Miracle-dz/UniFAR-FTUs huggingface dataset:
CHEMICAL COMPOSITION AND MICROBIAL DYNAMICS OF BUDU FERMENTATION , A TRADITIONAL MALAYSIAN FISH SAUCE

The chemical and microbiological changes during spontaneous budu fermentation were elucidated on monthly basis (1–12 months). A signifi cant increase (P<0.05) in pH, acidity, soluble protein, total protein, and moisture content was observed during budu fermentation, except for the fat content. The total microbial load decreased gradually from the initial of 6.13±0.01 to 3.45±0.13 log CFU g–1 after 12 months of fermentation. Overall, 150 isolates were identifi ed, with a majority of bacteria (77%), followed by yeasts (12%) and 11% of unconfi rmed species. Micrococcus luteus was the predominant strain that initiated the fermentation before it was replaced by Staphylococcus arlettae that exists throughout the fermentation. This study confi rmed that lactic acid bacteria and yeasts often coexist with other microorganisms, even though a microbiological succession usually takes place both between and within species, which shaped the chemical and sensory characteristics of the fi nal product. In addition, some of the isolates could be potentially valuable as starter cultures for further improved and controllable budu fermentation.
Enhanced dissolution and bioavailability of gliclazide using solid dispersion techniques

Gliclazide is practically insoluble in water and its bioavailability is limited by dissolution rate. To enhance the dissolution rate and bioavailability the present study was aimed to formulate solid dispersions using different water soluble polymers such as polyethylene glycol 4000 (PEG 4000), polyethylene glycol 6000 (PEG 6000) using fusion method and polyvinyl pyrrolidone K- 30 (PVP K 30) by solvent evaporation method. The interaction of gliclazide with the hydrophilic polymers was studied by Differential Scanning Calorimetry (DSC), Fourier Transformation-Infrared Spectroscopy (FTIR) and X-Ray diffraction analysis. Solid dispersions were characterized for physicochemical properties like drug content, surface morphology and dissolution studies. Various factors like type of polymer and ratio of the drug to polymer on the solubility and dissolution rate of the drug were also evaluated. Pharmacokinetic studies of optimized formulation were compared with pure drug and marketed formulation in wistar rats. The dissolution of the pure drug and solid dispersion prepared with PVP K 30 (1:1) showed 38.3 + 4.5 % and 95 + 5.2 % release respectively within 30 min. Peak plasma concentration of pure drug, solid dispersion (PVP K 30) and marketed formulation was found to be 8.76 + 2.5, 16.04 + 5.5 and 9.24 + 3.6 μg/ml respectively, from these results it was observed that there is two fold increase in peak plasma concentration compared to pure drug. Solid dispersion is an effective technique in increasing solubility, dissolution rate and bioavailability of the poorly soluble drugs. Keywords: Gliclazide; solubility; solid dispersion; pharmacokinetics; peak plasma concentration; half life
Soil water content and temperature as independent or confounded factors controlling soil respiration in a temperate mixed hardwood forest

Variation in soil temperature can account for most of the seasonal and diel variation in soil CO2 efflux, but the temperature effect is not always consistent, and other factors such as soil water content are known to influence soil respiration. The objectives of this research were to study the spatial and temporal variation in soil respiration in a temperate forested landscape and to evaluate temperature and soil water functions as predictors of soil respiration. Soil CO2 fluxes were measured with chambers throughout an annual cycle in six study areas at the Harvard Forest in central Massachusetts that include soil drainage classes from well drained to very poorly drained. The mean annual estimate of soil CO2 efflux was 7.2 Mg ha–1, but ranged from 5.3 in the swamp site to 8.5 in a well‐drained site, indicating that landscape heterogeneity is related to soil drainage class. An exponential function relating CO2 fluxes to soil temperature accounted for 80% of the seasonal variation in fluxes across all sites (Q10 = 3.9), but the Q10 ranged from 3.4 to 5.6 for the individual study sites. A significant drought in 1995 caused rapid declines in soil respiration rates in August and September in five of the six sites (a swamp site was the exception). This decline in CO2 fluxes correlated exponentially with decreasing soil matric potential, indicating a mechanistic effect of drought stress. At moderate to high water contents, however, soil water content was negatively correlated with soil temperature, which precluded distinguishing between the effects of these two confounded factors on CO2 flux. Occurrence of high Q10 values and variation in Q10 values among sites may be related to: (i) confounding effects of high soil water content; (ii) seasonal and diel patterns in root respiration and turnover of fine roots that are linked to above ground phenology and metabolism; and (iii) variation in the depth where CO2 is produced. The Q10 function can yield reasonably good predictions of annual fluxes of CO2, but it is a simplification that masks responses of root and microbial processes to variation in temperature and water content throughout the soil.
Diversity of Rhizobium leguminosarum bv . viceae Strains Isolated from Different Schemes in Shendi Area

An attempt has been made to evaluate the diversity of sixteen Rhizobium leguminosarum bv. viceae strains isolated from different schemes in Shendi area. Morphological and cultural characteristics were performed viz: colony morphology, Gram staining and motility. Biochemical and physiological tests include acid base production, oxidase and catalast tests were carried out. The effects of antibiotics on the growth of Rhizobium strains on YEMA media were tested using measurement of diameters of the growth inhibition zones. Growth of pure rhizobial isolates on (YEM) medium having variable range of pH (5.5 to 8.5) and different concentrations of NaCl (0.5 6.6 %) were recorded. The genetic diversity of the eleven studied strains were examined and screened for the polymorphism and were amplified using two different RAPD primers (OPC9 and OPY14). The isolates studied were motile, gram negative and rod shaped and catalase and oxidase positive bacteria. Regardless the location of isolation. Rhizobium strains tested showed significant differences (P < 0.05) in their sensitivity to the antibiotics. Strain SHUOS1F34, SHUMAF6 and SHUGF37 were the most sensitive strains where as strain SHUJ15F2, SHUSSF4 and SHUR2F36 were the most tolerant ones to almost all antibiotics tested. With the exception of strain SHUNOF35, which tolerate high pH values upto 8.5, the growth rate of all strains increased steadily with increasing pH from 5.5 reaching the maximum at pH 6.5 to 7.5 and declined then after to 8.5. In all the tested strains the growth rate decreased with increasing salt concentration from 0.5 upto 6%. The two RAPD primers gave amplification products and they were reproducible. A total of 88 fragments were detected representing 15 different loci with 100% polymorphism. The most relative lines were strains SHUTR2F36 and SHUGO3F42 with 79% similarity. According to the similarity indices, the eleven strains were grouped into four Clusters
Proximate and Elemental Composition of Methanolic Extract of Boswellia dalzielii Hutch. (Frankincense Tree: Burseracea)

This study is aimed at investigating the proximate contents, concentrations of some micro/macro elements and anions of the stem bark and leaves of B. dalzielii with the view of validating its use as forage and medicinal by man in the treatment of diarrhoea, dysentery and in wound healing. The stem bark and leaves of B. dalzielii were collected from Bagale-Giere Local Government Area, Adamawa State, Nigeria. Proximate analysis was conducted following methods of Association of Official Analytical Chemists and the results showed that the stem bark had the higher dry matter (90.94 %), nitrogen free extract (54.13 %), crude fibre (30.65 %), and ash (8.34 %), while crude proteins (4.63 %), fats (21.20 %), carbohydrates (57.76 %) and moisture content (12.41 %) were estimated to be higher in the leaves of this plant. The levels of 11 elements (Ca, Mg, Na, K, Fe, Cd, Cu, Ni, Zn, Cr, Pb) were determined using atomic absorption spectrophotometer, the anions (nitrates, phosphates and sulphates) were estimated using smart spectrophotometer. The results revealed higher concentrations of macro elements and microelements in the leaves sample except for Cr concentration which was higher (4.0 x 10±0.00) mg/g in the stem bark than in the leaves (3.80 x 10±0.01) mg/g. In both the samples Pb was not detected.The concentrations of nitrates, phosphates and sulphates were higher in the leaves (1.52 x 10, 4.0 x 10, 1.33 x 10) mg/g than the stem bark (1.40 x 10 3.0 x 10, 1.24 x 10) mg/g respectively.The proximate, elemental and anions concentrations for these parts of B. dalzielii were mostly found within the permissible limit set by World Health Organization.
Measurement of infrared optical constants with visible photons

We demonstrate a new scheme for infrared spectroscopy with visible light sources and detectors. The technique relies on the nonlinear interference of correlated photons, produced via spontaneous parametric down conversion in a nonlinear crystal. Visible and infrared photons are split into two paths and the infrared photons interact with the sample under study. The photons are reflected back to the crystal, resembling a conventional Michelson interferometer. Interference of the visible photons is observed and it is dependent on the phases of all three interacting photons: pump, visible and infrared. The transmission coefficient and the refractive index of the sample in the infrared range can be inferred from the interference pattern of visible photons. The method does not require the use of potentially expensive and inefficient infrared detectors and sources, it can be applied to a broad variety of samples, and it does not require a priori knowledge of sample properties in the visible range.
Towards inferring causal gene regulatory networks from single cell expression Measurements

Single-cell transcriptome sequencing now routinely samples thousands of cells, potentially providing enough data to reconstruct causal gene regulatory networks from observational data. Here, we present Scribe, a toolkit for detecting and visualizing causal regulatory interactions between genes and explore the potential for single-cell experiments to power network reconstruction. Scribe employs Restricted Directed Information to determine causality by estimating the strength of information transferred from a potential regulator to its downstream target. We apply Scribe and other leading approaches for causal network reconstruction to several types of single-cell measurements and show that there is a dramatic drop in performance for "pseudotime” ordered single-cell data compared to true time series data. We demonstrate that performing causal inference requires temporal coupling between measurements. We show that methods such as “RNA velocity” restore some degree of coupling through an analysis of chromaffin cell fate commitment. These analyses therefore highlight an important shortcoming in experimental and computational methods for analyzing gene regulation at single-cell resolution and point the way towards overcoming it.
Virulence of Agrobacterium tumefaciens requires lipid homeostasis mediated by the lysyl‐phosphatidylglycerol hydrolase AcvB

Agrobacterium tumefaciens transfers oncogenic T‐DNA via the type IV secretion system (T4SS) into plants causing tumor formation. The acvB gene encodes a virulence factor of unknown function required for plant transformation. Here we specify AcvB as a periplasmic lysyl‐phosphatidylglycerol (L‐PG) hydrolase, which modulates L‐PG homeostasis. Through functional characterization of recombinant AcvB variants, we showed that the C‐terminal domain of AcvB (residues 232–456) is sufficient for full enzymatic activity and defined key residues for catalysis. Absence of the hydrolase resulted in ~10‐fold increase in L‐PG in Agrobacterium membranes and abolished T‐DNA transfer and tumor formation. Overproduction of the L‐PG synthase gene (lpiA) in wild‐type A. tumefaciens resulted in a similar increase in the L‐PG content (~7‐fold) and a virulence defect even in the presence of intact AcvB. These results suggest that elevated L‐PG amounts (either by overproduction of the synthase or absence of the hydrolase) are responsible for the virulence phenotype. Gradually increasing the L‐PG content by complementation with different acvB variants revealed that cellular L‐PG levels above 3% of total phospholipids interfere with T‐DNA transfer. Cumulatively, this study identified AcvB as a novel virulence factor required for membrane lipid homeostasis and T‐DNA transfer.
High‐dose linaclotide is effective and safe in patients with chronic constipation: A phase III randomized, double‐blind, placebo‐controlled study with a long‐term open‐label extension study in Japan

A previous phase II dose‐ranging study of linaclotide in a Japanese chronic constipation (CC) population showed that 0.5 mg was the most effective dose. This study aimed to verify the hypothesis that 0.5 mg of linaclotide is effective and safe in Japanese CC patients.
A Brief Review on Concurrent Training: From Laboratory to the Field

The majority of sports rely on concurrent training (CT; e.g., the simultaneous training of strength and endurance). However, a phenomenon called “Concurrent training effect” (CTE), which is a compromise in adaptation resulting from concurrent training, appears to be mostly affected by the interference of the molecular pathways of the underlying adaptations from each type of training segments. Until now, it seems that the volume, intensity, type, frequency of endurance training, as well as the training history and background strongly affect the CTE. High volume, moderate, continuous and frequent endurance training, are thought to negatively affect the resistance training-induced adaptations, probably by inhibition of the Protein kinase B—mammalian target of rapamycin pathway activation, of the adenosine monophosphate-activated protein kinase (AMPK). In contrast, it seems that short bouts of high-intensity interval training (HIIT) or sprint interval training (SIT) minimize the negative effects of concurrent training. This is particularly the case when HIIT and SIT incorporated in cycling have even lower or even no negative effects, while they provide at least the same metabolic adaptations, probably through the peroxisome proliferator-activated receptor-γ coactivator (PGC-1a) pathway. However, significant questions about the molecular events underlying the CTE remain unanswered.
Effect of Baseline Impedance on Ablation Lesion Dimensions: A Multimodality Concept Validation From Physics to Clinical Experience

Background Radiofrequency ablation using irrigated catheters is performed using a power-controlled mode. However, lesion size is dependent on current delivery at a particular impedance, such that a power value alone may not reflect actual energy delivery, resulting in lesion size variability at similar power settings. We hypothesized that modulating baseline impedance at fixed power settings affects ablation lesion dimensions. Methods In 20 ex vivo swine hearts, radiofrequency ablation was performed using an irrigated catheter at a fixed power setting of 30 W per 20 seconds and a multistepped impedance load (100–210&OHgr;). In 4 in vivo thigh muscle preparations and right atria, ablation was performed using similar power settings at 3 baseline impedances: low (90–130&OHgr;), intermediate (131–180&OHgr;), and high (181–224&OHgr;). The relationship between baseline impedance, current, and lesion dimensions was examined. Results Baseline impedance had a strong negative correlation with current squared (I2) for all experimental models: ex vivo (R=−0.94; P<0.0001), thigh muscle (R=−0.93; P<0.0001), and right atria (R=−0.94; P<0.0001). Lesion dimensions at similar power settings were highly variable and directly related to I2 (width [R=0.853], depth [R=0.814]). In the thigh muscle, lesion depth was 8.2±0.7, 6.5±0.8, and 4.2±0.5 mm for low, intermediate, and high impedance, respectively (P<0.0001). In right atria lines, low baseline impedance resulted in wider lines (7.2±1.4 mm) relative to intermediate (5.8±1.8 mm) and high impedance (4.7±1.7 mm; P<0.0001). Conclusions Radiofrequency ablation in a power control mode results in variable lesion dimensions that are partially related to differences in baseline impedance and current output. Ablation at a lower baseline impedance results in increased current output and lesion dimensions.
Continuity and discontinuity in human cortical development and change from embryonic stages to old age

The human cerebral cortex is highly regionalized. We aimed to test whether principles of regionalization could be traced from embryonic development throughout the human lifespan. A data-driven fuzzy-clustering approach was used to identify regions of coordinated longitudinal development of cortical surface area (SA) and thickness (CT) over 1.5 years (n = 301, 4-12 years). First, the SA clusters were compared to patterns from embryonic cortical development. The earliest sign of cortical regionalization is the emergence of morphometric gradients in the cerebral vesicles, with a major gradient running along the anterior-posterior (AP) axis. We found that the principal divide for the developmental SA clusters extended from the inferior-posterior to the superior-anterior cortex, corresponding to the embryonic morphometric AP gradient. Second, embryonic factors showing a clear AP gradient were identified, and tests revealed significant differences in gene expression of these factors between the anterior and posterior clusters. Further, each identified developmental SA and CT cluster showed distinguishable lifespan trajectories in a larger longitudinal dataset (4-88 years, 1633 observations). This means that regions that developed together also changed together throughout life, demonstrating continuity in regionalization of cortical changes. The AP divide in SA development also characterized genetic patterning obtained in an adult twin sample, but otherwise regionalized CT development adhered more to the genetic boundaries. Finally, SA and CT clusters showed differential relationships to cognitive functions. In sum, the results suggest that development of cortical regionalization is a continuous process from the embryonic stage throughout human life. Significance statement (120 words) The protomap and the radial unit theories of brain development have shown that graded expression patterns of several factors are responsible for shaping the ultimately highly partitioned and specialized neocortical landscape. The present study shows that the major anterior-posterior gradient of embryonic development can be detected in the regional cortical expansion profiles of children. The study further demonstrates that brain regions that develop together during childhood also tend to change together throughout the lifespan. This suggests that regional cortical development is a continuous process through the entire life, and that early-life factors have life-long impacts on this process.
Identification of key candidate genes, pathways and related prognostic values in ER-negative/HER2-negative breast cancer by bioinformatics analysis.

PURPOSE Breast cancer possesses different molecular expressions and biological behaviors. The purpose of this study was to identify the key genes, pathways, and related prognostic values in estrogen receptor (ER)-negative/human epidermal growth factor 2 (HER2)-negative breast cancer by bioinformatics analysis. METHODS The mRNA expression profiles of GSE20194 and GSE23988 were obtained from the Gene Expression Omnibus (GEO) database. Differently expressed genes (DEGs) were analyzed by GEO2R. A functional and pathway enrichment analysis of DEGs was conducted using DAVID. A protein-protein interaction (PPI) network was constructed using STRING and a module analysis of the PPI network was conducted using Cytoscape software. Survival analysis of hub genes was analyzed using the Kaplan-Meier plotter online tool. RESULTS 108 ER-negative/HER2-negative and 172 ER-positive/HER2-negative breast cancer samples were collected from the datasets GSE20194 and GSE23988. A total of 355 DEGs were identified in the ER-negative/HER2-negative samples, including 140 up-regulated and 215 down-regulated genes. The PPI network of DEGs consisted of 265 nodes and 648 edges. A significant module (12 nodes and 56 edges) was acquired from the PPI network of DEGs. Geneontology (GO) and pathway enrichment analysis demonstrated that this module was mainly related with transcription, cell proliferation, binding, and pathways in the PI3K-Akt signaling pathway. The high expression of CCNE1, KRT16, and MYBL2 was associated with worse relapse-free survival (RFS) and overall survival (OS) in ER-negative/HER2-negative breast cancer. CONCLUSIONS An integrated bioinformatics analysis was utilized to discover key candidate genes and pathways in ER-negative/HER2-negative breast cancer. This can improve the understanding of molecular mechanisms and provide potential candidate genes for diagnosis, prognosis, and individualized therapy.
Modified MXene/Holey Graphene Films for Advanced Supercapacitor Electrodes with Superior Energy Storage

MXene films are attractive for advanced supercapacitor electrodes requiring high volumetric energy density due to their high redox capacitance combined with extremely high packing density. However, the self‐restacking of MXene flakes unavoidably decreases the volumetric performance, mass loading, and rate capability. Herein, a simple strategy is developed to prepare a flexible and free‐standing modified MXene/holey graphene film by filtration of the alkalized MXene and holey graphene oxide dispersions, followed by a mild annealing treatment. After terminal groups (F/OH) are removed, the increased proportion of Ti atoms enables more pseudocapacitive reaction. Meanwhile, the embedded holey graphene effectively prevents the self‐restacking of MXene and forms a high nanopore connectivity network, which is able to immensely accelerate the ion transport and shorten transport pathways for both ion and electron. When applied as electrode materials for supercapacitors, it can deliver an ultrahigh volumetric capacitance (1445 F cm−3) at 2 mV s−1, excellent rate capability, and high mass loading. In addition, the assembled symmetric supercapacitor demonstrates a fantastic volumetric energy density (38.6 Wh L−1), which is the highest value reported for MXene‐based electrodes in aqueous electrolytes. This work opens a new avenue for the further exploration of MXene materials in energy storage devices.