Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of Babesia species in hunting dogs in Ogun State South West Nigeria

Dogs are commonly used for hunting in Nigeria and they may harbour parasites without showing any clinical features. Babesiosis is a worldwide, tick-borne, protozoal haemoparasitic disease caused by parasites of genus Babesia. This study assessed by means of microscopy and Polymerase Chain Reaction (PCR), the presence of Babesia species in 109 indigenous Nigerian hunting dogs. One hundred and nine hunting dogs were sampled from 21 different locations, from May 2014 to March 2015 with ages ranging from less than 1 to greater than 6 years. The average weight of the dogs studied was 12.20±0.33kg with the mean Packed Cell Volume (PCV) of 35.2±0.86% and mean age of 3.01±0.23 years. Using microscopy 24 (22%) of the dogs were positive for Babesia species. There were no statistically significant differences in the gender (p=0.84), age (p= 0.71), weight (p= 0.45) and PCV (p=0.87) of infected and non-infected dogs. With PCR assay, 52 (47.7%) of the sampled dogs were positive to Babesia spp. Of which 18 (34.6%) were male and 34(65.4%) were females. There were no statistical significance between the presence of Babesia spp. and sex (p=0.11) also with PCV (p=0.06) of hunting dogs but there were significant differences in their ages (p=0.04) and weights (p= 0.01) Using PCR as a gold standard the specificity and sensitivity of microscopy for detecting Babesia were 77.2% and 21.2 % respectively. The positive predictive value for microscopy was 45.8% while the negative predictive value was 51.8% with a diagnostic accuracy of 50%. The implication of the presence of the parasite in the study areas is discussed.
The distinction between randomized clinical trials (RCTs) and preliminary feasibility and pilot studies: what they are and are not.

Feasibility and pilot studies play an important role in the preliminary planning of a proposed full-size randomized clinical trial (RCT). In essence, feasibility studies are used to help develop trial interventions or outcome measures, whereas pilot studies replicate, in miniature, a planned full-size RCT. However, the terms used for these preliminary studies are sometimes considered synonymous, and in practice may overlap considerably or be combined. The important issue is not the distinction between these: the important distinction is between such preliminary studies and a proper RCT. J Orthop Sports Phys Ther 2014;44(8):555–558. doi:10.2519/jospt.2014. 0110
The Conserved YAGL Motif in Human Metapneumovirus Is Required for Higher-Order Cellular Assemblies of the Matrix Protein and for Virion Production

ABSTRACT YXXL motifs in cellular and viral proteins have a variety of functions. The matrix (M) protein of the respiratory pathogen human metapneumovirus (hMPV) contains two such conserved motifs—YSKL and YAGL. We mutated these sequences to analyze their contributions to hMPV infectivity. The mutant clones were capable of intracellular replication; however, the YAGL but not YSKL mutants were defective at spreading in infected cultures. We improved the reverse genetics system for hMPV and generated cell lines that stably expressed selectable, replicating full-length genomes for both the wild type and the mutant clones, allowing microscopic and biochemical analyses of these viruses. YAGL mutants produced normal cellular levels of M protein but failed to release virions, while ectopic coexpression of wild-type M generated particles that were restricted to a single cycle of infection. The YAGL motif did not act as a late (L) domain, however, since hMPV budding was independent of the cellular endosomal sorting complex required for transport (ESCRT) machinery and because replacement of the YAGL motif with classical L domains generated defective viruses. Instead, the YAGL mutants had defective M assemblies lacking a normal filamentous appearance and showed poor extractability from the cell compared to the wild-type protein. The mutant proteins were not grossly misfolded, however, as they interacted with cellular membranes and coassembled with wild-type M proteins. Thus, the YAGL motif is an important determinant of hMPV assembly. Furthermore, the selectable hMPV genomes described here should extend the use of reverse genetics systems in the analysis of spreading-defective viruses.
PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors

Among the various databases dedicated to the identification of protein families and domains, PROSITE is the first one created and has continuously evolved since. PROSITE currently consists of a large collection of biologically meaningful motifs that are described as patterns or profiles, and linked to documentation briefly describing the protein family or domain they are designed to detect. The close relationship of PROSITE with the SWISS-PROT protein database allows the evaluation of the sensitivity and specificity of the PROSITE motifs and their periodic reviewing. In return, PROSITE is used to help annotate SWISS-PROT entries. The main characteristics and the techniques of family and domain identification used by PROSITE are reviewed in this paper.
Construction of Partial MDS (PMDS) and Sector-Disk (SD) Codes with Two Global Parity Symbols

Partial MDS (PMDS) codes are erasure codes combining local (row) correction with global additional correction of entries, while Sector-Disk (SD) codes are erasure codes that address the mixed failure mode of current RAID systems. It has been an open problem to construct general codes that have the PMDS and the SD properties, and previous work has relied on Monte-Carlo searches. In this paper, we present a general construction that addresses the case of any number of failed disks and in addition, two erased sectors. The construction requires a modest field size. This result generalizes previous constructions extending RAID~5 and RAID~6.
Prehospital sudden death from ischaemic heart disease. A postmortem study.

SUMMARY A detailed postmortem study of the myocardium and coronary arteries was performed on 114 men and 37 women who died suddenly outside hospital. Data on the disease history and certain risk factors were collected through an 'Ischaemic Heart Disease Register'. Men and women did not differ with respect to history of previous symptoms of ischaemic heart disease or necropsy findings. A history of hypertension and the previous use of digitalis or diuretics tended to be more frequent in women than in men but current smoking was more common in men (69%) than in women (43%). Of the subjects in whom necropsy revealed an old myocardial infarction, 86 per cent had a history of symptomatic ischaemic heart disease but a previous myocardial infarction was known in only 42 per cent of them. A definite recent myocardial infarction was found in 26 per cent and an early infarction in 51 per cent. About half of the patients with a definite recent or an early myocardial infarction, and half of those with no recent myocardial infarct, died at once. Fourteen per cent of the subjects died after symptoms lasting 2 hours or more. a no
Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia

Histone modification is an important mechanism regulating both gene expression and the establishment and maintenance of cellular phenotypes during development. Regulation of histone acetylation via histone acetylases and deacetylases (HDACs) appears to be particularly crucial in determining gene expression patterns. In this study we explored the effect of HDAC inhibition on the life cycle of the human pathogen Giardia lamblia, a highly reduced parasitic protozoan characterized by minimized cellular processes. We found that the HDAC inhibitor FR235222 increased the level of histone acetylation and induced transcriptional regulation of ∼2% of genes in proliferating and encysting parasites. In addition, our analyses showed that the levels of histone acetylation decreased during differentiation into cysts, the infective stage of the parasite. Importantly, FR235222 treatment during encystation reversed this histone hypo‐acetylation and potently blocked the formation of cysts. These results provide the first direct evidence for epigenetic regulation of gene expression in this simple eukaryote. This suggests that regulation of histone acetylation is involved in the control of Giardia stage differentiation, and identifies epigenetic mechanisms as a promising target to prevent Giardia transmission.
Intra-project transfer of knowledge in information systems development firms

Purpose – The focus of this paper is on knowledge transfer. The purpose is to investigate intra‐project knowledge‐transfer practice in information systems development (ISD) firms applying a Scrum methodology.Design/methodology/approach – Case study of ISD projects and empirical data obtained using in‐depth interviews following a semi‐structured approach were employed.Findings – One of the main findings showed that Scrum team members believed in the usefulness of knowledge transfer. The study observed extensive personal exchange of knowledge through, for example, meetings and networks, including dialog with the client. The mechanisms observed in creating knowledge transfer were: lean and dynamic documentation, cross‐functional teams, client consultation and feedback, intra‐project meetings, application of project tools and techniques, and management of changes.Research limitations/implications – Future research should investigate other organizations and countries, so that these findings may be generalized.
ENZYMATICALLY PRODUCED SUBUNITS OF PROTEINS FORMED BY PLASMA CELLS IN MICE

Gamma globulin and antibody obtained from inbred C3H mice are split by papain and cysteine into fragments roughly one-third the size of the original Molecule (S 20,w = 3.5S). The papain digests were characterized by starch gel electrophoresis and immunological methods. The highly heterogeneous fragments could be divided into two groups with distinct antigenic determinants (S and F), which were separated by DEAE ion-exchange cellulose chromatography. Approximately two-thirds of the fragments had S antigenic groupings and one-third had F antigenic groupings. These data are consistent with the view that mouse gamma globulin is split by papain and cysteine into three major fragments, two of which are of the S type and one of the F type. Antibody activity of the original molecule was present in the S fragments. Although the S fragments did not precipitate the antigen (hemocyanin) they were shown to bind antigen specifically in the manner of univalent antibodies. The S fragments of normal γ-globulin were very heterogeneous with a broad spectrum of electrophoretic mobilities. Comparison of S fragments from slow and fast migrating globulins showed that the mobilities of the original γ-globulin samples were largely reflected in the mobilities of their S fragments. Additional observations indicated that the F fragments also may help to determine the electrophoretic mobility of intact γ-globulin molecules. S fragments of differing electrophoretic mobility were shown to have the same antigenic determinants, indicating that the structural differences responsible for the electrophoretic mobility differences were not involved in the antigenic groupings identified with rabbit antisera. The F fragments of normal γ-globulin migrated more rapidly than the S fragments, were less heterogeneous, and showed several bands on starch gel electrophoresis. The F fragments differed antigenically from the S fragments, and had no antibody activity. Two groups of F fragments (F and F') were detected with some antisera. The γ-myeloma protein (5563) formed in a C3H plasma cell tumor and similarly fragmented by treatment with papain and cysteine, produced much more discrete S and F components than were found in the normal γ-globulin digest. The electrophoretic properties of the myeloma protein fragments were within the range observed for normal γ-globulin fragments. Although the γ-myeloma protein shares antigenic determinants with normal γ-globulins it lacks some of the antigenic groupings present in the γ-globulin preparation. Both S and F fragments from the myeloma protein share antigenic determinants with the corresponding fragments from normal γ-globulin. In addition, both S and F fragments of normal γ-globulin possess antigenic groupings not present in fragments of the γ-myeloma protein, accounting for the antigenic deficiency observed on comparison of the γ-myeloma protein with normal γ-globulins.
Evolution of Local Mutation Rate and Its Determinants

Mutation rate varies along the human genome, and part of this variation is explainable by measurable local properties of the DNA molecule. Moreover, mutation rates differ between orthologous genomic regions of different species, but the drivers of this change are unclear. Here, we compare the local mutation rates of several species. We show that these rates are very similar between human and apes, implying that their variation has a strong underlying cryptic component not explainable by the known genomic features. Mutation rates become progressively less similar in more distant species, and these changes are partially explainable by changes in the local genomic features of orthologous regions, most importantly, in the recombination rate. However, they are much more rapid, implying that the cryptic component underlying the mutation rate is more ephemeral than the known genomic features. These findings shed light on the determinants of mutation rate evolution.
ik3-1/Cables is associated with Trap and Pctaire2.

ik3-1/Cables is associated with and phosphorylated by cdk3 in self-replicating cells. In postmitotic neurons, it may serve as an adaptor molecule, functionally connecting c-abl and cdk5, and supporting neurite growth. Here, we cloned cDNAs coding for mouse Trap (tudor repeat associator with Pctaire 2) to interact with ik3-1. ik3-1 interacts with a region of mouse Trap containing the C-terminal tudor repeat domains 4 and 5 (corresponding to amino acids 881-1086 of mouse Trap). Furthermore, the N-terminal 93-amino-acid domain of ik3-1 is essential for ik3-1 interaction with Trap. Moreover, ik3-1 is coimmunoprecipitated with Pctaire 2 from COS7 cells, although we could not clarify whether ik3-1 is directly associated with Pctaire 2 or indirectly associated with Pctaire 2 through Trap. In vitro kinase assay indicated that ik3-1 does not activate phosphorylation of myelin basic protein or histione H 1 by the Pctaire 2-mediated kinase. These findings led us to speculate that through ik3-1, the Pctaire family and Trap may be functionally connected with cdk3 or cdk5.
Safety and tolerability of carbamylated erythropoietin in Friedreich's ataxia

Erythropoietin (EPO) derivatives have been found to increase frataxin levels in Friedreich's ataxia (FRDA) in vitro. This multicenter, double‐blind, placebo‐controlled, phase II clinical trial aimed to evaluate the safety and tolerability of Lu AA24493 (carbamylated EPO; CEPO).
Mortality Risk After Hip Fracture

Objective To determine the mortality risk following hip fracture and identify factors predictive of increased mortality. Design Retrospective review of prospectively collected data. Setting Tertiary care orthopaedic hospital. Background Approximately 250,000 hip fractures occur annually in the United States. The greatest mortality risk following hip fracture has been demonstrated to be within the first 6 months of fracture, and some studies report that the risk approaches expected mortality after 6 months. However, more recent studies have demonstrated that an increased risk of mortality may persist for several years postfracture. The purpose of this study was to assess the excess mortality associated with hip fracture at up to 2 years postinjury. Methods All patients with a hip fracture who were admitted to our institution over a 10-year period were evaluated. Criteria for inclusion included: Caucasian, age 65 or older, previously ambulatory, and home dwelling. Patients were followed prospectively to determine the mortality risk associated with hip fracture over a 2-year follow-up period. Mortality was compared to a standardized population and standardized mortality ratios were calculated. Results Eight hundred thirty-six patients met the inclusion criteria and were included. The mortality risk was highest within the first 3 months following fracture, with standardized mortality ratios approaching that of the control population by two years. Patients age 65–84 had higher mortality risk when compared with patients age ≥85. American Society of Anesthesiologists classification was predictive of increased mortality risk in younger patients, with these patients having triple the mortality risk when compared to the reference population at 2-year follow-up. More elderly patients had minimal excess mortality associated with hip fracture at 1- and 2-year follow-up, regardless of ASA classification. Conclusion The data demonstrate that hip fracture is not associated with significant excess mortality amongst patients older than age 85. Amongst younger patients, however, those with ASA classifications of 3 or 4 have significant excess mortality following hip fracture that persists up to 2 years after injury.
Flow Extremes as Spatiotemporal Control Points on River Solute Fluxes and Metabolism

Floods are dominant controls on export of solutes from catchments. In contrast, low‐flow periods such as droughts are potentially dominant control points for biogeochemical processing, enhancing spatiotemporal variation in solute concentrations, stream metabolism, and nutrient uptake. Using complementary time series (i.e., an Eulerian reference frame) and longitudinal profiling (i.e., a Lagrangian reference frame), we investigated hydrologic controls on temporal and spatial variation in solute flux and metabolism in the Lower Santa Fe River (FL, USA), where highly colored surface water mixes with exceptionally clear groundwater from springs. Gage measurements suggest groundwater inputs ranged from <1% (during extreme floods) to 86% (during extreme drought) of total discharge (Q). Mass transport of most solutes was dominated by high‐Q periods. Most solute C‐Q relationships exhibited statistically significant slope breakpoints near the transition between surface and groundwater dominance. In particular, parameters controlling water column light attenuation were chemostatic above median Q but markedly reduced at low Q. As a result, river metabolism and assimilatory nitrate (NO3−) uptake were consistently suppressed at high Q and enhanced at low Q, with greater variability in response to drivers other than water column light transmittance. Spatial variation in solute concentrations was also enhanced at low Q, induced by discrete groundwater inflow and biogeochemical processing along the reach. Contrasting reference frames yielded corroborative evidence for transport dominance at high Q, which damps spatiotemporal heterogeneity. In contrast, low‐Q periods enable localized mixing controls on solute concentrations and high rates of metabolism and nutrient processing that increase spatiotemporal variability.
Maximum mutual information multi-phone units in direct modeling

This paper introduces a class of discriminative features for use in maximum entropy speech recognition models. The features we propose are acoustic detectors for discriminatively determined multi-phone units. The multi-phone units are found by computing the mutual information between the phonetic subsequences that occur in the training lexicon, and the word labels. This quantity is a function of an error model governing our ability to detect phone sequences accurately (an otherwise informative sequence which cannot be reliably detected is not so useful). We show how to compute this mutual information quantity under a class of error models efficiently, in one pass over the data, for all phonetic sub-sequences in the training data. After this computation, detectors are created for a subset of highly informative units. We then define two novel classes of features based on these units: associative and transductive. Incorporating these features in a maximum entropy based direct model for Voice-Search outperforms the baseline by 24% in sentence error rate.
Evolution of Dominance in Metabolic Pathways

Dominance is a form of phenotypic robustness to mutations. Understanding how such robustness can evolve provides a window into how the relation between genotype and phenotype can evolve. As such, the issue of dominance evolution is a question about the evolution of inheritance systems. Attempts at explaining the evolution of dominance have run into two problems. One is that selection for dominance is sensitive to the frequency of heterozygotes. Accordingly, dominance cannot evolve unless special conditions lead to the presence of a high frequency of mutant alleles in the population. Second, on the basis of theoretical results in metabolic control analysis, it has been proposed that metabolic systems possess inherent constraints. These hypothetical constraints imply the default manifestation of dominance of the wild type with respect to the effects of mutations at most loci. Hence, some biologists have maintained that an evolutionary explanation is not relevant to dominance. In this article, we put into question the hypothetical assumption of default metabolic constraints. We show that this assumption is based on an exclusion of important nonlinear interactions that can occur between enzymes in a pathway. With an a priori exclusion of such interactions, the possibility of epistasis and hence dominance modification is eliminated. We present a theoretical model that integrates enzyme kinetics and population genetics to address dominance evolution in metabolic pathways. In the case of mutations that decrease enzyme concentrations, and given the mechanistic constraints of Michaelis-Menten-type catalysis, it is shown that dominance of the wild type can be extensively modified in a two-enzyme pathway. Moreover, we discuss analytical results indicating that the conclusions from the two-enzyme case can be generalized to any number of enzymes. Dominance modification is achieved chiefly through changes in enzyme concentrations or kinetic parameters such as kcat, both of which can alter saturation levels. Low saturation translates into higher levels of dominance with respect to mutations that decrease enzyme concentrations. Furthermore, it is shown that in the two-enzyme example, dominance evolves as a by-product of selection in a manner that is insensitive to the frequency of heterozygotes. Using variation in kcat as an example of modifier mutations, it is shown that the latter can have direct fitness effects in addition to dominance modification effects. Dominance evolution can occur in a frequency-insensitive manner as a result of selection for such dual-effects alleles. This type of selection may prove to be a common pattern for the evolution of phenotypic robustness to mutations.