection.

OBJECTIVE The purposes of this study were to evaluate the expression of p16(INK4a) (referred as to p16) and Ki-67 in cervical intraepithelial neoplasia (CIN), and the correlation between high-risk human papillomavirus (HPV) infection and the above biomarkers. METHODS We analyzed 31 patients who were diagnosed with CIN at Kwandong University Myongji Hospital from October 2006 to September 2007. CIN specimens (CIN1, 12; CIN2, 6; CIN3, 13) were obtained by colposcopy-directed biopsy (CDB) or loop electrical excision procedure (LEEP). The expressions of p16 and Ki-67 were evaluated by immunohistochemical methods with antibodies to p16 and Ki67. The immunohistochemical staining results were classified into four grades: 0, 1, 2 and 3. HPV genotyping or Hybrid Capture-II test was used to detect high-risk HPV. RESULTS The expression of p16 (p<0.001) and Ki-67 (p=0.003) were positively associated with CIN grade. p16 expressions increased significantly with high-risk HPV infection (p=0.014), especially HPV type 16 and 58. Ki-67 expression was not related with high-risk HPV. There was positive correlation between the expression of the p16 and Ki-67 (p=0.007). CONCLUSION CIN grade were positively related to the expression of p16 and Ki-67. p16 expressions of high-risk HPV specimens significantly increased more than Ki-67. Therefore, in the diagnosis of CIN and high-risk HPV infection, p16 can be a useful biomarker.
Influence of Rate and Volume of Infusion on the Kinetics of 0.9% Saline and 7.5% Saline/6.0% Dextran 70 in Sheep

We examined whether volume kinetic variables obtained during infusion of a short bolus of 0.9% saline (NS) or 7.5% saline/6.0% dextran 70 (HSD) predict the dilution-time curve resulting from a 20-min infusion of the same fluid. Each of six conscious, splenectomized sheep (mean body weight, 36 ± 3 kg), on 4 different days, in a random order, received each of 4 IV boluses: NS at a rate of 1.2 mL · kg−1 · min−1 over 5 min or 20 min or 4.0 mL/kg of HSD over 2 min or 20 min. One, 2, and 3-volume kinetic models were fitted to the dilution of the arterial hemoglobin concentration and the urinary excretion as sampled during 180 min. The maximum dilution of arterial plasma at the end of the 5-min and 20-min infusions of NS was approximately 10% and 22%, respectively, and after the 2-min and 20-min infusions of HSD, maximum dilution was 24% and 21%, respectively. The median absolute performance error was virtually identical when the mean variable estimates from the 5-min infusion of NS were used to predict the individual dilution-time curves of the 5-min (mean, 0.027 dilution units) and 20-min (mean, 0.027) infusions and when the 2-min infusion of HSD was used to predict the dilution during the individual 2-min (mean, 0.050) and 20-min infusions (mean, 0.047). Computer simulations indicated that the difference at the end of infusion between the volume effects of NS and HSD is larger after longer infusions. We concluded that the volume kinetic variables obtained during a short infusion can be used to predict the outcome of a longer one, even if the longer infusion also delivers a larger volume.
Characterizing the Number of Optimal Index Codes and Their Relation to Min–Max Probability of Error Performance

An index coding problem arises when there is a single source with a number of messages and multiple receivers each wanting a subset of messages knowing a different set of messages a priori. The noiseless index coding problem is to identify the minimum number of transmissions (optimal length) to be made by the source through a noiseless channel so that all receivers can decode their wanted messages using the transmitted symbols and their respective prior information. Recently (A. Thomas, R. Kavitha, A. Chandramouli, and B. Sundar Rajan, “Optimal index coding with min-max probability of error over fading channels,” in Proc. IEEE 26th Annu. Int. Symp. Pers. Indoor Mobile Radio Commun., Hong Kong, 2015, pp. 889–894), it is shown that different optimal length codes perform differently in a noisy channel for single-uniprior index coding problems. Towards identifying the best optimal length index code, one needs to know the number of optimal length index codes. In this paper, we consider unicast index coding problems and present results on the number of optimal length index codes making use of the representation of an index coding problem by an equivalent network code. Our formulation results in matrices of smaller sizes compared to the approach of Koetter and Medard (R. Koetter and M. Medard, “An algebraic approach to network coding,” IEEE/ACM Trans. Netw., vol. 11, no. 5, pp. 782–795, Oct. 2003.). Our formulation leads to a lower bound on the minimum number of optimal length codes possible for all unicast index coding problems (L. Ong and C. K. Ho, “Optimal index codes for a class of multicast networks with receiver side information,” in Proc. IEEE Int. Conf. Commun., 2012, pp. 2213–2218), which is met with equality for several special cases of the unicast index coding problem. Furthermore, for noisy broadcast channels, a method to identify the best among the optimal length codes for unicast index coding problems in terms of minimum–maximum error probability is presented.
Renal Iodine Dye Risk, Age, and the Acute Coronary Syndrome

In this issue of Angiology, Toso et al assessed the occurrence of acute kidney injury (AKI) in 128 of 615 patients, as defined by network criteria for AKI in the Italian Elderly Acute Coronary Syndrome (ACS) study, involving patients 75 years. They surprisingly reported that their elderly patients who underwent coronary angiography with iodine dye did not have increased rates of AKI. Consideration of this observation is warranted.
The Concentration of the 35-kDa Surfactant Apoprotein in Amniotic Fluid from Normal and Diabetic Pregnancies

ABSTRACT: A specific, enzyme-linked immunoabsorbent assay was used to determine the concentration of the 35,000 mol wt surfactant apoprotein (SP-A) in samples of amniotic fluid obtained from nondiabetic (n = 358) and diabetic (n = 29) women. The enzyme-linked immunoabsorbent assay was performed with rabbit antibodies directed against SP-A present in lavage fluid from a patient with alveolar proteinosis. Amniotic fluid SP-A concentrations increased as a function of gestational age, from <3 μg/ml at 30–31 wk to 24 μg/ml at 40–41 wk, and were positively correlated with the lecithin to sphingomyelin ratio (p < 0.01). SP-A concentrations also increased as a function of gestational age in shake test positive samples (p < 0.05), but were unchanged in shake test-negative samples. There was no difference in the surfactant apoprotein concentration of male compared with female fetuses at any gestational age. In amniotic fluid obtained from 20 diabetic women, SP-A levels were significantly less than in nondiabetic pregnancies that were matched for gestational age and sex of the fetus (p < 0.05). The SP-A concentrations in amniotic fluids obtained from nine women who were diabetic and hypertensive and from 10 hypertensive women were not different from matched controls. The relationships described above were valid whether the SP-A concentration was expressed per mg protein or per ml amniotic fluid. These data are suggestive that the concentration of amniotic fluid SP-A is decreased in diabetic pregnancies.
Risk of heart failure among postmenopausal women: a secondary analysis of the randomized trial of vitamin D plus calcium of the women's health initiative.

BACKGROUND Vitamin D supplementation may be an inexpensive intervention to reduce heart failure (HF) incidence. However, there are insufficient data to support this hypothesis. This study evaluates whether vitamin D plus calcium (CaD) supplementation is associated with lower rates of HF in postmenopausal women and whether the effects differ between those at high versus low risk for HF. METHODS AND RESULTS Analyses were restricted to 35 983 (of original 36 282) women aged 50 to 79 years old in the Women's Health Initiative randomized trial of CaD supplementation who were randomized 1:1 in a double-blinded fashion to receive 1000 mg/d of calcium plus 400 IU/d of vitamin D3 or placebo. Overall, 744 adjudicated incident HF cases (intervention, 363; control, 381) occurred during a median follow-up of 7.1 (interquartile range, 1.6) years. CaD supplementation, compared with placebo, was not associated with reduced HF risk in the overall population, hazard ratio, 0.95; P=0.46. However, CaD supplementation had differential effects (P interaction=0.005) in subgroups stratified by baseline risk status of HF defined by the presence (high risk=17 449) or absence (low risk=18 534) of pre-existing HF precursors including coronary heart diseases, diabetes mellitus, or hypertension: 37% (hazard ratio, 0.63 [95% confidence interval, 0.46-0.87]) lower risk of HF in the low-risk versus hazard ratio, 1.06; P=0.51, in the high-risk subgroups. CONCLUSIONS CaD supplementation did not significantly reduce HF incidence in the overall cohort, however, it was beneficial among postmenopausal women without major HF precursors while of little value in high-risk subgroups. Additional studies are warranted to confirm these findings and investigate the underlying mechanism. CLINICAL TRIAL REGISTRATION URL http://www.clinicaltrials. gov. Unique identifier: NCT00000611.
Analyzing Speech to Detect Financial Misreporting

We examine whether vocal markers of cognitive dissonance are useful for detecting financial misreporting. We use speech samples of CEOs during earnings conference calls, and generate vocal dissonance markers using automated vocal emotion analysis software. We begin by assessing construct validity for the software‐generated dissonance markers by correlating them with four dissonance‐from‐misreporting proxies obtained in a laboratory setting. We find a positive association between these proxies and vocal dissonance markers generated by the software, suggesting the software's dissonance markers have construct validity. Applying the software to CEO speech, we find that vocal dissonance markers are positively associated with the likelihood of irregularity restatements. The diagnostic accuracy levels are 11% better than chance and of similar magnitude to models based solely on financial accounting information. Moreover, the association between vocal dissonance markers and irregularity restatements holds even after controlling for financial accounting and linguistic‐based predictors. Our results provide new evidence on the role of vocal cues in detecting financial misreporting.
Learning boolean functions

Although various formal models of learning have been studied in the past, a realistic model taking into consideration the time required for learning has not been proposed. Recently, Valiant [8] proposed a general learning model based on the theory of computational complexity, gave a definition of learnability, and obtained various classes of learnable concepts. Based on this model, this paper investigates various objects of learning.
Agreement of immunosuppression regimens described in Medicare pharmacy claims with the Organ Procurement and Transplantation Network survey.

The Organ Procurement and Transplantation Network (OPTN) collects intermittent survey data on immunosuppressive medication use that are studied frequently as research measures. Pharmacy billing claims may provide an accurate measure of immunosuppression use over time. Herein is characterized the agreement of Medicare pharmacy claims for immunosuppressive medications with OPTN reports. Data were drawn from the United States Renal Data System. Participants received a kidney transplant in 2000 to 2001 and had an OPTN record and a Medicare pharmacy claim for an immunosuppressive drug at transplant discharge and 6 mo and 1 yr after transplantation. The concordance (kappa) of the OPTN and claims (+/-30 d of survey) for indicated medication use was compared, and sensitivity, specificity, and predictive values for claims were computed, assuming OPTN as a "gold standard. " Clinical trial participation and regimen changes were examined as explanations for discordance. A total of 4357 eligible subjects were identified. Concordance over observation ranged from excellent for calcineurin inhibitors (kappa > 0.86) to generally very good for adjunctive agents (kappa = 0.49 to 0.75) to poor for corticosteroids (kappa <0.15). Claims demonstrated high positive predictive values (> or =97%) but low negative predictive values (< or =13%) for OPTN-reported corticosteroid use. Regimen changes (28 to 75%) but not clinical trial participation (< or =21%) were identified frequently among cases with discordant indications of nonsteroid medication use. Close agreement of Medicare billing claims and the OPTN for indicated use of nonsteroid immunosuppressive medications supports both as useful measures of drug exposure. Low detection rates of OPTN-indicated corticosteroid use within claims require further examination.
Diethyl [(4-nitrobenzamido)(phenyl)methyl]phosphonate

In the title compound, C18H21N2O6P, the dihedral angle between the benzene and phenyl rings is 85.1 (2)°. In the crystal, molecules are linked via pairs of N—H⋯O(=P) hydrogen bonds, forming inversion dimers with graph-set notation R 2 2(10). One of the ethyl groups is disordered over two sets of sites, with occupancies 0.746 (11) and 0.254 (11).
The responses of Golgi tendon organs to stimulation of different combinations of motor units.

1. Afferent discharges were recorded from stretch receptors identified as Golgi tendon organs, in the medial gastrocnemius and soleus muscles of the cat. 2. The response of a tendon organ was recorded during stimulation of one or more motor units selected for the intensity of discharge elicited from the receptor during twitch and tetanic contractions. 3. Repetitive stimulation of a single motor unit could evoke in a tendon organ a firing rate of up to 174 impulses/sec. The mean rate for a total of 90 motor units was 65 (+/‐ 32 S.D.) impulses/sec. No significant difference in effectiveness could be detected between motor units covering a wide range of contraction speeds, tetanic tensions and susceptibility to fatigue. 4. The response of a tendon organ to contraction of several motor units in combination was greater than from stimulating any one motor unit alone but less than predicted from the algebraic sum of individual responses. 5. The relation between firing rate and tension was plotted for combined stimulation of up to ten motor units. The relation was found to be a straight line provided the size of the response elicited by each motor unit in the stimulated bundle was similar or when responses were ranked according to their intensity. When one motor unit evoked a much more powerful response than others it tended to dominate the discharge and disturb the linearity. 6. Evidence is provided that the sites of stimulus transduction for motor units which exert their effect directly on the receptor can be relatively independent of one another. It is argued that on such occasions summation of responses may be attributed to mechanisms operating at the level of impulse generation.