Miracle-dz/UniFAR-FTUs huggingface dataset:
GlycA: A Composite Nuclear Magnetic Resonance Biomarker of Systemic Inflammation.

BACKGROUND Nuclear magnetic resonance (NMR) spectra of serum obtained under quantitative conditions for lipoprotein particle analyses contain additional signals that could potentially serve as useful clinical biomarkers. One of these signals that we named GlycA originates from a subset of glycan N-acetylglucosamine residues on enzymatically glycosylated acute-phase proteins. We hypothesized that the amplitude of the GlycA signal might provide a unique and convenient measure of systemic inflammation. METHODS We developed a spectral deconvolution algorithm to quantify GlycA signal amplitudes from automated NMR LipoProfile(®) test spectra and assessed analytic precision and biological variability. Spectra of acute-phase glycoproteins and serum fractions were analyzed to probe the origins of the GlycA signal. GlycA concentrations obtained from archived NMR LipoProfile spectra of baseline plasma from 5537 participants in the Multi-Ethnic Study of Atherosclerosis (MESA) were used to assess associations with demographic and laboratory parameters including measures of inflammation. RESULTS Major acute-phase protein contributors to the serum GlycA signal are α1-acid glycoprotein, haptoglobin, α1-antitrypsin, α1-antichymotrypsin, and transferrin. GlycA concentrations were correlated with high-sensitivity C-reactive protein (hsCRP) (r = 0.56), fibrinogen (r = 0.46), and interleukin-6 (IL-6) (r = 0.35) (all P < 0.0001). Analytic imprecision was low (intra- and interassay CVs 1.9% and 2.6%, respectively) and intraindividual variability, assessed weekly for 5 weeks in 23 healthy volunteers, was 4.3%, lower than for hsCRP (29.2%), cholesterol (5.7%), and triglycerides (18.0%). CONCLUSIONS GlycA is a unique inflammatory biomarker with analytic and clinical attributes that may complement or provide advantages over existing clinical markers of systemic inflammation.
Prevalence of Malaria in Patients Attending the General Hospital Makarfi, Makarfi Kaduna – State, North-Western Nigeria

Nigeria is a high endemic country for malaria. Its large population, diverse weather conditions and cultures make it a bit difficult implementing the same malaria control measures throughout the country. Prevalence studies are therefore essential for better understanding and implementation of intervention programs. This study determined some malariometric parameters such as malaria prevalence, transmission based on age and gender, parasite density, fever and anaemia in patients attending General Hospital Makarfi, during the malaria transmission season. All participants were screened microscopically for malaria and classified into 3 groups: under 5 years, 5 – 15 years and above 15. A total of 1173 participants were screened out of which 419 (35.7%) were positive. The geometric mean parasite density was 15,108 parasite/µL of blood. Children aged 5 – 15 years had a statistically significant higher infection rate compared to the other groups. Males were more prone to malaria than females. Presence of parasitaemia, fever or anaemia did not correlate with the presence of malaria. Some of the positive patients had high parasite densities and yet asymptomatic. More malariometric surveys are needed in Nigeria in order to adopt control efforts that best suit rural areas and smaller communities especially during peak malaria transmission season.
Smoking during pregnancy and vision difficulties in children: a systematic review

Cigarette smoking during pregnancy is a major public health concern. Intra‐uterine exposure to maternal cigarette smoking is associated with increased risks of growth and neurodevelopmental problems during childhood and later life. Few studies have focussed on visual difficulties in children in the context of maternal smoking during pregnancy. A systematic search of online databases was carried out between February and May 2013 to examine the trend in visual outcomes in children exposed to maternal cigarette smoking during intra‐uterine life. Twenty‐four non‐randomized studies were identified. Each study was rated for quality using the Newcastle‐Ottawa Scale. Most studies (n = 18) reported fetal exposure to active or passive maternal cigarette smoking to be associated with an increased risk of adverse visual outcomes in children. In particular, there were higher rates of strabismus, refractive errors and retinopathy among children of women who smoked during pregnancy. These findings suggest that fetal exposure to cigarette smoke is a significant risk factor for visual problems during later life and that certain visual faculties, such as the intraocular muscles and retinal neurons, are more affected than others. The findings provide evidence in support of public health policies aimed at reducing fetal exposure to smoking by advising both women and their partners to quit smoking during pregnancy.
Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida

Gallic acid (3,4,5‐trihydroxybenzoic acid, GA) is widely distributed in nature, being a major phenolic pollutant and a commonly used antioxidant and building‐block for drug development. We have characterized the first complete cluster (gal genes) responsible for growth in GA in a derivative of the model bacterium Pseudomonas putida KT2440. GalT mediates specific GA uptake and chemotaxis, and highlights the critical role of GA transport in bacterial adaptation to GA consumption. The proposed GA degradation via the central intermediate 4‐oxalomesaconic acid (OMA) was revisited and all enzymes involved have been identified. Thus, GalD is the prototype of a new subfamily of isomerases that catalyses a biochemical step that remained unknown, i.e. the tautomerization of the OMAketo generated by the GalA dioxygenase to OMAenol. GalB is the founding member of a new family of zinc‐containing hydratases that converts OMAenol into 4‐carboxy‐4‐hydroxy‐2‐oxoadipic acid (CHA). galC encodes the aldolase catalysing CHA cleavage to pyruvic and oxaloacetic acids. The presence of homologous gal clusters outside the Pseudomonas genus sheds light on the evolution and ecology of the gal genes in GA degraders. The gal genes were used for expanding the metabolic abilities of heterologous hosts towards GA degradation, and for engineering a GA cellular biosensor.
Short-term outcomes of laparoscopic total gastrectomy for gastric cancer: a comparative study with laparoscopic distal gastrectomy at a high-volume center

Abstract Background: Laparoscopic distal gastrectomy (LDG) for gastric cancer has gradually gained popularity. However, laparoscopic total gastrectomy (LTG) has been reported rarely when compared with LDG. This study was designed to evaluate the surgical outcomes as well as the morbidity and mortality of LTG compared with LDG to confirm the feasibility and safety of LTG. Material and methods: We reviewed the data of patients at our institution undergoing LTG (n = 448) or LDG (n = 956) for gastric cancer between January 2008 and July 2016. Then the clinical characteristics and perioperative clinical outcomes of the two groups were compared. Results: Except for tumor size and stage, there were no statistically significant differences in the clinicopathological parameters between the groups. LTG was associated with significantly longer operation time, late time to postoperative diet, and longer hospital stay compared with the LDG group. Overall complications developed in 60 patients (13.4%) and surgical complications in 48 patients (10.7%) after LTG. Postoperative complications were less frequent in the LDG group than in the LTG group (8.4% versus 13.4%, p < .01), and fewer surgical complications were observed with LDG than with LTG (7.5% versus 10.7%, p = .05). Conclusions: The results of LTG were favorable even though are not inferior to those of LDG. LTG for gastric cancer is technically feasible and safe. However, because of the limits of this study, other high-quality studies are needed for further evaluation.
Feature Centric Volume Visualization

This thesis presents techniques and algorithms for the effective exploration of volumetric datasets. The visualization techniques are designed to focus on user specified features of interest. The proposed techniques are grouped into four chapters namely feature peeling, computation and visualization of fabrication artifacts, locally adaptive marching cubes, and comparative visualization for parameter studies of dataset series. The presented methods enable the user to efficiently explore the volumetric dataset for features of interest. Feature peeling is a novel rendering algorithm that analyzes ray profiles along lines of sight. The profiles are subdivided according to encountered peaks and valleys at so called transition points. The sensitivity of these transition points is calibrated via two thresholds. The slope threshold is based on the magnitude of a peak following a valley, while the peeling threshold measures the depth of the transition point relative to the neighboring rays. This technique separates the dataset into a number of feature layers. Fabrication artifacts are of prime importance for quality control engineers for first part inspection of industrial components. Techniques are presented in this thesis to measure fabrication artifacts through direct comparison of a reference CAD model with the corresponding industrial 3D X-ray computed tomography volume. Information from the CAD model is used to locate corresponding points in the volume data. Then various comparison metrics are computed to measure differences (fabrication artifacts) between the CAD model and the volumetric dataset. The comparison metrics are classified as either geometry-driven comparison techniques or visual-driven comparison techniques. The locally adaptive marching cubes algorithm is a modification of the marching cubes algorithm where instead of a global iso-value, each grid point has its own iso-value. This defines an iso-value field, which modifies the case identification process in the algorithm. An iso-value field enables the algorithm to correct biases within the dataset like low frequency noise, contrast drifts, local density variations, and other artifacts introduced by the measurement process. It can also be used for blending between different iso-surfaces (e.g., skin, and bone in a medical dataset). Comparative visualization techniques are proposed to carry out parameter studies for the special application area of dimensional measurement using industrial 3D X-ray computed tomography. A dataset series is generated by scanning a specimen multiple times by varying parameters of the scanning device. A high resolution series is explored using a planar reformatting based visualization system. A multi-image view and an edge explorer are proposed for comparing and visualizing gray values and edges of several datasets simultaneously. For fast data retrieval and convenient usability the datasets are bricked and efficient data structures are used.
Serum antibodies after vaccination with Haemophilus influenzae type b capsular polysaccharide and responses to reimmunization: no evidence of immunologic tolerance or memory.

Haemophilus influenzae type b capsular polysaccharide vaccine was given in Finland in 1974 to approximately 50,000 infants and children, whose serum anti-H influenzae type b capsular polysaccharide levels have been followed for 3 1/2 years. The serum antibodies induced by the vaccination proved short-lived (less than 6 months) in the infants younger than 18 months. Elevated serum antibody levels were detectable for 1 1/2 years but less than 3 1/2 years in the children who were vaccinated when 18 to 35 months old. In the children who were 3 to 5 years old when vaccinated, the elevated anti-H influenzae type b capsular polysaccharide levels persisted for at least 3 1/2 years. Therefore, children vaccinated at the age of 18 months may need a new dose of vaccine 1 to 1 1/2 years after the first dose in order to be protected for the period of high susceptibility, until the age of approximately 7 years. Some of the vaccinated children were reimmunized 3 1/2 years after the first dose, and the anti-H influenzae type b capsular polysaccharide levels in their sera were studied in a similar manner. At no time did the anti-H influenzae type b capsular polysaccharide levels after the reimmunization differ from the anti-H influenzae type b capsular polysaccharide levels seen after the first vaccination in children of the same age. (ABSTRACT TRUNCATED AT 250 WORDS)
Increased hepatic platelet activating factor (PAF) and PAF receptors in carbon tetrachloride induced liver cirrhosis

Background and aims: The liver is a major site for the synthesis and actions of platelet activating factor (PAF), a potent hepatic vasoconstrictor and systemic vasodilator. As PAF is implicated in portal hypertension and hyperdynamic circulation associated with liver cirrhosis, we characterised changes in the hepatic PAF system in experimental cirrhosis. Methods: In rats made cirrhotic by carbon tetrachloride (CCl4) administration for eight weeks, we determined hepatic levels of PAF and its cognate receptor, and the effects of PAF and PAF antagonist (BN52021) on portal and arterial pressure. Results: Compared with control rats, cirrhotic rats had higher hepatic PAF levels, higher apparent hepatic efflux of PAF, and higher PAF levels in arterial blood (p<0.01, p<0.01, p<0.05, respectively). Relative to controls, cirrhotic livers had elevated hepatic PAF receptors (by mRNA and protein levels and [3H]PAF binding), higher (p<0.01) baseline hepatic portal pressure, and an augmented (p = 0.03) portal pressure response to PAF infusion (1 μg/kg). Portal infusion of BN52021 (5 mg/kg) showed that elevated endogenous PAF was responsible for 23% of the cirrhotic portal pressure increase but made no contribution to systemic hypotension. Finally, increased PAF receptor density was observed in the contractile perisinusoidal stellate cells isolated from cirrhotic livers relative to those from control livers. Conclusions: In cirrhosis, increased hepatic release of PAF elevates systemic PAF; in combination with upregulated hepatic PAF receptors in stellate cells, this contributes to portal hypertension.
Phrasing and Focus in Bengali

Part of the reason why these questions have not been adequately answered in the past is the lack of variety in the data collected and analyzed in previous studies. In order to set up an empirically-testable model of Bengali prosody within the framework of Intonational Phonology (Pierrehumbert 1980, Beckman & Pierrehumbert 1986, Pierrehumbert & Beckman 1988; see Ladd 1996 for review), the current study examines an extensive set of recordings of various types of sentences produced by a group of 25 adult native speakers of Standard Bangladeshi Bengali, collected in a recent experiment. Each speaker read 57 sentences aloud into a hand-held microphone connected via a USB cable to a laptop. The sentences were mostly made up of vowels and sonorant consonants. Their pragmatic, semantic, syntactic, and phonological properties were manipulated to test for: (a) different boundary tones, by using particular particles (e.g. focus clitics, interrogative particles) and punctuation (e.g. commas, question marks), and (b) the realization of focus domains, by using particular words of varying size and by using context sentences (i.e. preceding wh-questions eliciting focus on particular constituents). Recordings were made in WaveSurfer (Sjölander & Beskow 2005), and pitch events were analyzed in Praat (Boersma & Weenink 2005). Observations and measurements made using this new corpus of data reveal three fundamental facts that have been previously overlooked or refuted:
Catching Up Faster by Switching Sooner: A Prequential Solution to the AIC-BIC Dilemma

Bayesian model averaging, model selection and its approximations such as BIC are generally statistically consistent, but sometimes achieve slower rates of convergence than other methods such as AIC and leave-one-out cross-validation. On the other hand, these other methods can be inconsistent. We identify the catch-up phenomenonas a novel explanation for the slow convergence of Bayesian methods. Based on this analysis we define the switch distribution, a modifica tion of the Bayesian marginal distribution. We show that, under broad conditions, model selection and prediction based on the switch distribution is both consistent and achieves optimal convergence rates, thereby resolving the AIC-BIC dilemma. The method is practical; we give an efficient implementation. Th e switch distribution has a data compression interpretation, and can thus be viewed as a “prequential” or MDL method; yet it is different from the MDL methods that are usually considered in the literature. We compare the switch distribution to Bayes factor model selection and leave-one-out cross-validatio n.
Vapreotide acetate for the treatment of esophageal variceal bleeding

Variceal bleeding is a life-threatening complication of portal hypertension. The recommended treatment includes the early administration of a vasoactive drug. Vapreotide is a somatostatin analogue with a different receptor affinity to octreotide. It decreases portal pressure and blood flow of collateral circulation in rats with cirrhosis. The pivotal study of early administration of vapreotide in patients with cirrhosis and variceal bleeding has shown a significant improvement in bleeding control and, in the subset of patients with significant bleeding, a significant reduction in mortality. In addition, a meta-analysis of four randomized studies has shown a significant improvement in bleeding control. Vapreotide administrated via the intravenous route is simple to use, with practically no contraindications and few, usually minor, side effects.
Mutation in a novel connexin-like gene (Gjf1) in the mouse affects early lens development and causes a variable small-eye phenotype.

PURPOSE The purpose of the study was the characterization of the novel small-eye mutant Aey12 in the mouse. METHODS The eyes of the mutants were described morphologically and histologically and by in situ hybridization. RESULTS The homozygotes were viable and fully fertile, which identifies Aey12 as a new microphthalmia phenotype in the mouse, different from Maf or Pax6 mutants. Histologic analysis indicated the presence of the lens vesicle; however, the primary fiber cells did not elongate properly. Genome-wide linkage analysis mapped the mutation to the proximal region of chromosome 10 between the markers D10Mit206 and D10Mit189. Among the positional candidate genes, one EST (expressed sequence tag), D230044M03Rik, encodes a connexin-like protein. A G-->T point mutation was identified at cDNA position 96, resulting in an R32Q amino acid exchange in a transmembrane domain. The mutation leads to a loss of an SsiI restriction site, which is present in five wild-type mouse strains (102, C3H, C57BL/6, DBA, and JF1). The gene is expressed in the posterior part of the lens vesicle, where the primary fiber elongation starts. In the mutants, the expression pattern of Pax6, Prox1, Six3, and Crygd are modified, but not the pattern of Pax2. CONCLUSIONS The mutated mouse gene belongs to the family of connexin-encoding genes (gene symbols Gja-Gje). Together with its rat and human homologues, it defines a new subgroup, referred to as Gjf1. The mouse mutant described herein offers a new functional candidate gene for microphthalmia-related disorders at the corresponding locus on human chromosome 6, area q24.
From resource to female defence: the impact of roosting ecology on a bat's mating strategy

With their extraordinary species richness and diversity in ecological traits and social systems, bats are a promising taxon for testing socio-ecological hypotheses in order to get new insights into the evolution of animal social systems. Regarding its roosting habits, proboscis bats form an extreme by occupying sites which are usually completely exposed to daylight (e.g. tree trunks, vines or rocks). This is accompanied by morphological and behavioural adaptations to remain cryptic in exposed day roosts. With long-term behavioural observations and genetic parentage analyses of individually marked proboscis bats, we assessed its social dispersion and male mating strategy during day and night. Our results reveal nocturnal male territoriality—a strategy which most closely resembles a resource-defence polygyny that is frequent also in other tropical bats. Its contrasting clumped social dispersion during the day is likely to be the result of strong selection for crypsis in exposed roosts and is accompanied by direct female defence in addition to male territoriality. To the best of our knowledge, such contrasting male mating strategies within a single day–night cycle have not been described in a vertebrate species so far and illustrate a possible evolutionary trajectory from resource-defence to female-defence strategy by small ecologically driven evolutionary steps.
Do Fish Perceive Anaesthetics as Aversive?

This study addresses a fundamental question in fish welfare: are the anaesthetics used for fish aversive? Despite years of routine general use of many agents, within both scientific research and aquaculture, there is a paucity of information regarding their tolerance and associated behavioural responses by fish. This study examined nine of the most commonly used fish anaesthetic agents, and performed preference tests using adult mixed sex zebrafish (Danio rerio), the most commonly held laboratory fish. Video tracking software quantified swimming behaviour related to aversion for each anaesthetic at 50% of its standard recommended dose compared with clean water in a flow-through chemotaxic choice chamber. Results suggest that several commonly used anaesthetics were aversive, including two of the most commonly recommended and used: MS222 (ethyl 3-aminobenzoate methanesulphate) and benzocaine. For ethical best practice, it is recommended that compounds that are aversive, even at low concentration, should no longer be used routinely for anaesthesia or indeed the first step of humane euthanasia of adult zebrafish. Two agents were found not to induce aversive behavioural responses: etomidate and 2,2,2 tribromoethanol. For the millions of adult zebrafish used in laboratories and breeding worldwide, etomidate appears best suited for future routine humane use.
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1  Abstract—Due to their capacity-achieving property, polar codes have become one of the most attractive channel codes. To date, the successive cancellation list (SCL) decoding algorithm is the primary approach that can guarantee outstanding error-correcting performance of polar codes. However, the hardware designs of the original SCL decoder have large silicon area and long decoding latency. Although some recent efforts can reduce either the area or latency of SCL decoders, these two metrics still cannot be optimized at the same time. This paper, for the first time, proposes a general log-likelihood-ratio (LLR)-based SCL decoding algorithm with multi-bit decision. This new algorithm, referred as LLR-2 K b-SCL, can determine 2 K bits simultaneously for arbitrary K with the use of LLR messages. In addition, a reduced-data-width scheme is presented to reduce the critical path of the sorting block. Then, based on the proposed algorithm, a VLSI architecture of the new SCL decoder is developed. Synthesis results show that for an example (1024, 512) polar code with list size 4, the proposed LLR-2 K b-SCL decoders achieve significant reduction in both area and latency as compared to prior works. As a result, the hardware efficiency of the proposed designs with K=2 and 3 are 2.33 times and 3.32 times of that of the state-of-the-art works, respectively.