Miracle-dz/UniFAR-FTUs huggingface dataset:
Physico-chemical Meat Qualities of Loin and Top Round Beef from Holstein Calves with Different Slaughtering Ages

The objective of this study was to investigate the physico-chemical and sensory properties of loin (m. longissimus dorsi) and top round (m. semimembranosus) beef from 3-, 6-, 9-, and 12 mon-old Holstein calves. For both loin and top round muscles, the moisture contents were decreased, whereas the protein and fat contents were increased, as the slaughtering age increased. In terms of meat color, for both muscle types, CIE L* values were decreased, whereas CIE a* values and myoglobin content increased as the slaughtering age increased. pH values were significantly higher in the 3 mon-old group than in the other groups. The Warner–Bratzler shear force (WBSF) values were lowest for loin muscles from the 12 mon-old group; however, there was no significant difference for top round muscle among the 4 age groups. Cooking loss for both loin and top round muscles were significantly higher for the 3 mon-old group than for the other groups. The water holding capacity (WHC) of both muscles were highest for the 12 mon-old groups (p<0.05). In fatty acid composition of the 12 mon-old groups, loin muscles had significantly higher levels of C14:0, C16:1n7, C18:1n9, and mono-unsaturated fatty acids (MUFA), and top round muscles had significantly higher levels of C16:1n7, C18:1n7, C18:1n9, MUFA, MUFA/SFA. Loin muscle from the 3- and 12 mon-old groups had significantly higher scores for tenderness and overall likeness. Top round muscle from the 9- and 12 mon-old groups had significantly higher scores for overall likeness than those from the other age groups.
Emerald Article: Net neutrality and the value chain for video

AbstractPurpose – Video distribution over the internet leads to heated net-neutrality related debates betweennetwork operators and over-the-top application providers. The purpose of this paper is to analyze thisdebate from a new perspective that takes into account all of the assets that companies try to exploit inthe so-called battle for eyeballs in video distribution.Design/methodology/approach – The systematic value chain analysis is used to determine the pointsalong the value chain where net neutrality interacts with video distribution. The inputs to the analysis arethe existing and proposed policy measures for net neutrality in Europe and in the USA, and a number ofnet neutrality incidents that have led to discussions earlier.Findings – The paper ﬁnds that the current and proposed policy measures aimed at net neutrality eachcontribute to a certain extent to their intended effects. However, the analysis also shows that they arelikely to lead to new debates in other parts of the value chain, as players try to compensate the loss ofinﬂuence or revenue streams by rearranging the ways in which they exploit their assets.Practical implications – Further and new debates are expected in the areas of peering andinterconnection, distribution of resources between over-the-top and managed services and the role ofdevices with tightly linked search engines, recommendation systems and app stores.Originality/value – The new perspectives offered by our value-chain based analysis are valuable forpolicy makers who aim to promote net neutrality and simultaneously stimulate competition andinnovation throughout the value chain.Keywords Net neutrality, Value chain, Video distribution, Internet, Over-the-top, Regulation,Transparency, No blocking, Managed services, Europe, United States of AmericaPaper type Research paper
IGHV1-69-Encoded Antibodies Expressed in Chronic Lymphocytic Leukemia React with Malondialdehyde–Acetaldehyde Adduct, an Immunodominant Oxidation-Specific Epitope

The immunoglobulins expressed by chronic lymphocytic leukemia (CLL) B cells are highly restricted, suggesting they are selected for binding either self or foreign antigen. Of the immunoglobulin heavy-chain variable (IGHV) genes expressed in CLL, IGHV1-69 is the most common, and often is expressed with little or no somatic mutation, and restricted IGHD and IGHJ gene usage. We found that antibodies encoded by one particular IGHV1-69 subset, designated CLL69C, with the HCDR3 encoded by the IGHD3-3 gene in reading frame 2 and IGHJ6, specifically bound to oxidation-specific epitopes (OSE), which are products of enhanced lipid peroxidation and a major target of innate natural antibodies. Specifically, CLL69C bound immunodominant OSE adducts termed MAA (malondialdehyde–acetaldehyde-adducts), which are found on apoptotic cells, inflammatory tissues, and atherosclerotic lesions. It also reacted specifically with MAA-specific peptide mimotopes. Light chain shuffling indicated that non-stochastically paired L chain of IGLV3-9 contributes to the antigen binding of CLL69C. A nearly identical CLL69C Ig heavy chain was identified from an MAA-enriched umbilical cord phage displayed Fab library, and a derived Fab with the same HCDR3 rearrangement displayed identical MAA-binding properties. These data support the concept that OSE (MAA-epitopes), which are ubiquitous products of inflammation, may play a role in clonal selection and expansion of CLL B cells.
Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., Two New Alveolate Phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and Their Contributions to Reconstructing the Ancestral State of Alveolates and Eukaryotes

The evolutionary and ecological importance of predatory flagellates are too often overlooked. This is not only a gap in our understanding of microbial diversity, but also impacts how we interpret their better-studied relatives. A prime example of these problems is found in the alveolates. All well-studied species belong to three large clades (apicomplexans, dinoflagellates, and ciliates), but the predatory colponemid flagellates are also alveolates that are rare in nature and seldom cultured, but potentially important to our understanding of alveolate evolution. Recently we reported the first cultivation and molecular analysis of several colponemid-like organisms representing two novel clades in molecular trees. Here we provide ultrastructural analysis and formal species descriptions for both new species, Colponema vietnamica n. sp. and Acavomonas peruviana n. gen. n. sp. Morphological and feeding characteristics concur with molecular data that both species are distinct members of alveolates, with Acavomonas lacking the longitudinal phagocytotic groove, a defining feature of Colponema. Based on ultrastructure and molecular phylogenies, which both provide concrete rationale for a taxonomic reclassification of Alveolata, we establish the new phyla Colponemidia nom. nov. for the genus Colponema and its close relatives, and Acavomonidia nom. nov. for the genus Acavomonas and its close relatives. The morphological data presented here suggests that colponemids are central to our understanding of early alveolate evolution, and suggest they also retain features of the common ancestor of all eukaryotes.
Subarachnoid Hemorrhage-Induced Hydrocephalus in Rats

Background and Purpose— Hydrocephalus is an important complication of subarachnoid hemorrhage (SAH). We investigated the occurrence of acute hydrocephalus in a rat SAH model. Methods— SAH was induced by endovascular perforation in adult male Sprague-Dawley rats (n=36). Sham rats (n=8) underwent the same procedure without perforation. MRI was performed 24 hours after SAH and the volume of the ventricular system and extent of T2* hypointensity lesions were measured. We defined hydrocephalus as ventricular volume > +3 SDs above the mean in sham animals. SAH grade was determined and brains were used for histology, immunohistochemistry, Perls staining, and Western blot analysis. Ventricular wall damage was defined as percentage of ependymal surface disruption. Results— All surviving rats (n=27) after SAH had ventricular enlargement (33.6±4.7 versus 13.5±1.4 mm3 in sham animals, P<0.01). Ventricular volume correlated with SAH severity (r=0.48; P<0.05). Out of 27 SAH rats, 12 demonstrated hydrocephalus and all had intraventricular blood accumulation. Rats with hydrocephalus had more severe ventricular wall damage (7.4±1.2%) than the sham animals (0.6±0.2%; P<0.01) and rats without hydrocephalus (1.1±0.2%; P<0.01). Periventricular iron deposition was observed and heme oxygenase-1 and Iba-1 expression were markedly increased in hydrocephalus rats. Conclusions— SAH causes ventricular enlargement in a rat endovascular perforation model, with hydrocephalus occurring in 44% of animals at 24 hours. Rats with hydrocephalus had more severe SAH, intraventricular hemorrhage, and greater ventricular wall damage.
Hatching for Motion Picture Production

This paper presents a hatching algorithm which – while also allows for an implementation in real‐time – is integrated into the production pipeline of computer generated motion picture. Motion picture production pipelines impose special functional and quality requirements. From the functional point of view, the stages of modeling, 3D rendering, and compositing form a pipeline without feed‐back, and frames are rendered independently, possibly on different computers. Thus, no temporal data can be shared between them while flicker free animation needs to be generated. Quality requirements can be grasped as that of dual consistency: the generated hatching must consistently follow object movement and deformation, and, at the same time, it should have a consistent pattern and density in image‐space to provide the hand‐crafted look. In order to meet both requirements, we apply a particle based method and develop an image‐space density control mechanism using rejection sampling and low‐discrepancy sequences. We also discuss the decomposition of rendering tasks according to the main stages of the production pipeline and demonstrate how the artist can define the illustration style in a convenient way.
Social-demographics, health behaviors, and telomere length in the Mexican American Mano a Mano Cohort

In the current study, we examined cross-sectional associations among social-demographics, lifestyle behaviors, and relative telomere length (RTL) in peripheral blood leukocytes, as well as longitudinal relationships among major chronic diseases, weight gain, and RTL, among 12,792 Mexican Americans aged 20 to 85 years in the Mano-A-Mano, the Mexican American Cohort. As expected, RTL was inversely correlated with age (ρ=-0.15, ρ<0.001). In the multivariate analysis, we found that RTL was positively correlated with levels of education (ρ=0.021), self-insurance (ρ=0.041), body mass index (BMI) (ρ<0.001), and sleeping time per day (ρ for trend<0.001), and RTL was inversely correlated with sitting time per day (ρ for trend =0.001). In longitudinal analysis, we found that longer RTL was modestly but positively associated with increased risks of overall cancer (adjusted hazard ratio (adj.HR)=1.05, 95% conference interval (95%CI)=1.02-1.09). In quartile analysis, 4th quartile (longest RTL) was associated with 1.53-fold increased risk of overall cancer (adj.HR=1.53, 95%CI=1.11-2.10), compared to 1st quartile (shortest RTL). RTL was reversely associated with the risk of type-2 diabetes (adj.HR=0.89, 95%CI=0.82-0.94). In quartile analysis, 4th quartile (longest RTL) was associated with 48% decreased risk of typle-2 diabetes (adj.HR=0.52, 95%CI=0.32-0.70), compared to 1st quartile (shortest RTL). In addition, longer RTL was a positive predictor of at least 10% weight gain (adj.HR=1.03, 95%CI=1.00-1.05). In summary, our results in Mexican Americans support the notion that telomere length is a biological mechanism by which social demographics and health behaviors “get under the skin” to affect health.
Positive and Negative Symptoms of Schizotypy and the Five-Factor Model: A Domain and Facet Level Analysis

In this study, we investigated the Five-factor model in the concurrent prediction of positive symptom schizotypy as measured by the Magical Ideation (Eckblad & Chapman, 1983) and Perceptual Aberration (Chapman, Chapman, & Raulin, 1978) scales and negative symptom schizotypy as measured by the Physical Anhedonia (Chapman, Chapman, & Raulin, 1976) and Revised Social Anhedonia (Eckblad, Chapman, Chapman, & Mishlove, 1982; Mishlove & Chapman, 1985) scales. Previous studies suggest that these measures reflect the core symptoms found in schizotypal and schizoid personality disorder (Bailey, West, Widiger, & Freiman, 1993). Negative symptoms were significantly predicted by Neuroticism (+), Extraversion (-), Openness (-), and Agreeableness (-) domains of the Revised NEO Personality Inventory (NEO-PI-R; Costa & McCrae, 1992). Additionally, positive symptoms were significantly predicted by Neuroticism (+), Openness (+), and Agreeableness (-). In addition, we examined the validity of lower order traits in describing these symptoms of character pathology. These findings lend further support for the use of domain and facet scales of the NEO-PI-R in the identification of personality pathology.
Quantifying heterogeneity and dynamics of clonal fitness in response to perturbation

The dynamics of heterogeneous clonal lineages within a cell population, in aggregate, shape both normal and pathological biological processes. Studies of clonality typically relate the fitness of clones to their relative abundance, thus requiring long‐term experiments and limiting conclusions about the heterogeneity of clonal fitness in response to perturbation. We present, for the first time, a method that enables a dynamic, global picture of clonal fitness within a mammalian cell population. This novel assay allows facile comparison of the structure of clonal fitness in a cell population across many perturbations. By utilizing high‐throughput imaging, our methodology provides ample statistical power to define clonal fitness dynamically and to visualize the structure of perturbation‐induced clonal fitness within a cell population. We envision that this technique will be a powerful tool to investigate heterogeneity in biological processes involving cell proliferation, including development and drug response. J. Cell. Physiol. 230: 1403–1412, 2015. © 2015 Wiley Periodicals, Inc., A Wiley Company
Activity‐dependent excitability changes in normal and demyelinated rat spinal root axons.

Myelinated nerve fibres with a reduced safety factor for conduction due to demyelination are easily blocked by trains of impulses. To find out why, in vivo recordings from rat ventral root fibres demyelinated with diphtheria toxin have been supplemented with in vivo and in vitro recordings from normal fibres. Despite a small rise in extracellular potassium activity, normal fibres were invariably hyperpolarized by intermittent trains of impulses. This hyperpolarization resulted in an increase in threshold and also in an enhancement of the depolarizing after‐potential and the superexcitable period. Replacement of NaCl in the extracellular solution by LiCl completely blocked both the membrane hyperpolarization and the threshold increase which were normally observed during intermittent trains of impulses. At demyelinated nodes which were blocked by trains of impulses (10‐50 Hz), conduction block was preceded by a rise in threshold current and in an increase in internodal conduction time, but by no detectable reduction in the outward current generated by the preceding node. It was found possible to prevent the threshold from changing during a train by automatic adjustment of a d.c. polarizing current. This 'threshold clamp' prevented the conduction failure and virtually abolished the changes in internodal conduction time. The threshold changes were attributed to hyperpolarization, as in normal fibres, since (a) the polarizing current required to prevent them was always a depolarizing current, and (b) they were accompanied by an increase in superexcitability. The post‐tetanic depression that can follow continuous trains of impulses was attributed to the combination of increased threshold and enhanced superexcitable period due to hyperpolarization. It is concluded that the susceptibility of these demyelinated fibres to impulse trains is not due to a membrane depolarization induced by extracellular potassium accumulation but to a membrane hyperpolarization as a consequence of electrogenic sodium pumping.
Interventions for non-metastatic squamous cell carcinoma of the skin: systematic review and pooled analysis of observational studies

Objectives To assess the effects of treatments for non-metastatic invasive squamous cell carcinoma (SCC) of the skin using evidence from observational studies, given the paucity of evidence from randomised controlled trials. Design Systematic review of observational studies. Data sources Medline, Embase, to December 2012. Review methods Observational studies of interventions for primary, non-metastatic, invasive, SCC of the skin that reported recurrence during follow-up, quality of life, initial response to treatment, adverse events, cosmetic appearance, or death from disease. Studies were excluded if data for primary cutaneous SCC was not separable from other data. Data were extracted independently by two reviewers. Meta-analysis was performed where appropriate using a random effects model to estimate the pooled proportion of an event with 95% confidence intervals. Results 118 publications were included, covering seven treatment modalities. Pooled estimates of recurrence of SCCs were lowest after cryotherapy (0.8% (95% confidence interval 0.1% to 2%)) and curettage and electrodesiccation (1.7% (0.5% to 3.4%)), but most treated SCCs were small, low risk lesions. After Mohs micrographic surgery, the pooled estimate of local recurrence during variable follow-up periods from 10 studies was 3.0% (2.2% to 3.9%), which was non-significantly lower than the pooled average local recurrence of 5.4% (2.5% to 9.1%) after standard surgical excision (12 studies), and 6.4% (3.0% to 11.0%) after external radiotherapy (7 studies). After an apparently successful initial response of SCCs to photodynamic therapy, pooled average recurrence of 26.4% (12.3% to 43.7%; 8 studies) was significantly higher than other treatments. Evidence was limited for laser treatment (1 study) and for topical and systemic treatments (mostly single case reports or small non-comparative series with limited follow-up). Conclusions Many observational studies have looked at different treatment modalities for SCC, but the evidence base for the effectiveness of these interventions is poor. Comparison of outcomes after different treatments should be interpreted cautiously owing to biases inherent in the types of study included, and lack of direct comparisons to enable the estimation of relative treatment effect. Further evidence is needed to develop a prognostic model and stratify individuals at high risk of developing SCC, to improve the evidence base for this common cancer and to optimise clinical management. Protocol registration International Prospective Register of Systematic Reviews (PROSPERO) registration number CRD42011001450.
Gene regulatory network inference: A semi-supervised approach

Gene Regulatory Network (GRN) represents the regulatory interactions between genes. Experimental methods are capable of determining the nature of gene regulation in a given system, but are time-consuming and expensive. High-throughput technologies produce large number of gene expression data. These data along with additional information from heterogeneous data sources enable computational biologists to infer transcriptional gene regulations on genome-scale. Use of computational methods to infer gene regulatory networks from biological experimental data is a challenging task. Many studies have been conducted using unsupervised and supervised methods to achieve this task; however, such methods usually yield low prediction accuracy. The key issue of this problem is that, the negative training samples are not available for learning and the available positive training samples are insufficient. In this article, we propose a two-step semi-supervised method. First, a small number of reliable negative samples are extracted using clustering technique. Then, we utilize this negative samples for classification using an iterative procedure. We have applied this method to simulated as well as experimental gene expression dataset of Escherichia coli and evaluated the performance.
Impact of azacitidine before allogeneic stem-cell transplantation for myelodysplastic syndromes: a study by the Société Française de Greffe de Moelle et de Thérapie-Cellulaire and the Groupe-Francophone des Myélodysplasies.

PURPOSE To investigate the impact of prior-to-transplantation azacitidine (AZA) on patient outcome after allogeneic stem-cell transplantation (alloSCT) for myelodysplastic syndrome (MDS). PATIENTS AND METHODS Of the 265 consecutive patients who underwent alloSCT for MDS between October 2005 and December 2009, 163 had received cytoreductive treatment prior to transplantation, including induction chemotherapy (ICT) alone (ICT group; n = 98), AZA alone (AZA group; n = 48), or AZA preceded or followed by ICT (AZA-ICT group; n = 17). At diagnosis, 126 patients (77%) had an excess of marrow blasts, and 95 patients (58%) had intermediate-2 or high-risk MDS according to the International Prognostic Scoring System (IPSS). Progression to more advanced disease before alloSCT was recorded in 67 patients. Donors were sibling (n = 75) or HLA-matched unrelated (10/10; n = 88). They received blood (n = 142) or marrow (n = 21) grafts following either myeloablative (n = 33) or reduced intensity (n = 130) conditioning. RESULTS With a median follow-up of 38.7 months, 3-year outcomes in the AZA, ICT, and AZA-ICT groups were 55%, 48%, and 32% (P = .07) for overall survival (OS); 42%, 44%, and 29% (P = .14) for event-free survival (EFS); 40%, 37%, and 36% (P = .86) for relapse; and 19%, 20%, and 35% (P = .24) for nonrelapse mortality (NRM), respectively. Multivariate analysis confirmed the absence of statistical differences between the AZA and the ICT groups in terms of OS, EFS, relapse, and NRM. CONCLUSION With the goal of downstaging underlying disease before alloSCT, AZA alone led to outcomes similar to those for standard ICT.