Miracle-dz/UniFAR-FTUs huggingface dataset:
Cow Lying Behaviour and Bedding Quality Changes during Five Weeks on a Stand-Off Pad

Simple Summary New Zealand dairy farmers place cows in uncovered off-paddock facilities for a part (e.g., 18 h) of the day to reduce their impact on pasture during winter. Lying time is a key indicator of whether these hybrid pasture systems are meeting welfare requirements. While it is easy to measure lying time in a research setting using accelerometers, it is not yet common to measure it on farm, and more convenient indicators are needed. We investigated the lying behaviour of dairy cows as bedding quality deteriorated over a five-week period to determine what measures may be useful as farmer-friendly indicators of cow welfare. The daily lying time of the two groups of cows on bedding according to normal farm practice (NFP) declined over the five weeks and was significantly less than that of cows on fresh bedding during the last 10 days of the trial. The fresh woodchip bedding contained less than 65% moisture throughout the trial. By week 3 and week 4, the moisture content of the lying surface exceeded 75% for NFP Group 2 and Group1, respectively. A bedding moisture threshold of 75% assessed by a ‘gumboot score’ and cows lying rather than grazing when on pasture may be useful farmer-friendly indicators of cow welfare because of their relationship with reduced lying time. Abstract Bedding quality and cow lying time were measured during five weeks in a normal farm practice (NFP) off-paddock system with no bedding refreshment. Two groups of 100 non-lactating dairy cows were compared to groups of 8 cows with fresh bedding (FB). The cows were on a woodchip pad for 18 h/d at a space allowance of 5.4 m2/cow, with 6 h/d on pasture for 5 weeks. Lying times were recorded continuously for 60 cows per group using accelerometers. Bedding moisture content was measured weekly. Data for each NFP group were analysed and compared with those of their respective FB group using repeated measures. The lying time declined over five weeks from 11.6 h/day during the first week to 5.6 h/day during the fifth week (SED = 0.3; F1,25 = 351.56; p < 0.001). The moisture content of the bedding increased over the five weeks and was significantly higher for both NFP groups (NFP Group 1: F5,59 = 8.33; p < 0.001; NFP Group 2: F5,61 = 5.54; p < 0.001) than those of the respective FB groups. The percentage of total time lying when in the paddock increased for the NFP groups, reaching 15% in the last week of the trial. During five weeks on a stand-off pad, bedding quality deteriorated, and cows lay down less, to such an extent that welfare was compromised.
Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs

ABSTRACT To investigate the dynamics of circRNA expression in pig testes, we designed specific strategies to individually study circRNA production from intron lariats and circRNAs originating from back-splicing of two exons. By applying these methods on seven Total-RNA-seq datasets sampled during the testicular puberty, we detected 126 introns in 114 genes able to produce circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparing our RNA-seq datasets to datasets from the literature (embryonic cortex and postnatal muscle stages) revealed highly abundant intronic and exonic circRNAs in one sample each in pubertal testis and embryonic cortex, respectively. This abundance was due to higher production of circRNA by the same genes in comparison to other testis samples, rather than to the recruitment of new genes. No global relationship between circRNA and mRNA production was found. We propose ExoCirc-9244 (SMARCA5) as a marker of a particular stage in testis, which is characterized by a very low plasma estradiol level and a high abundance of circRNA in testis. We hypothesize that the abundance of testicular circRNA is associated with an abrupt switch of the cellular process to overcome a particular challenge that may have arisen in the early stages of steroid production. We also hypothesize that, in certain circumstances, isoforms and circular transcripts from different genes share functions and that a global regulation of circRNA production is established. Our data indicate that this massive production of circRNAs is much more related to the structure of the genes generating circRNAs than to their function. Abbreviations: PE: Paired Ends; CR: chimeric Read; SR: Split Read; circRNA: circular RNA; NC: non conventional; ExoCirc-RNA: exonic circular RNA; IntroLCirc-: name of a porcine intronic lariat circRNA; ExoCirc-: name of a porcine exonic circRNA; IntronCircle-: name of a porcine intron circle; sisRNA: stable intronic sequence RNA; P: porcine breed Pietrain; LW: porcine breed Large White; RT: reverse transcription/reverse transcriptase; Total-RNA-seq: RNA-seq obtained from total RNA after ribosomal depletion; mRNA-seq: RNA-seq of poly(A) transcripts; TPM: transcripts per million; CR-PM: chimeric reads per million; RBP: RNA binding protein; miRNA: micro RNA; E2: estradiol; DHT: dihydrotestesterone
HIV in Young Men Who Have Sex with Men: A Review of Epidemiology, Risk and Protective Factors, and Interventions

Epidemiological studies have found that young men who have sex with men (YMSM) represent the majority of young people infected with HIV annually in the United States. Further, they are one of the few risk groups to show an increase in the rate of infections in recent years. In addition to these disparities in prevalence and infection rates, there is an inequity in prevention and intervention research on this population. The purpose of this article is to review the existing YMSM literature on HIV epidemiology, correlates of risk, and intervention research. The article concludes that promising future directions for basic research include a focus on multiple clustering health issues, processes that promote resiliency, the role of family influences, and the development of parsimonious models of risk. In terms of intervention research, the article suggests that promising future directions include Internet-based intervention delivery, integration of biomedical and behavioral approaches, and interventions that go beyond the individual level to address partnership, structural, community, and network factors.
The role of routine nasolacrimal sac biopsy during endoscopic dacryocystorhinostomy

Most patients who undergo endoscopic dacryocystorhinostomy (DCR) have a diagnosis of idiopathic nasolacrimal duct obstruction. The purpose of this study was to examine the impact of routine biopsy of the lacrimal sac performed at time of DCR on subsequent patient diagnosis and treatment.
Influence of culture and age on the self-reference effect

ABSTRACT Relating information to oneself can enhance memory for young and older adults. However, most studies investigating self-referencing have focused on Western populations, for whom the self is considered an independent and distinct entity. Whether self-referencing as a mnemonic strategy similarly benefits East Asians, cultures associated with interdependent self-construal, has been investigated little, particularly with age. In this study, we investigated the effect of self-reference on memory for both younger and older adults from American and Taiwanese cultures, predicting that self-referencing would be a less effective strategy for younger and older adults from Taiwan compared to Americans. Results reveal some cultural differences with age, with Taiwanese older adults benefitting less from self-referencing than younger Taiwanese, though the effect did not differ with age for Americans, or between younger adults across cultures. Thus, our results suggest that the potential mnemonic benefits of self-referencing may be limited in older adults from Eastern cultures.
Gender-specific associations of malocclusion traits with oral health-related quality of life in a Finnish adult population.

AIM The aim of this cross-sectional study was to investigate gender-specific associations of different malocclusion traits with oral health-related quality of life (OHRQoL) among Finnish adults. MATERIAL AND METHODS The study material comprised 1885 subjects from the Northern Finland Birth Cohort 1966. A clinical oral examination including registration of occlusion was carried out in connection with a 46-year follow-up examination. The 14-item Oral Health Impact Profile (OHIP-14) was used to measure OHRQoL. Subgroups with increased/decreased overjet, deep bite, open bite, lateral crossbite, and scissor bite were selected for further analysis. Subjects with normal occlusion were selected to form the normal occlusion group. Differences between subgroups and the normal occlusion group were evaluated for both genders separately. Education, number of teeth, caries, and orthodontic treatment history were chosen as confounding variables. Multivariate Poisson regression analyses were conducted to assess the effect of independent variables on OHRQoL. RESULTS After adjustments, decreased overjet, open bite, and scissor bite were associated with higher OHIP severity in women (P < 0.01). In men, deep bite was associated with higher OHIP severity (P = 0.007). Different malocclusion traits had associations with some OHIP dimension either in men or women. Orthodontic treatment history had a positive effect on OHRQoL in both genders. CONCLUSION The associations of malocclusion traits with OHRQoL differed between genders, with women reporting more impacts. Deviations from normal occlusion were generally found to have a negative impact on OHRQoL, but most of the adults with malocclusion seem to adapt to their condition.
Comparative Evaluation Of Diametral Tensile Strength Of Phosphate Bonded Investment Materials After Drying By Various Methods”–An Invitro Study

The study is to evaluate and compare the Diametral Tensile strength of Phosphate bonded Investment materials (Wirovest, Cromocasting Fast and Accuvest) after drying by Air dried method, Conventional Hot air oven method and Microwave oven method.A total of 90 cylindrical specimens were prepared from three different commercially available phosphate bonded investment materials. Thus 30 samples for each material were prepared and 10 of each were Air dried for 60 minutes, 10 were dried in a Conventional Hot air oven for 60 minutes at 265℃ to 300℃ and 10 were dried in Microwave oven with 600 watts t frequency of 2450 MHz for 10 minutes. All the samples were subjected to diametral compression test using a computer coordinated Universal testing machine at 2 hour interval at a crosshead speed of 0.5 cm/min.The results illustrate that the method of Microwave drying of the samples of all the materials could withstand high compressive loads when compared to the other two methods i.e., Air dried and Hot air oven dried methods respectively. And the material Wirovest is considered to be the one with high diametral tensile strengths of all the compared phosphate bonded investment materials.Within the limitations of this study, the Mean Diametral tensile strengths of the Microwave oven dried samples were highest, followed by the Hot air oven dried samples and Air dried samples. The Mean Diametral tensile strengths of the Wirovest material show highest values than Cromocasting fast investment material and Accuvest material.
Serum Iron Levels and Copper-to-Zinc Ratio in Sickle Cell Disease

Background and Objectives: Altered copper and zinc homeostasis may influence the antioxidant defense system and consequently lead to oxidative stress and associated complications in sickle cell disease (SCD) patients. Iron levels have been reported to increase in sickle cell patients due to frequent blood transfusion, chronic intravenous haemolysis and increased absorption of iron from the gastrointestinal tract. These elevated levels of iron may also lead to extensive oxidative damage. The current study evaluated serum levels of iron, copper and zinc in SCD patients and “healthy” controls. Materials and Methods: The study was a cross-sectional one, comprising 90 SCD patients with Haemoglobin SS and Haemoglobin SC genotypes and 50 HbAA “healthy” controls. Serum levels of iron, copper and zinc were measured using a Flame Atomic Absorption Spectrometer (Variant 240FS manufactured by VARIAN Australia Pty Ltd, VIC, Australia). Copper and zinc ratios were calculated and analyzed. Results: Serum levels of iron and copper were significantly elevated in the SCD patients, compared to their “healthy” counterparts (p < 0.001). These levels were further increased in patients with haemoglobin SS in vaso-occlusive crises (HbSS VOCs). Serum zinc levels were, however, significantly lower in the SCD patients, particularly during vaso-occlusion. The copper-to-zinc ratio was also found to be significantly higher in the SCD patients. Conclusion: Elevated copper-to-zinc ratio may be a biomarker of sickle cell oxidative stress and associated complications. The ratio may also be informative for the management of sickle cell oxidative burden. The significantly lower levels of zinc in the SCD patients may warrant zinc supplementation.
Correlation between the motility of the proximal antrum and the high‐frequency power of heart rate variability in freely moving rats

Cardiac vagal tone can be monitored non‐invasively via electrocardiogram measurements of the high‐frequency power spectrum of heart rate variability (HF‐HRV). Vagal inputs to the upper GI tract are cumbersome to measure non‐invasively. Although cardiac and GI vagal outputs arise from distinct brainstem nuclei, the nucleus ambiguus, and the dorsal motor nucleus of the vagus, respectively, we aim to test the hypotheses that in freely moving rats HF‐HRV power is correlated to proximal antral motility and can be altered by high levels of circulating estrogen and vagal‐selective treatments known to affect antral motility.
A national survey on routines regarding sedation in Swedish intensive care units

Abstract Background: Previous studies concerning sedation in Swedish intensive care units (ICU) have shown variability in drug choices and strategies. Currently, there are no national guidelines on this topic. As an update to a Nordic survey from 2004, and as a follow-up to a recently introduced quality indicator from the Swedish Intensive Care Registry, we performed a national survey. Methods: A digital survey was sent to the ICUs in Sweden, asking for sedation routines regarding hypnosedatives, analgosedatives, protocols, sedation scales, etc. Results: Fifty out of 80 ICUs responded to the survey. All units used sedation scales, and 88% used the RASS scale; 80% used written guidelines for sedation. Propofol and dexmedetomidine were the preferred short-term hypnosedatives. Propofol, dexmedetomidine, and midazolam were preferred for long-term hypnosedation. Remifentanil, morphine, and fentanyl were the most frequently used agents for analgosedation. Conclusions: All ICUs used a sedation scale, an increase compared with previous studies. Concerning the choice of hypno- and analgosedatives, the use of dexmedetomidine, clonidine, and remifentanil has increased, and the use of benzodiazepines has decreased since the Nordic survey in 2004.
Topac: Alignment of gene Regulatory Networks Using Topology-Aware Coloring

We consider the problem of finding a subnetwork in a given biological network (i.e. target network) that is most similar to a given small query network. We aim to find the optimal solution (i.e. the subnetwork with the largest alignment score) with a provable confidence bound. There is no known polynomial time solution to this problem in the literature. Alon et al. has developed a state-of-the-art coloring method that reduces the cost of this problem. This method randomly colors the target network prior to alignment for many iterations until a user-supplied confidence is reached. Here we develop a novel coloring method, named k-hop coloring (k is a positive integer), that achieves a provable confidence value in a small number of iterations without sacrificing the optimality. Our method considers the color assignments already made in the neighborhood of each target network node while assigning a color to a node. This way, it preemptively avoids many color assignments that are guaranteed to fail to produce the optimal alignment. We also develop a filtering method that eliminates the nodes that cannot be aligned without reducing the alignment score after each coloring instance. We demonstrate both theoretically and experimentally that our coloring method outperforms that of Alon et al., which is also used by a number network alignment methods, including QPath and QNet, by a factor of three without reducing the confidence in the optimality of the result. Our experiments also suggest that the resulting alignment method is capable of identifying functionally enriched regions in the target network successfully.
The Effects of Pavement Types on Soil Bacterial Communities across Different Depths

Pavements have remarkable effects on topsoil micro-organisms, but it remains unclear how subsoil microbial communities respond to pavements. In this study, ash trees (Fraxinus Chinensis) were planted on pervious pavement (PP), impervious pavement (IPP), and non-pavement (NP) plots. After five years, we determined the soil bacterial community composition and diversity by high-throughput sequencing of the bacterial 16S rRNA gene. The results of our field experiment reveal that the presence of pavement changed soil bacterial community composition and decreased the Shannon index, but had no impact on the Chao 1 at the 0–20 cm layer. However, we achieved the opposite result at a depth of 20–80 cm. Furthermore, there was a significant difference in bacterial community composition using the Shannon index and the Chao 1 at the 80–100 cm layer. Soil total carbon (TC), total nitrogen (TN), available phosphorus (AP), NO3−-N, and available potassium (AK) were the main factors that influenced soil bacterial composition and diversity across different pavements. Soil bacterial composition and diversity had no notable difference between PP and IPPs at different soil layers. Our results strongly indicate that pavements have a greater impact on topsoil bacterial communities than do subsoils, and PPs did not provide a better habitat for micro-organisms when compared to IPPs in the short term.
Effect of Alirocumab on Mortality After Acute Coronary Syndromes

whereas an association parameter >0 indicates that nonfatal and fatal event times are associated. Treatment effects on nonfatal and fatal events are summarized separately by HRs and corresponding 95% CIs. Point estimates and corresponding 95% CIs are also generated for association parameters. Additional details of the model are provided in the Methods in the online-only Data Supplement. To determine the association between baseline LDL-C and death, patients were classified according to baseline levels of LDL-C in prespecified categories of <80 mg/dL (2.07 mmol/L), 80 to <100 mg/dL (2.07 to <2.59 mmol/L), and ≥ 100 mg/ dL (2.59 mmol/L). To assess the relationship between LDL-C achieved on alirocumab at month 4 and the subsequent risk of death, a spline plot was created, with an HR of 1 set to the median value of achieved LDL-C in that treatment group. The latter analysis was performed post hoc and was adjusted for age, region, diabetes mellitus status, and baseline LDL-C.
Mantle Source Characteristics of Alkali Basalts and Basanites in an Extensional Intracontinental Plate Setting, Western Anatolia, Turkey: Implications for Multi-stage Melting

The alkaline volcanic province of Western Anatolia is characterized by intra-continental plate alkali olivine basalts and basanites extruded along localized extensional basins during Late Miocene (<11 Ma) to Quaternary (>0.13 Ma) time. The rocks are characterized by low 87Sr/86Sr (0.70311-0.70325) and high 143Nd/144Nd (0.51293-0.51298) ratios; they have OIB-like trace-element patterns characterized by enrichment in LILE, HFSE, and L-MREE, and a slight depletion in HREE relative to N-MORB. Trace-element modeling indicates that the mafic magmas formed by variable degrees (˜2% -10%) of partial melting of an isotopically homogenous garnet-bearing mantle source. The degree of melting decreased progressively from early-formed alkali olivine basalts to later basanites. Major- and trace-element systematics reveal two distinct depth ranges of melt segregation from the source mantle: (1) garnet and spinel + garnet stability zone for the Late Miocene rocks; and (2) spinel and spinel + garnet stability zone for the Quaternary rocks. Source concentrations, calculated using an inverse numerical method, show that the mantle from which the alkaline magmas were generated was enriched in all incompatible elements (e.g., LILE, HFSE, and LMREE) relative to depleted MORB mantle (DMM) and primitive mantle (PM) compositions. The isotopically depleted nature of the alkaline rocks relative to bulk silicate earth (BSE) further indicates that this enrichment is a recent event related to small-degree, multi-stage melting processes that involve local metasomatism of the mantle.
Preparation of Ion-Exchanged TEMPO-Oxidized Celluloses as Flame Retardant Products

Cellulose, as one of the most abundant natural biopolymers, has been widely used in textile industry. However, owing to its drawbacks of flammability and ignitability, the large-scale commercial application of neat cellulose is limited. This study investigated some TEMPO-oxidized cellulose (TOC) which was prepared by selective TEMPO-mediated oxidation and ion exchange. The prepared TOC was characterized by Fourier transform infrared (FT-IR) spectroscopy and solid-state 13C-nuclear magnetic resonance (13C-NMR) spectroscopy. The thermal stability and combustion performance of TOC were investigated by thermogravimetry analysis (TG), microscale combustion calorimetry (MCC) and limiting oxygen index (LOI). The results demonstrated that the thermal stability of TOC was less than that of the pristine material cellulose, but the peak of heat release rate (pHHR) and the total heat release (THR) of all TOC were significantly reduced. Additionally, the LOI values of all TOC products were much higher 25%. In summary, the above results indicated that the modified cellulose with carboxyl groups and metal ions by selective oxidation and ion exchange endows efficient flame retardancy.
Influence of Late Treatment on How Chronic Myeloid Leukemia Responds to Imatinib

INTRODUCTION In Brazil, patients with chronic myeloid leukemia (CML) in the chronic phase were not given first-line imatinib treatment until 2008. Therefore, there was a long period of time between diagnosis and the initiation of imatinib therapy for many patients. This study aims to compare the major molecular remission (MMR) rates of early versus late imatinib therapy in chronic phase CML patients. METHODS Between May 2002 and November 2007, 44 patients with chronic phase CML were treated with second-line imatinib therapy at the Hematology Unit of the Ophir Loyola Hospital (Belém, Pará, Brazil). BCR-ABL transcript levels were measured at approximately six-month intervals using quantitative polymerase chain reaction. RESULTS The early treatment group presented a 60% probability of achieving MMR, while the probability for those patients who received late treatment was 40%. The probability of either not achieving MMR within one year of the initiation of imatinib therapy or losing MMR was higher in patients who received late treatment (79%), compared with patients who received early treatment (21%, odds ratio=5.75, P=0.012). The probability of maintaining MMR at 30 months of treatment was 80% in the early treatment group and 44% in the late treatment group (P=0.0005). CONCLUSIONS For CML patients in the chronic phase who were treated with second-line imatinib therapy, the probability of achieving and maintaining MMR was higher in patients who received early treatment compared with those patients for whom the time interval between diagnosis and initiation of imatinib therapy was longer than one year.