Miracle-dz/UniFAR-FTUs huggingface dataset:
Strategy for identification & characterization of Bartonella henselae with conventional & molecular methods

Background & objectives: Bartonella henselae is a fastidious gram-negative bacterium usually causing self limiting infections in immunocompetent individuals but often causes potentially life threatening infection, such as bacillary angiomatosis in immunocompromised patients. Both diagnosis of infections and research into molecular mechanisms of pathogenesis have been hindered by lack of appropriate and reliable diagnostic techniques. We undertook this study to standardize methods to characterize B. henselae in clinical samples to diagnose Bartonella infection correctly. Methods: B. henselae ATCC 49882 strain was procured from American type culture collection, USA. This strain was revived and maintained in the laboratory, and identification and characterization of this strain was done by conventional and molecular techniques, which included culture on various media, staining by different methods including electron microscopy, biochemical analysis by conventional methods and API, polymerase chain reaction (PCR) for amplification of citrate synthase gene followed by restriction fragment length polymorphism (RFLP). Results: This organism was biochemically inert due to slow growth and generated unique identification code with API. The amplification of the citrate-synthase gene with primers yielded a 381 bp product followed by specific RFLP profile for B. henselae. Interpretation & conclusions: Bartonella is fastidious and fragile organism and should be handled carefully. Extra effort and careful observation are required to isolate and characterize this organism.
Knowledge Integration as a Source of Competitive Advantage in Large Croatian Enterprises

The paper discusses the integration of codified and tacit knowledge as a potential source of competitive advantage. The management of explicit knowledge is viewed through knowledge management practices, whereas the management of tacit knowledge is conceptualised through strategic human resource management. The paper presents the empirical results of testing of low- and high-synergy models of knowledge integration on a representative sample of large Croatian enterprises.
massachusetts institute of technology — artificial intelligence laboratory Improving Multi-class Text Classification with Naive Bayes

There are numerous text documents available in electronic form. More and more are becoming available every day. Such documents represent a massive amount of information that is easily accessible. Seeking value in this huge collection requires organization; much of the work of organizing documents can be automated through text classification. The accuracy and our understanding of such systems greatly influences their usefulness. In this paper, we seek 1) to advance the understanding of commonly used text classification techniques, and 2) through that understanding, improve the tools that are available for text classification. We begin by clarifying the assumptions made in the derivation of Naive Bayes, noting basic properties and proposing ways for its extension and improvement. Next, we investigate the quality of Naive Bayes parameter estimates and their impact on classification. Our analysis leads to a theorem which gives an explanation for the improvements that can be found in multiclass classification with Naive Bayes using Error-Correcting Output Codes. We use experimental evidence on two commonly-used data sets to exhibit an application of the theorem. Finally, we show fundamental flaws in a commonly-used feature selection algorithm and develop a statistics-based framework for text feature selection. Greater understanding of Naive Bayes and the properties of text allows us to make better use of it in text classification. Thesis Supervisor: Tommi Jaakkola Title: Assistant Professor of Electrical Engineering and Computer Science
DNA Polymerase δ Is Highly Processive with Proliferating Cell Nuclear Antigen and Undergoes Collision Release upon Completing DNA*

In most cells, 100-1000 Okazaki fragments are produced for each replicative DNA polymerase present in the cell. For fast-growing cells, this necessitates rapid recycling of DNA polymerase on the lagging strand. Bacteria produce long Okazaki fragments (1-2 kb) and utilize a highly processive DNA polymerase III (pol III), which is held to DNA by a circular sliding clamp. In contrast, Okazaki fragments in eukaryotes are quite short, 100-250 bp, and thus the eukaryotic lagging strand polymerase does not require a high degree of processivity. The lagging strand polymerase in eukaryotes, polymerase δ (pol δ), functions with the proliferating cell nuclear antigen (PCNA) sliding clamp. In this report, Saccharomyces cerevisiae pol δ is examined on model substrates to gain insight into the mechanism of lagging strand replication in eukaryotes. Surprisingly, we find pol δ is highly processive with PCNA, over at least 5 kb, on Replication Protein A (RPA)-coated primed single strand DNA. The high processivity of pol δ observed in this report contrasts with its role in synthesis of short lagging strand fragments, which require it to rapidly dissociate from DNA at the end of each Okazaki fragment. We find that this dilemma is solved by a “collision release” process in which pol δ ejects from PCNA upon extending a DNA template to completion and running into the downstream duplex. The released pol δ transfers to a new primed site, provided the new site contains a PCNA clamp. Additional results indicate that the collision release mechanism is intrinsic to the pol3/pol31 subunits of the pol δ heterotrimer.
A Two-Stage Penalized Least Squares Method for Constructing Large Systems of Structural Equations

We propose a two-stage penalized least squares method to build large systems of structural equations based on the instrumental variables view of the classical two-stage least squares method. We show that, with large numbers of endogenous and exogenous variables, the system can be constructed via consistent estimation of a set of conditional expectations at the first stage, and consistent selection of regulatory effects at the second stage. While the consistent estimation at the first stage can be obtained via the ridge regression, the adaptive lasso is employed at the second stage to achieve the consistent selection. The resultant estimates of regulatory effects enjoy the oracle properties. This method is computationally fast and allows for parallel implementation. We demonstrate its effectiveness via simulation studies and real data analysis.
Astrocytic localization of kynurenine aminotransferase II in the rat brain visualized by immunocytochemistry

Kynurenic acid (KYNA), a metabolite of the kynurenine pathway of tryptophan degradation, is a neuroinhibitory agent present in the mammalian brain. Endogenous KYNA preferentially affects the α7 nicotinic acetylcholine (α7nACh) receptor and, possibly, the glycine co‐agonist (glycineB) site of the NMDA receptor. Functionally relevant fluctuations in brain KYNA occur under both physiological and pathological conditions, affecting cholinergic and glutamatergic neurotransmission. Kynurenine aminotransferase II (KAT II), the major biosynthetic enzyme of KYNA in the rat brain, catalyzes the irreversible formation of KYNA from its immediate bioprecursor, kynurenine. We now purified rat kidney KAT II to homogeneity, generated a polyclonal rabbit anti‐rat KAT II antibody, and purified the antibody using routine biochemical methods. The antibody selectively recognized KAT II by Western blot analysis and in immunotitration experiments. Used for immunocytochemistry, the antibody revealed discrete, specific staining of KAT II‐positive astrocyte‐like cells throughout the adult rat brain. The presence of KAT II in astrocytes was confirmed by double fluorescence immunostaining with an antibody against the astrocyte‐specific marker glial fibrillary acidic protein (GFAP). No specific labeling was detected in neurons or microglia. However, KAT II‐positive astrocytes were intimately associated with select neuron populations, supporting a neuromodulatory role of KYNA. Intense staining was frequently seen around brain capillaries, with astrocytic end feet contacting the capillary wall. This may explain the rapid access of blood‐derived kynurenine to KAT II‐containing astrocytes. The new anti‐KAT II antibody should be useful in the further elucidation of the presumed role of KYNA in brain physiology and pathology. © 2006 Wiley‐Liss, Inc.
Robust Fusion of Uncertain Information

A technique is presented to combine n data points, each available with point-dependent uncertainty, when only a subset of these points come from N \ll n sources, where N is unknown. We detect the significant modes of the underlying multivariate probability distribution using a generalization of the nonparametric mean shift procedure. The number of detected modes automatically defiens N, while the appurtenance of a point to the basin of attraction of a mode provides the fusion rule.
A new instrument to measure sexual function in women with urinary incontinence or pelvic organ prolapse.

OBJECTIVE Our aim was to develop a condition-specific, reliable, validated, and self-administered instrument to evaluate sexual function in women with pelvic organ prolapse or urinary incontinence. STUDY DESIGN The questionnaire was designed after review of the literature and of nonspecific validated instruments. The study was completed in 2 phases. In phase 1 a total of 83 women completed both our questionnaire and the Incontinence Impact Questionnaire-7, with 20 women undergoing test-retest reliability analyses. Item analysis was based on the internal consistency, the correlations with the Incontinence Impact Questionnaire-7, the patient's age and self-rating of satisfaction, and the results of reliability testing. For final validation the questionnaire was administered in phase 2 to 99 women. Factor and item analyses were repeated, results were correlated with the Sexual History Form-12, and comparison was made between patients with high depression scores and those with low depression scores on the Symptom Questionnaire. RESULTS Factor analysis identified 3 domains, labeled Behavioral/Emotive, Physical, and Partner-Related. Sexual function scores were highly correlated with scores on the Sexual History Form-12 for the questionnaire (r = -0.74; P <.001) and for both the Behavioral/Emotive and the Partner-Related domains (r = -0.79 and -0.5, respectively; P <.001). The Physical domain was correlated with scores on the Incontinence Impact Questionnaire-7 (r = -0.63; P <.001). Women with high depression scores on the Symptom Questionnaire had significantly lower scores on the final questionnaire, in comparison with women without depression (P <.001). CONCLUSION We developed a condition-specific, validated, and reliable instrument, containing 31 items divided into 3 domains, to evaluate sexual functioning in women with urinary incontinence or pelvic organ prolapse.
Inflammation enhances cardiovascular risk and mortality in hemodialysis patients.

BACKGROUND Atherosclerosis, a major problem in patients on chronic hemodialysis, has been characterized as an inflammatory disease. C-reactive protein (CRP), the prototypical acute phase protein in humans, is a predictor of cardiovascular mortality in the general population. We hypothesize that several of the classic, as well as nontraditional, cardiovascular risk factors may respond to acute phase reactions. An activated acute phase response may influence or predict cardiovascular risk. METHODS In 280 stable hemodialysis patients, serum lipids, apolipoproteins (apo) A-I and B, lipoprotein(a) [Lp(a)], fibrinogen, and serum albumin (Salb) were determined in relation to CRP and serum amyloid A (SAA), two sensitive markers of an acute phase response. Mortality was monitored prospectively over a two year period. RESULTS Serum CRP and SAA were found to be elevated (more than 8 and more than 10 mg/liter, respectively) in 46% and 47% of the patients in the absence of clinically apparent infection. Patients with elevated CRP or SAA had significantly higher serum levels of Lp(a), higher plasma fibrinogen, and lower serum levels of high-density lipoprotein cholesterol, apo A-I, and Salb than patients with normal CRP or SAA. The rise in Lp(a) concentration was restricted to patients exhibiting high molecular weight apo(a) isoforms. During follow-up, 72 patients (25.7%) had died, mostly due to cardiovascular events (58%). Overall mortality and cardiovascular mortality were significantly higher in patients with elevated CRP (31% vs. 16%, P < 0.0001, and 23% vs. 5%, P < 0.0001, respectively) or SAA (29% vs. 19%, P = 0.004, and 20 vs. 10%, P = 0.008, respectively) and were also higher in patients with Salb of lower than 40 g/liter (44% vs. 14%, P < 0.0001, and 34% vs. 6%, P < 0.0001, respectively). Univariate Cox regression analysis demonstrated that age, diabetes, pre-existing cardiovascular disease, body mass index, CRP, SAA, Salb, fibrinogen, apo A-I, and Lp(a) were significantly associated with the risk of all-cause and cardiovascular mortality. During multivariate regression analysis, SAA, fibrinogen, apo A-I, and Lp(a) lost their predictive values, but age and CRP remained powerful independent predictors of both overall death and cardiovascular death. CONCLUSION These results suggest that a considerable number of hemodialysis patients exhibit an activated acute phase response, which is closely related to high levels of atherogenic vascular risk factors and cardiovascular death. The mechanisms of activated acute phase reaction in patients on chronic hemodialysis remain to be identified. A successful treatment of the inflammatory condition may improve long-term survival in these patients.
Integer and polynomial multiplication: towards optimal toom-cook matrices

Karatsuba and Toom-Cook are well-known methods used to multiply efficiently long integers. There have been different proposal about the interpolating values used to determine the matrix to be inverted and the sequence of operations to invert it. A deffinitive word about which is the optimal matrix (values) and the (number of) basic operations to invert it seems still not to have been said. In this paper we present some particular examples of useful matrices and a method to generate automatically, by means of optimised exhaustive searches on a graph, the best sequence of basic operations to invert them.
Changes in genetic diversity and differentiation in Red‐cockaded woodpeckers (Dryobates borealis) over the past century

Abstract Red‐cockaded woodpeckers (RCW; Dryobates borealis) declined after human activities reduced their fire‐maintained pine ecosystem to <3% of its historical range in the southeastern United States and degraded remaining habitat. An estimated 1.6 million RCW cooperative breeding groups declined to about 3,500 groups with no more than 10,000 birds by 1978. Management has increased RCW population abundances since they were at their lowest in the 1990s. However, no range‐wide study has been undertaken since then to investigate the impacts of this massive bottleneck or infer the effects of conservation management and recent demographic recoveries. We used mitochondrial DNA sequences (mtDNA) and nine nuclear microsatellite loci to determine if range‐wide demographic declines resulted in changes to genetic structure and diversity in RCW by comparing samples collected before 1970 (mtDNA data only), between 1992 and 1995 (mtDNA and microsatellites), and between 2010 and 2014 (mtDNA and microsatellites). We show that genetic diversity has been lost as detected by a reduction in the number of mitochondrial haplotypes. This reduction was apparent in comparisons of pre‐1970 mtDNA data with data from the 1992–1995 and 2010–2014 time points, with no change between the latter two time points in mtDNA and microsatellite analyses. The mtDNA data also revealed increases in range‐wide genetic differentiation, with a genetically panmictic population present throughout the southeastern United States in the pre‐1970s data and subsequent development of genetic structure that has remained unchanged since the 1990s. Genetic structure was also uncovered with the microsatellite data, which like the mtDNA data showed little change between the 1992–1995 and 2010–2014 data sets. Temporal haplotype networks revealed a consistent, star‐like phylogeny, suggesting that despite the overall loss of haplotypes, no phylogenetically distinct mtDNA lineages were lost when the population declined. Our results may suggest that management during the last two decades has prevented additional losses of genetic diversity.
Cocoa as a Limiting Factor on the Microbial Population of Saliva

Cocoa powder added to cariogenic diets fed to rats (H. J. KINKEL and J. NEWIGER, Deutsch Zahnaertzl Z 15:1083-85, 1960) and hamsters (A. STRALFORS, Arch Oral Biol 11:323-328, 1966; and 11:149-161, 1966) decreased the incidence of caries in these animals. According to Stralfors, both water-soluble and insoluble cocoa factors were found to be cariostatic. Unheated or autoclaved 5% concentrations of cocoa inhibited growth of Salmonella species (F. F. BIJSTA and M. L. SPECK, Appl Microbiol 18:424-425, 1968). This study was undertaken to determine the effect of cocoa powder on the in vitro growth of the microbial population of saliva. Brain-heart infusion agar* plus 0.1% yeast extract* was used as the control medium. Cocoa powder from three distributorswas added in 5% and 10% amounts. Specimens (36) of paraffin-stimulated saliva were collected at various times from 12 apparently normal individuals. Aliquots of 0.1 ml of a 1:100,000 dilution of saliva were inoculated on four plates each of the control medium, the control medium plus 5% cocoa, and the control medium plus 10% cocoa. Two plates of each of the three above series were incubated aerobically and the same number anaerobically for 72 hours. Colony counts were performed with a Quebec colony counter. A decided decrease in colony
Selective Killing Natural Products and Drugs in Oral Cancer Treatments

Copyright: © 2016 Chang HW. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Most cancer drugs are effective to kill cancer cells but also harm normal cells. Drugs and natural products with the selective killing effect may be helpful to solve this problem.
Uptake and Intracellular Fate of Francisella tularensis in Human Macrophages

Abstract: Francisella tularensis is an intracellular pathogen that survives and multiplies within host mononuclear phagocytes. We have shown that uptake of the bacterium by human macrophages occurs by a novel process, “looping phagocytosis,” in which the bacterium is engulfed in a spacious, asymmetric, pseudopod loop. Whereas looping phagocytosis is resistant to treatment of the F. tularensis with formalin, proteases, or heat, the process is abolished by oxidation of the bacterial carbohydrates with periodate, suggesting a role for preformed surface carbohydrate molecules in triggering looping phagocytosis. Following uptake, F. tularensis initially resides in a spacious vacuole at the periphery of the cell, but this vacuole rapidly shrinks in size. The nascent F. tularensis vacuole transiently acquires early endosomal markers, but subsequently exhibits an arrested maturation, manifest by only limited amounts of lysosome‐associated membrane glycoproteins (consistent with limited interaction with late endosomes), nonfusion with lysosomes, and minimal acidification. In ultrastructural studies, we have observed that the F. tularensis phagosome displays a novel feature in that many of the phagosomes acquire an electron dense fibrillar coat. This fibrillar coat forms blebs and vesicles, and with time, is seen to be fragmented and disrupted. With increasing time after infection, increasing numbers of the F. tularensis are found free in the macrophage cytoplasm, such that by 14 h after infection, less than 15% of the bacteria are surrounded by any discernible phagosomal membrane. Further research is needed to determine the mechanisms underlying looping phagocytosis, and the maturational arrest, fibrillar coat formation, and disruption of the phagosome.
Tikhonov type regularization methods for inverse mixed variational inequalities

In this paper, we focus on a Tikhonov type regularization method for inverse mixed variational inequalities. Existence of solutions of the inverse mixed variational inequalities and its regularized problem are established. We also present the relationships among three coercivity conditions for inverse mixed variational inequalities. Finally, the nonemptiness and boundedness for the solutions set of the regularized problem are derived under some mild conditions.
A Suggestion for a High-Speed Parallel Binary Divider

A family of four procedures to compute the inverse 1/X of a given binary number X normalized between 0.5 and 1 is described. The quotient is obtained in redundant binary form, i.e., in a base 2 code in which digits can assume any positive or negative integer value. All methods here described can be implemented by combinatorial networks; the dividers realized in this way are very fast because all carry propagations take place at the same time.
Cardiac Troponin T Isoforms Affect the Ca2+Sensitivity and Inhibition of Force Development

At least four isoforms of troponin T (TnT) exist in the human heart, and they are expressed in a developmentally regulated manner. To determine whether the different N-terminal isoforms are functionally distinct with respect to structure, Ca2+ sensitivity, and inhibition of force development, the four known human cardiac troponin T isoforms, TnT1 (all exons present), TnT2 (missing exon 4), TnT3 (missing exon 5), and TnT4 (missing exons 4 and 5), were expressed, purified, and utilized in skinned fiber studies and in reconstituted actomyosin ATPase assays. TnT3, the adult isoform, had a slightly higher α-helical content than the other three isoforms. The variable region in the N terminus of cardiac TnT was found to contribute to the determination of the Ca2+ sensitivity of force development in a charge-dependent manner; the greater the charge the higher the Ca2+ sensitivity, and this was primarily because of exon 5. These studies also demonstrated that removal of either exon 4 or exon 5 from TnT increased the cooperativity of the pCa force relationship. Troponin complexes reconstituted with the four TnT isoforms all yielded the same maximal actin-tropomyosin-activated myosin ATPase activity. However, troponin complexes containing either TnT1 or TnT2 (both containing exon 5) had a reduced ability to inhibit this ATPase activity when compared with wild type troponin (which contains TnT3). Interestingly, fibers containing these isoforms also showed less relaxation suggesting that exon 5 of cardiac TnT affects the ability of Tn to inhibit force development and ATPase activity. These results suggest that the different N-terminal TnT isoforms would produce different functional properties in the heart that would directly affect myocardial contraction.