Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of substrate adaptation on the microbial fermentation and microbial composition of faecal microbiota of weaning piglets studied in vitro

The in vitro cumulative gas production technique can be used to assess microbial activity of a complex community, in relation to fermentation of a particular energy source. Therefore, in combination with an in vivo study to examine the effects of two different diets for weaning piglets, microbial activities of faeces were compared from animals on the two different diets. The two diets were: CHO diet [containing added fermentable carbohydrates, including sugarbeet pulp (SBP) and wheat starch (WST)], and control diet without any added fermentable carbohydrates. Neither diet contained antibiotics or extra added copper. Twenty-four piglets were selected from 12 litters (two per litter), weaned at 4 weeks of age (neither creep feeding nor any antibiotic treatment before and during the study), and introduced to one of the two diets. After 9 days on the diet, faecal samples were collected from selected animals, and tested for their activity in terms of gas production kinetics, and end-products such as volatile fatty acids, ammonia and dry matter disappearance of the two test substrates SBP and WST. The bacterial diversity was also analysed before and after in vitro fermentation using denaturing gradient gel electrophoresis analysis of amplified 16S rRNA genes. There were differences both in kinetics and end-products of the substrates. More interestingly, significant differences were detected between inocula, although mainly in terms of fermentation kinetics of the two substrates. With the CHO inoculum, SBP was fermented faster than with the control, while this effect was reversed for WST. Significantly higher diversity, as measured by DGGE fingerprint analysis, was detected in the microbial community enrichment on SBP as compared with WST at the end of fermentation. The difference between the kinetics of SBP compared with WST fermentation by faecal microbiota from the CHO diet fed piglets suggests better adaptation to SBP fermentation than to WST fermentation. The WST fermentation was more unexpected, given that a significant amount of starch is known to be fermentable by the small intestinal microbiota. It was concluded that the microbial community composition and activity in the GIT may be changed in response to diet, and that this change can be detected in vitro. Copyright © 2005 Society of Chemical Industry
Growth at elevated CO2 leads to down-regulation of photosynthesis and altered response to high temperature in Quercus suber L. seedlings

The effects of growth at elevated CO 2 on the response to high temperatures in terms of carbon assimilation (net photosynthesis, stomatal conductance, amount and activity of Rubisco, and concentrations of total soluble sugars and starch) and of photochemistry (for example, the efficiency of excitation energy captured by open photosystem II reaction centres) were studied in cork oak (Quercus suber L.). Plants grown in elevated CO 2 (700 ppm) showed a down-regulation of photosynthesis and had lower amounts and activity of Rubisco than plants grown at ambient CO 2 (350 ppm), after 14 months in the greenhouse. At that time plants were subjected to a heat-shock treatment (4 h at 45°C in a chamber with 80% relative humidity and 800-1000 μmol m -2 s -1 photon flux density). Growth in a CO 2 -enriched atmosphere seems to protect cork oak leaves from the short-term effects of high temperature. Elevated CO 2 plants had positive net carbon uptake rates during the heat shock treatment whereas plants grown at ambient CO 2 showed negative rates. Moreover, recovery was faster in high CO 2 -grown plants which, after 30 min at 25°C, exhibited higher net carbon uptake rates and lower decreases in photosynthetic capacity (A max ) as well as in the efficiency of excitation energy captured by open photosystem II reaction centres (F v /F m ) than plants grown at ambient CO 2 . The stomata of elevated CO 2 plants were also less responsive when exposed to high temperature.
Rock hyrax (Procavia capensis) den site selection: preference for artificial sites

Context Objective assessments of habitat requirements for endangered species are often lacking when planning management strategies, and inappropriate landscape manipulation can sometimes turn an endangered species into a pest. Recent expansive population growth of the rock hyrax Procavia capensis in northern Israel has been attributed largely to the proliferation of man-made boulder piles on the fringes of new residential developments. Aims The hyrax is a protected species, but when in proximity to residential areas it can be a garden pest and is medically important as a reservoir of cutaneous leishmaniasis. Management should thus consider preservation of hyrax populations in combination with minimising pest potential. We examined the hypothesis that hyraxes prefer artificial boulder piles to natural outcrop crevices as den sites. Methods We surveyed all 57 potential den sites in a 1 × 1 km area around a village in northern Israel, and conducted logistic regression to examine the correlation of hyrax presence with site type (pile or crevice), size, distance from the village, distance from other den sites and network centrality within the den site network. We used the Aikaike information criterion (AIC) to compare logistic models. Key results Occupancy was well predicted by site type, site size, and distance from other sites, explaining 59% of the variation in the logistic regression. These three predictors were selected both by considering the combination of predictors that gave the lowest AIC value, and also by the stepwise logistic algorithm. Conclusions and implications Hyrax den site preference, and in particular preference for boulder piles over natural crevices, should be integrated into managing this species simultaneously for conservation and pest control in the face of continuing residential encroachment on natural areas.
Palaeoecological perspectives on pattern and process in plant diversity and distribution adjustments: a comment on recent developments *

Two developments in the understanding of the relationship between sedimentary pollen assemblages, vegetation and plant diversity are discussed. The Prentice model of vegetation–pollen relationships has improved our understanding of how and at what scale sedimentary pollen records vegetation. The modelling framework allows improved palaeoecological study designs that may, potentially, give important new insights into processes of plant migrations in response to climate change. Also, reconstructions of plant communities and landscape openness may be improved. Competing hypotheses for the relationship between vegetation and palynological diversity are discussed and it is concluded that more attention should be focused on evenness aspects of palynological diversity and on hypothesis testing.
The Effects of Bacterial Inoculants on the Fermentation, Aerobic Stability and Rumen Degradability Characteristics of Wheat Silages*

This study was carried out to determine the effects of lactic acid bacteria (LAB) inoculants on the fermentation, aerobic stability and in situ rumen degradability characteristics of wheat silages. Wheat was harvested at the early dough stage. Inoculant-1188 (Pioneer ¤ , USA) and Sil-All (Alltech, UK) were used as LAB inoculants. Inoculants were applied to silages at 1.5 x 10 6 cfu/g levels. Wheat material was ensiled in 1.5-l special anaerobic jars, equipped with a lid enabling gas release only. Three jars from each group were sampled for chemical and microbiological analysis 2, 4, 8, 15 and 50 days after ensiling. At the end of the ensiling period all silages were subjected to an aerobic stability test for 5 days. In addition, in situ rumen degradability characteristics were determined in the silages. Both homofermentative LAB inoculants improved the fermentation characteristics of wheat silages. At the end of the ensiling period inoculants increased the lactobacilli and decreased yeast and mold numbers of the silages. However, both LAB inoculants led to higher CO2 production and impaired the aerobic stability of the silages. The in situ degradability characteristics of the wheat silages were not affected by the inoculant treatment.
Frequency of aberrant promoter methylation of p15INK4b and O6-methylguanine-DNA methyltransferase genes in b-cell non-Hodgkin lymphoma: A pilot study

The methylation status of the target promoter sequences of p15 INK4B (p15) and O 6 -methylguanine-DNA methyltransferase (MGMT) genes was studied by methylation-specific PCR in 10 adult patients with de novo B-cell non- Hodgkin lymphoma (B-NHL). The aberrant hypermethylation of the p15 gene was more frequent (50%) compared to the hypermethylation of the MGMT gene (30%), and was detected in different types of B-NHL in both genes. Hyper- methylation of the MGMT gene occurred exclusively in association with the hypermethylation of the p15 gene. All lymphoma patients with hypermethylation of the p15 and/or MGMT genes had a higher clinical stage of the disease (IV - V). We show the association of anemia and/or thrombocytopenia with the hypermethylation of the p15 gene, ascribing the p15 gene as a potential prognostic marker in B-NHL. Comethylation of MGMT with the p15 gene represents a novel finding and presents both genes as candidates for future studies of the hypermethylation profiles of B-NHL.
Creatinine

Purpose of reviewTo summarize the history and current findings for creatinine as a renal biomarker and try to predict its future, looking at new biomarkers for kidneys (neutrophil gelatinase-associated lipocalin and cystatin C) and comparing current development to other diseases (troponins and procalcitonin). Recent findingsIn general, biomarkers are used for diagnosis, severity classification, outcome prediction, and most importantly, outcome modification. Creatinine can be used for the first three (except for outcome modification). Multiple clinical studies have shown that new renal biomarkers, especially neutrophil gelatinase-associated lipocalin and cystatin C, can diagnose acute kidney injury more rapidly and accurately, have a better relationship with disease severity, and predict outcome of patients with acute kidney injury more accurately, than creatinine. However, to prove the true superiority of the new renal biomarkers to creatinine, more clinical studies will be required. Such studies include interventional ones that can improve outcome (especially mortality) of patients with acute kidney injury and ones showing relationship of the markers with beneficial effects of specific interventions. SummaryUnless enough evidence accumulates, considering the history, familiarity, and recent findings related to outcome, creatinine will continue to be used and dominate in clinical practice.
Spatial distribution of interstitial assemblages in the floodplain of the rhǒne river

Interstitial invertebrate assemblages of the Rhǒne River were studied at the scale of the entire alluvial plain. Ten stations, located in five former channels, were sampled with a Bou-Rouch pump at 50 and 100 cm depth. The chemical characteristics of the interstitial water allowed the differentiation of stations without hydrological connections with the subterranean habitats, stations fed by surface water coming through the bank sediments and stations fed by true groundwater. The faunal assemblages reflect the difference between connected and isolated stations but did not demonstrate any differences related to the origin of the water. In fact the interstitial assemblages are distributed along a gradient from the margin of the floodplain (stations with a high physical stability associated with the absence of flood periods) to the area close to the main channel regularly influenced by floods. These results demonstrate that both groundwater characteristics and the position of the station in the floodplain influence the spatial distribution of interstitial fauna in the alluvial valley of the Rhǒne River.
Expressions of B7-H4 and B7-H3 Proteins and Effect of Sorafenib on their Expressions in Different Human Hepatoma Cell Lines

Purpose : To study whether B7-H3 and B7-H4 proteins can be candidate drug targets for preventing and treating hepatoma. Methods : Western blot assay was used to study the expressions of B7-H3 and B7-H4 proteins and the effect of sorafenib on their expressions in different human hepatoma cell lines (HepG2, Hep3B, BEL- 7402, BEL-7404, BEL-7405, QGY-7701, QGY-7703, SMMC-7721, MHCC97H, MHCC97L, HCCLM3 and HCCLM6). 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was used to study the cytotoxicity of sorafenib against different human hepatoma cell lines. Results : The expressions of B7-H3 (0.26 - 0.84 μM) and B7-H4 (0.18 - 0.78 μM) proteins in different human hepatoma cell lines were significantly (p < 0.01) up-regulated, compared with that of the normal human liver cell line (HL-7702) (0.09 and 0.08 μM). Sorafenib was cytotoxic on Hep3B, BEL-7404, MHCC97H, HCCLM3 and HCCLM6 cells with half-maximal inhibitory concentration (IC 50 ) of 14.56, 9.14, 9.46, 17.21 and 9.29 μM, respectively. After treatment with sorafenib at concentrations of 5, 10 and 20 μM, the expressions of B7-H3 protein in MHCC97H, HCCLM3 and HCCLM6 cells and the expressions of B7-H4 protein in Hep3B, BEL-7404 and MHCC97H cells were significantly (p < 0.01) down-regulated, compared with that of the control. Conclusion : Over-expression of B7-H3 and B7-H4 proteins is common in different human hepatoma cell lines and thus, B7-H3 and B7-H4 proteins may be regarded as candidate drug targets for preventing and treating hepatoma. Keywords : Hepatoma, B7-H3, B7-H4, Sorafenib, Over-expression, Cytotoxic activity, Down-regulation
Practice parameter: Management of dementia (an evidence-based review): Report of the Quality Standards Subcommittee of the American Academy of Neurology

Objective To define and investigate key issues in the management of dementia and to make literature-based treatment recommendations. MethodsThe authors searched the literature for four clinical questions: 1) Does pharmacotherapy for cognitive symptoms improve outcomes in patients with dementia? 2) Does pharmacotherapy for noncognitive symptoms improve outcomes in patients with dementia? 3) Do educational interventions improve outcomes in patients and/or caregivers? 4) Do other nonpharmacologic interventions improve outcomes in patients and/or caregivers? ResultsCholinesterase inhibitors benefit patients with AD (Standard), although the average benefit appears small; vitamin E likely delays the time to clinical worsening (Guideline); selegiline, other antioxidants, anti-inflammatories, and estrogen require further study. Antipsychotics are effective for agitation or psychosis in patients with dementia where environmental manipulation fails (Standard), and antidepressants are effective in depressed patients with dementia (Guideline). Educational programs should be offered to family caregivers to improve caregiver satisfaction and to delay the time to nursing home placement (Guideline). Staff of long-term care facilities should also be educated about AD to minimize the unnecessary use of antipsychotic medications (Guideline). Behavior modification, scheduled toileting, and prompted voiding reduce urinary incontinence (Standard). Functional independence can be increased by graded assistance, skills practice, and positive reinforcement (Guideline).
Antagonism of Bacterial Extracellular Metabolites to Freshwater-Fouling Invertebrate Zebra Mussels, Dreissena polymorpha

We investigated the antagonism of indigenous bacteria isolated from stressed mussels and their extracellular metabolites on the adult zebra mussel, Dreissena polymorpha. Selective bacterial isolates including Aeromonas media, A. salmonicida, A. veronii, and Shewanella putrefaciens, showed strong lethality against adult mussels and 100% mortality was observed within 5 days of incubation. Bacterial metabolites, fractionated and concentrated from stationary-phase culture supernatants of these bacterial isolates, displayed varying degrees of antagonistic effects on zebra mussels. Among the three size fractions examined, 10 kDa, the most lethal fraction seems to be >10 kDa for three of the four isolates tested. Further chemical analyses of these size fractions revealed that the predominant constituents were polysaccharides and proteins. No 2-keto-3-deoxyoctanoic acid (2-KDO), deoxyribonucleic acids (DNA) or uronic acid were detectable. Extraction of supernatants of two antagonistic isolates with polar solvent suggested that polar molecules are present in the active fraction. Our data suggest that extracellular metabolites produced by antagonistic bacteria are also involved in disease development in zebra mussels and elucidation of the mechanisms involved may offer a novel strategy for control of biofouling invertebrates.
A comparison of physiological, morphological and growth responses of 13 hybrid poplar clones to flooding

Summary Effects of a 30-day fl ooding period on some morphological and physiological changes and on relative growth rate (RGR) of 13 hybrid poplar clones, belonging to four different parentages i.e. T × N, T × D, D × N and N × E (with T = Popolus trichocarpa , N = P. nigra , D = P. deltoids and E = P. euramericana ) were studied under controlled conditions. Responses of the 13 clones to fl ooding differed, and they varied with duration of fl ooding period. Stomatal conductance was not reduced in any of the plants during the fi rst few days of fl ooding. However , in trees of some clones , stomata opened and then closed as fl ooding was prolonged. Net photosynthesis rates (Pn) of fl ooded trees of some clones decreased during fl ooding, but in some fl ooded clones it returned to the value of the control following a period of decrease. RGR was reduced by fl ooding in 10 clones and was correlated with reduction of Pn. Other responses to fl ooding included formation of adventitious roots and relative amount of carbon allocated to the aboveand below-ground tissues. Based on the dendrogram from the hierarchical cluster analysis, the 13 clones tested could be divided into two groups. Clones 58-280, DN-34, 311-93, DN-70, Simplot, R-419 and OP-367 were grouped into a cluster with high tolerance to fl ooding; clones 309-74, PC-1, DN-14273, 195-529, NE-353 and R-247 into a cluster with low tolerance to fl ooding.
Identification of insilico 3D structure of amylase (Drosophila melanogaster) and comparative computational studies

Comparative studies are useful in the prediction of validated 3D structure of a query protein (Amylase). Modeler is used for structure prediction of amylase. All the structural models are verified by results of ramachandran plot, Whatif server, Prosa (ll) and Procheck (Checks the stereochemical quality of a protein structure, producing a number of postscript plots analyzing its overall and residue-by- residue geometry. Predicted and validated structure (after comparative study) is useful in structure based drug designing, protein-DNA interactions, study of protein-protein interactions and protein-ligand binding. Amylase is an enzyme that breaks down starch into sugar. Amylase is present in human saliva, where it begins the chemical process of digestion. The pancreas also makes amylase (alpha amylase) to break down dietary starch into disaccharides which are converted by other enzymes to glucose to supply the body with energy. There are 3 subunits of amylase, α, β and γ. A higher than normal concentration may reflect one of several medical conditions, including acute inflammation of the pancreas, macroamylasemia and perforated peptic ulcer, urine and blood amylase levels may also be elevated with a variety of other conditions, such as ovarian cancer, lung cancer, tubal pregnancy, mumps, intestinal obstruction, or perforated ulcers. Key words: Amylase, ramachandran plot, stereochemical, 3D structure, modeler.
WALLABY pre-pilot survey: Radio continuum properties of the Eridanus supergroup

Abstract We present the highest resolution and sensitivity $\sim$ $1.4\,$ GHz continuum observations of the Eridanus supergroup obtained as a part of the Widefield Australian Square Kilometer Array Pathfinder (ASKAP) L-band Legacy All-sky Blind surveY (WALLABY) pre-pilot observations using the ASKAP. We detect 9461 sources at 1.37 GHz down to a flux density limit of $\sim$ $0.1$ mJy at $6.1''\times 7.9''$ resolution with a median root mean square of 0.05 mJy beam $^{-1}$ . We find that the flux scale is accurate to within 5 % (compared to NVSS at 1.4 GHz). We then determine the global properties of eight Eridanus supergroup members, which are detected in both radio continuum and neutral hydrogen (HI) emission, and find that the radio-derived star formation rates (SFRs) agree well with previous literature. Using our global and resolved radio continuum properties of the nearby Eridanus galaxies, we measure and extend the infrared-radio correlation (IRRC) to lower stellar masses and inferred SFRs than before. We find the resolved IRRC to be useful for: (1) discriminating between active galactic nuclei and star-forming galaxies; (2) identifying background radio sources; and (3) tracing the effects of group environment pre-processing in NGC 1385. We find evidence for tidal interactions and ram-pressure stripping in the HI, resolved spectral index and IRRC morphologies of NGC 1385. There appears to be a spatial coincidence (in projection) of double-lobed radio jets with the central HI hole of NGC 1367. The destruction of polycyclic aromatic hydrocarbons by merger-induced shocks may be driving the observed WISE W3 deficit observed in NGC 1359. Our results suggest that resolved radio continuum and IRRC studies are excellent tracers of the physical processes that drive galaxy evolution and will be possible on larger sample of sources with upcoming ASKAP radio continuum surveys.
WhisperX: Time-Accurate Speech Transcription of Long-Form Audio

Large-scale, weakly-supervised speech recognition models, such as Whisper, have demonstrated impressive results on speech recognition across domains and languages. However, their application to long audio transcription via buffered or sliding window approaches is prone to drifting, hallucination&repetition; and prohibits batched transcription due to their sequential nature. Further, timestamps corresponding each utterance are prone to inaccuracies and word-level timestamps are not available out-of-the-box. To overcome these challenges, we present WhisperX, a time-accurate speech recognition system with word-level timestamps utilising voice activity detection and forced phoneme alignment. In doing so, we demonstrate state-of-the-art performance on long-form transcription and word segmentation benchmarks. Additionally, we show that pre-segmenting audio with our proposed VAD Cut&Merge strategy improves transcription quality and enables a twelve-fold transcription speedup via batched inference.