Miracle-dz/UniFAR-FTUs huggingface dataset:
Treated Olive Cake as a Non-forage Fiber Source for Growing Awassi Lambs: Effects on Nutrient Intake, Rumen and Urine pH, Performance, and Carcass Yield

The objective of this study was to investigate the effects of partial replacement of wheat hay with sun-dried (SOC) or acid-treated SOC (ASOC) olive cake on nutrient intake and performance of Awassi lambs. An additional objective was to study the effects of acid treatment of olive cake (OC) on its chemical composition and nutritive value. On DM basis, sun-drying of OC did not dramatically affect its chemical composition. On the other hand, treating SOC with phosphoric acid decreased (p<0.05) SOC contents of neutral detergent fiber. Twenty seven male lambs (17.6±0.75 kg body weight) individually housed in shaded pens were randomly assigned to one of three dietary treatments (9 lambs/treatment). Dietary treatments were formulated to be isocaloric and isonitrogenous by replacing 50% of wheat hay in the control diet (CTL) with SOC or ASOC and to meet all nutrient requirements. Dietary treatments had no effects on nutrient intake or digestibility except for ether extract. Lambs fed the SOC diet had (p = 0.05) faster growth rate, greater final body weight, and greater total body weight gain in comparison with the CTL diet, but not different from the ASOC diet. Additionally, lambs fed the SOC diet had greater (p = 0.03) hot and cold carcass weights than the ASOC diet, but not different from the CTL diet. However, feed conversion ratios and dressing percentages were similar among dietary treatments. In conclusion, replacing half of dietary wheat hay with SOC improved performance of Awassi lambs with no detrimental effects on nutrients intake or digestibility. No further improvements in the nutritive value of SOC and lambs performance were detected when SOC was treated with acid.
G Protein–Coupled Receptor APJ and Its Ligand Apelin Act Downstream of Cripto to Specify Embryonic Stem Cells Toward the Cardiac Lineage Through Extracellular Signal-Regulated Kinase/p70S6 Kinase Signaling Pathway

Rationale: Pluripotent stem cells represent a powerful model system to study the early steps of cardiac specification for which the molecular control is largely unknown. The EGF-CFC (epidermal growth factor–Cripto/FRL-1/Cryptic) Cripto protein is essential for cardiac myogenesis in embryonic stem cells (ESCs). Objective: Here, we study the role of apelin and its G protein–coupled receptor, APJ, as downstream targets of Cripto both in vivo and in ESC differentiation. Methods and Results: Gain-of-function experiments show that APJ suppresses neuronal differentiation and restores the cardiac program in Cripto−/− ESCs. Loss-of-function experiments point for a central role for APJ/apelin in the gene regulatory cascade promoting cardiac specification and differentiation in ESCs. Remarkably, we show for the first time that apelin promotes mammalian cardiomyogenesis via activation of mitogen-activated protein kinase/p70S6 through coupling to a Go/Gi protein. Conclusions: Together our data provide evidence for a previously unrecognized function of APJ/apelin in the Cripto signaling pathway governing mesoderm patterning and cardiac specification in mammals.
Clonal Distribution of Superantigen Genes in Clinical Staphylococcus aureus Isolates

ABSTRACT Staphylococcus aureus is both a successful human commensal and a major pathogen. The elucidation of the molecular determinants of virulence, in particular assessment of the contributions of the genetic background versus those of mobile genetic elements (MGEs), has proved difficult in this variable species. To address this, we simultaneously determined the genetic backgrounds (spa typing) and the distributions of all 19 known superantigens and the exfoliative toxins A and D (multiplex PCR) as markers for MGEs. Methicillin- sensitive S. aureus strains from Pomerania, 107 nasal and 88 blood culture isolates, were investigated. All superantigen-encoding MGEs were linked more or less tightly to the genetic background. Thus, each S. aureus clonal complex was characterized by a typical repertoire of superantigen and exfoliative toxin genes. However, within each S. aureus clonal complex and even within the same spa type, virulence gene profiles varied remarkably. Therefore, virulence genes of nasal and blood culture isolates were separately compared in each clonal complex. The results indicated a role in infection for the MGE harboring the exfoliative toxin D gene. In contrast, there was no association of superantigen genes with bloodstream invasion. In summary, we show here that the simultaneous assessment of virulence gene profiles and the genetic background increases the discriminatory power of genetic investigations into the mechanisms of S. aureus pathogenesis.
Pattern of stress protein expression in human lung cell-line A549 after short- or long-term exposure to cadmium.

Exposure to cadmium is associated with the development of pulmonary damage such as emphysema and lung cancer. This metal is also a powerful inducer of stress proteins in many biologic models. The present study was undertaken to evaluate whether an overexpression of the heat shock protein (hsp)72 stress protein, which indicates repair of damaged proteins, could be a sensitive and early biomarker of environmental pollution by Cd. In comparative studies, we examined the effects of exposure to Cd (as CdCl(2)) on the growth rate of the A549 pulmonary cell line, and (by Western blot analyses) on the induction of the hsp72 stress protein and metallothioneins (MTs). CdCl(2) exposure was studied for periods of 2 hr to 1 month. For short-term exposure (2-6 hr) to Cd concentrations higher than 50 microM, an overexpression of hsp72 appeared 6 hr later, suggesting that hsp72 might be considered an early biomarker of acute exposure to Cd. For exposures lasting more than 4 days, lower doses of Cd (0.1-10 microM) similar to levels encountered in occupational exposure induced a significant increase of the hsp72 level. Because the increase of hsp72 occurs for doses that did not affect cell proliferation, our work supports the idea that its overexpression might be used as a sensitive indicator of occupational exposure to Cd. However, increased resistance to Cd appeared in A549 cells exposed for 1 month and overexpression of hsp72 disappeared simultaneously. It is possible that, in vivo, cell adaptation also occurs throughout chronic exposure to Cd, with a decrease of hsp induction as a consequence. A dose-related increase of MTs was found after 4 days of exposure to Cd concentrations ranging from 0.1 to 10 microM without change of overexpression during chronic exposure, suggesting that MT expression could be a more constant indicator of Cd pollution. Because 0.1 microM Cd (11 microg/L) induces hsp72 expression, showing the presence of damaged proteins, our work suggests that the maximum allowable biologic exposure limit should be lowered. ImagesFigure 1Figure 2Figure 3Figure 4Figure 5Figure 6Figure 7Figure 8Figure 9Figure 10
Relevant analyses of pathogenic bacteria and inflammatory factors in neonatal purulent meningitis

Pathogenic bacteria and inflammatory factors in neonatal purulent meningitis (PM) were investigated to explore the diagnostic value of inflammatory factors in PM, to clarify the etiology, and to provide evidence for rational clinical treatment. Seventy-four neonates who were diagnosed with PM and were bacteriogically positive in Daqing Longnan Hospital from January 2012 to December 2015 were retrospectively analyzed and used as observation group. Another 74 neonates simultaneously hospitalized with non-PM factors were selected as control group. The levels of C-reactive protein (CRP) and β 2 microglobulin (β2MG) in cerebrospinal fluid in pediatric patients were measured, and the separation culture and identification of pathogenic bacteria were carried out at the same time. The results showed that i) neonatal PM often lacked specific clinical manifestations; ii) high risk factors of neonatal PM included gestational age, body weight <2,500 g, neonatal asphyxia, premature rupture of membranes, and umbilical or pulmonary infection; iii) the levels of CRP and β2MG in the cerebrospinal fluid in the neonatal PM group were significantly higher than those in the control group (P<0.05), and the neonatal PM group had obviously decreased levels of CRP and β2MG in the cerebrospinal fluid after treatment compared with those before treatment (P<0.05); iv) the positive rate of Gram-negative bacilli (G-bacilli) showed an increasing trend year by year in the past 4 years. Seventy-four strains of bacteria were isolated from the cerebrospinal fluid in neonatal PM group, including 45 strains of Gram-positive cocci (G+cocci, accounting for 60.81%) and 29 strains of G-bacilli (accounting for 39.19%). Among them, the top three were Escherichia coli, coagulase-negative staphylococci (CNS) and Streptococcus. These findings indicated that for suspected PM pediatric patients with high risk factors, the inflammatory factors in cerebrospinal fluid and the etiology should be investigated via lumbar puncture as early as possible to confirm the diagnosis. Pathogenic bacteria of meningitis mainly are Escherichia coli, CNS and Streptococcus, and the characteristics of pathogenic bacteria should be considered during experiential medication. The incidence rate of PM due to Streptococcus has an upward tendency and great damage, needing to arouse high attention in clinic.
Assessing Sentiment Strength in Words Prior Polarities

Many approaches to sentiment analysis rely on lexica where words are tagged with their prior polarity - i.e. if a word out of context evokes something positive or something negative. In particular, broad-coverage resources like SentiWordNet provide polarities for (almost) every word. Since words can have multiple senses, we address the problem of how to compute the prior polarity of a word starting from the polarity of each sense and returning its polarity strength as an index between -1 and 1. We compare 14 such formulae that appear in the literature, and assess which one best approximates the human judgement of prior polarities, with both regression and classification models.
Managing an Assemble-to-Order System with Returns

We consider a multiproduct assemble-to-order (ATO) system, in which inventory is kept only at the component level and the finished products are assembled in response to customer demands. In addition to stochastic demand for finished products, the system experiences stochastic returns of subsets of components, which can then be used to satisfy subsequent demands. The system is managed over an infinite horizon using a component-level base-stock policy. We identify several ways in which returns complicate the behavior of the system, and we demonstrate how to handle these additional complexities when calculating or approximating key order-based performance metrics, including the immediate fill rate, the fill rate within a time window, and average backorders. We also present a method for computing a near-optimal base-stock policy. We use these results to address managerial questions on both operational and product-design levels. For example, we find that tracking product-based (as opposed to component-based) return information appears to provide much less value than tracking product-based demand information, and we explore the impact of the number of products, component lead times, and different patterns of component returns (joint versus independent returns, returns of common versus dedicated components) on the value of component commonality.
Biodiversity Offsets: A Cost-Effective Interim Solution to Seabird Bycatch in Fisheries?

The concept of biodiversity offsets is well established as an approach to environmental management. The concept has been suggested for environmental management in fisheries, particularly in relation to the substantial numbers of non-target species—seabirds in particular—caught and killed as incidental bycatch during fishing activities. Substantial areas of fisheries are being closed to protect these species at great cost to the fishing industry. However, other actions may be taken to offset the impact of fishing on these populations at lower cost to the fishing industry. This idea, however, has attracted severe criticism largely as it does not address the underlying externality problems created by the fishing sector, namely seabird fishing mortality. In this paper, we re-examine the potential role of compensatory mitigation as a fisheries management tool, although from the perspective of being an interim management measure while more long-lasting solutions to the problem are found. We re-model an example previously examined by both proponents and opponents of the approach, namely the cost effectiveness of rodent control relative to fishery area closures for the conservation of a seabird population adversely affected by an Australian tuna fishery. We find that, in the example being examined, invasive rodent eradication is at least 10 times more cost effective than area closures. We conclude that, while this does not solve the actual bycatch problem, it may provide breathing space for both the seabird species and the industry to find longer term means of reducing bycatch.
Category-specific visual responses : an intracranial study comparing gamma , beta , alpha , and ERP response selectivity

2009), attention (Lachaux et al., 2005; Tallon-Baudry et al., 2005), and different types of memory (Sederberg et al., 2006, 2007; van Vugt et al., 2010). Although spectral analysis has become a well-established technique in cognitive neuroscience, an important debate remains regarding whether low-amplitude GBR is more informative than high-amplitude intracerebral evoked response potentials (iERPs) as a neural marker of underlying mental processes. Reports often focus on either GBR or iERPs (Allison et al., 1994b; Halgren et al., 1994a,b, 1995a,b; McCarthy et al., 1999; Puce et al., 1999; Privman et al., 2007; Jacobs and Kahana, 2009) to reveal the high specificity of response to stimulation conditions, but recent studies combined both markers (Fisch et al., 2009; Engell and McCarthy, 2010). These markers show different stimulus response characteristics in terms of amplitude and latency, and it is still unknown whether they systematically reflect the same information processing. To investigate this issue, we decided to study the GBR patterns in relation to iERP and ABR amplitude in an experimental context requiring a high level of neuronal response specificity: visual object recognition. IntroductIon Several studies have shown that high-frequency neuronal activity in the brain is a marker of active information processing involved in perception, action, and cognition (Engel et al., 2001; Fell et al., 2001; Fries et al., 2001; Varela et al., 2001; Pesaran et al., 2002; Fries, 2009). Electroencephalography (EEG) and magnetoencephalography (MEG) have enabled observation of the behavior of this spectral signature in a variety of tasks, revealing its functional role not only in local neuronal processing but also in large-scale neuronal communication (Bauer et al., 2006). Other studies have turned to the high spatial resolution and high signal-to-noise ratio of intracerebral electroencephalography (iEEG) to describe fine amplitude modulations invisible to scalp EEG/MEG while preserving millisecond time resolution (Voytek et al., 2010). Recordings with these in cerebro implanted electrodes in humans have shown local broadband gamma activity modulated by visual perception (Lachaux et al., 2005; Canolty et al., 2006; Jacobs and Kahana, 2009), language processing (Canolty et al., 2006; Sahin et al., 2006; Jung et al., 2008; Lachaux et al., 2008; Mainy et al., 2008; Sahin et al., Category-specific visual responses: an intracranial study comparing gamma, beta, alpha, and ERP response selectivity
Sexual dysfunction: conceptual and measurement issues

Despite a standard classification and array of self-report questionnaires, there is little consensus about how to define and measure sexual dysfunction. Recently the debate has been influenced by the pharmaceutical industry, leading to an increasingly medicalised view of sexual difficulties. The aim of this thesis was to explore the meaning of sexual (dys)function to those who have and have not experienced sexual difficulties; and to use these meanings to create a conceptual model and population prevalence measure of sexual dysfunction for use in UK community surveys. Thirty-two semi-structured interviews were conducted with individuals recruited from a GP practice, an HIV/AIDS Charity and a Sexual Problems Clinic. The data were analysed using principles derived from Grounded Theory. Variation in individual meaning was expressed in terms of three distinct versions of functional sex - the erotic, the interpersonal and the mechanistic - which framed the purpose of sexual activity, the criteria determining ideal sex, and threats to this ideal. The data highlighted several coping strategies that individuals adopted when their lived reality failed to match their ideal: changing circumstances to fit goals, for instance by seeking a medical cure; changing goals to fit circumstances, for instance by lowering expectations; And living with the gap between ideal and actual experience, for instance by avoiding the problem. Choice of strategy and the likelihood of successful adjustment were influenced by the severity of the problem, causal attributions made about the problem, and the partnership context. Thirty-one potential components of a functioning sex life were identified from the data. Using evidence both from the literature and from this study, 12 of these components were selected for inclusion in a conceptual model of sexual function. This model was transformed into a 19-item draft prevalence measure of sexual dysfunction ready for psychometric testing and validation.
Prediction of coordination number and relative solvent accessibility in proteins

Knowing the coordination number and relative solvent accessibility of all the residues in a protein is crucial for deriving constraints useful in modeling protein folding and protein structure and in scoring remote homology searches. We develop ensembles of bidirectional recurrent neural network architectures to improve the state of the art in both contact and accessibility prediction, leveraging a large corpus of curated data together with evolutionary information. The ensembles are used to discriminate between two different states of residue contacts or relative solvent accessibility, higher or lower than a threshold determined by the average value of the residue distribution or the accessibility cutoff. For coordination numbers, the ensemble achieves performances ranging within 70.6–73.9% depending on the radius adopted to discriminate contacts (6Å–12Å). These performances represent gains of 16–20% over the baseline statistical predictor, always assigning an amino acid to the largest class, and are 4–7% better than any previous method. A combination of different radius predictors further improves performance. For accessibility thresholds in the relevant 15–30% range, the ensemble consistently achieves a performance above 77%, which is 10–16% above the baseline prediction and better than other existing predictors, by up to several percentage points. For both problems, we quantify the improvement due to evolutionary information in the form of PSI‐BLAST‐generated profiles over BLAST profiles. The prediction programs are implemented in the form of two web servers, CONpro and ACCpro, available at http://promoter.ics. uci.edu/BRNN‐PRED/. Proteins 2002;47:142–153. © 2002 Wiley‐Liss, Inc.
Identification of Alzheimer disease risk by functional magnetic resonance imaging.

BACKGROUND Functional magnetic resonance imaging plays a promising role in the preclinical characterization of Alzheimer disease (AD) for use in early diagnosis and in preventive drug trials. OBJECTIVE To determine whether functional magnetic resonance imaging can reliably distinguish risk groups for AD among cognitively normal middle-aged adults. DESIGN Cross-sectional case-control study. SETTING University of California, San Diego, Alzheimer Disease Research Center participants and San Diego community volunteers. PARTICIPANTS Twenty cognitively normal individuals (10 high risk and 10 low risk), aged 58 to 65 years, were divided into 2 groups based on the presence or absence of the apolipoprotein E epsilon4 allele and a positive family history of AD. MAIN OUTCOME MEASURES Word pairs were presented in a blocked design alternating between conditions of novel pairs, repeated pairs, and fixation. Whole-brain differences in blood oxygenation level-dependent brain responses between conditions were compared across risk groups. RESULTS Compared with the low-risk group, the high-risk group showed many areas of differential blood oxygenation level-dependent response in regions commonly associated with AD pathology (eg, the left medial temporal lobe). Furthermore, different patterns of association between left medial temporal lobe activity and memory performance were demonstrated. CONCLUSIONS Results support a theory of up-regulation in neuronal memory systems in people at risk for AD many years before the typical age at disease onset. They further demonstrate that functional magnetic resonance imaging is a viable technique to identify persons at risk for AD.
Noninvasive Quantitative In Vivo Mapping and Metabolism of Boronophenylalanine (BPA) by Nuclear Magnetic Resonance (NMR) Spectroscopy and Imaging

Abstract Bendel, P., Margalit, R. , Koudinova, N. and Salomon, Y. Noninvasive Quantitative In Vivo Mapping and Metabolism of Boronophenylalanine (BPA) by Nuclear Magnetic Resonance (NMR) Spectroscopy and Imaging. Radiat. Res. 164, 680–687 (2005). 10B-enriched l-p-boronophenylalanine (BPA) is one of the compounds used in boron neutron capture therapy (BNCT). In this study, several variations of nuclear magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) were applied to investigate the uptake, clearance and metabolism of the BPA-fructose complex (BPA-F) in normal mouse kidneys, rat oligodendroglioma xenografts, and rat blood. Localized 1H MRS was capable of following the uptake and clearance of BPA-F in mouse kidneys with temporal resolution of a few minutes, while 1H MRSI was used to image the BPA distribution in the kidney with a spatial resolution of 9 mm3. The results also revealed significant dissociation of the BPA-F complex to free BPA. This finding was corroborated by 1H and 11B NMR spectroscopy of rat blood samples as well as of tumor samples excised from mice after i.v. injection of BPA-F. This investigation demonstrates the feasibility of using 1H MRS and MRSI to follow the distribution of BPA in vivo, using NMR techniques specifically designed to optimize BPA detection. The implementation of such procedures could significantly improve the clinical efficacy of BNCT.