Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and crossbreeding parameters for incidence of recorded clinical lameness in New Zealand dairy cattle

AIM: To estimate genetic and crossbreeding parameters for the incidence of recorded clinical lameness in New Zealand dairy cattle. METHODS: Herd records from 76,357 cows, collected during the 2005/06 to 2008/09 milking seasons from 155 herds in the Livestock Improvement Corporation young sire progeny test scheme, were used to estimate genetic parameters and breed effects for incidence of recorded clinical lameness in HolsteinFriesian, Jersey and crossbred dairy cattle. Recorded clinical lameness was coded “1” for cows that presented at least one event of clinical lameness at any day during the season and “0” for unaffected cows. Genetic parameters were estimated using an animal model across breeds considering all and then only first lactation records. Heritability and repeatability of recorded clinical lameness were calculated from the variance component estimates both with and without logit transformation. RESULTS: The mean incidence of recorded clinical lameness per herd was 6.3 (min 2, max 34)%. The incidence of recorded clinical lameness in Holstein Friesian cows (mean 6.8, SE 0.24%) was higher than the incidence of recorded clinical lameness in crossbred (mean 6.1, SE 0.19%) and Jersey cows (mean 6.0, SE 0.28%) (p=0.0002). There was no difference in incidence between crossbred and Jersey cows (p=0.96). Estimates of the heritability of recorded clinical lameness as an untransformed trait were 0.053 (SE 0.014) for first lactation records and 0.016 (SE 0.003) for all lactation records. As a transformed (logit) trait heritabilities were 0.067 (SE 0.024) and 0.044 (SE 0.016) for first and all lactation records, respectively. The repeatability estimates of recorded clinical lameness were 0.071 (SE 0.005) and 0.107 (SE 0.011) for untransformed and logit transformed lactation records, respectively. Sire estimated breeding values for recorded clinical lameness showed the lowest values in Jersey sires, and ranged between -5 and 8%. CONCLUSIONS: Despite the low heritability of recorded clinical lameness, this study provided evidence that there is significant exploitable animal genetic variation. Selection of specific sires across and within breeds could be an option for increasing genetic resistance to lameness in New Zealand dairy cattle.
Associations between body condition, rumen fill, diarrhoea and lameness and ruminal acidosis in Australian dairy herds

AIMS: To investigate associations between ruminal acidosis and body condition score (BCS), prevalence of poor rumen fill, diarrhoea and lameness in dairy cows in New South Wales and Victoria, Australia. METHODS: This was a cross-sectional study conducted in 100 dairy herds in five regions of Australia. Feeding practices, diets and management practices of herds were assessed. Lactating cows within herds were sampled for rumen biochemistry (n = 8 per herd) and scored for body condition, rumen fill and locomotion (n = 15 per herd). The consistency of faecal pats (n = 20 per herd) from the lactating herd was also scored. A perineal faecal staining score was given to each herd. Herds were classified as subclinically acidotic (ACID), suboptimal (SO) and non-acidotic (Normal) when ≥3/8 cows per herd were allocated to previously defined categories based on rumen biochemical measures. Multivariate logistic regression models were used to examine associations between the prevalence of conditions within a herd and explanatory variables. RESULTS: Median BCS and perineal staining score were not associated with herd category (p >0.05). In the multivariate models, herds with a high prevalence of low rumen fill scores (≤2/5) were more likely to be categorised Normal than SO with an associated increased risk of 69% (p = 0.05). Herds that had a greater prevalence of lame cows (locomotion scores ≥3/5), had 103% higher risk of being categorised as ACID than SO (p = 0.034). In a multivariate logistic regression model, with herd modelled as a random effect, an increase of 1% of pasture in the diet was associated with a 5.5% increase in risk of high faecal scores (≥4/5) indicating diarrhoea (p = 0.001). CONCLUSIONS AND CLINICAL RELEVANCE: This study confirmed that herd categories based on rumen function are associated with biological outcomes consistent with acidosis. Herds that had a higher risk of lameness also had a much higher risk of being categorised ACID than SO. Herds with a high prevalence of low rumen scores were more likely to be categorised Normal than SO. The findings indicate that differences in rumen metabolism identified for herd categories ACID, SO and Normal were associated with differences in disease risk and physiology. The study also identified an association between pasture feeding and higher faecal scores. This study suggests that there is a challenge for farmers seeking to increase milk production of cows on pasture to maintain the health of cattle.
Association between placentome size, measured using transrectal ultrasonography, and gestational age in cattle

Abstract AIM: The aim of this study was to estimate whether fetal age could be accurately estimated using placentome size. METHODS: Fifty-eight cows with confirmed conception dates in two herds were used for the study. The length of the long axis and cross-sectional area of placentomes close to the cervix were measured once every 10 days between approximately 60–130 days of gestation and once every 15 days between 130–160 days of gestation. Four to six placentomes were measured using transrectal ultrasonography in each uterine horn. A linear mixed model was used to establish the factors that were significantly associated with log mean placentome length and to create an equation to predict gestational age from mean placentome length. Limits of agreement analysis was then used to evaluate whether the predictions were sufficiently accurate for mean placentome length to be used, in practice, as a method of determining gestational age. RESULTS: Only age of gestation (p<0.001) and uterine horn (p=0.048) were found to have a significant effect on log mean placentome length. From the three models used to predict gestational age the one that used log mean placentome length of all placentomes, adjusting for the effect of horn, had the smallest 95% limits of agreement; ±33 days. That is, predicted gestational age had a 95% chance of being between 33 days greater and 33.7 days less than actual age. This is approximately twice that reported in studies using measurement of fetal size. CONCLUSIONS: Measurement of placentomes near to the cervix using transrectal ultrasonography was easily achieved. There was a significant association between placentome size and gestational age, but between-cow variation in placentome size and growth resulted in poor agreement between placentome size and gestational age. CLINICAL RELEVANCE: Although placentomes can be easily visualised during diagnosis of pregnancy using transrectal ultrasonography, mean placentome size should not be used to estimate gestational age.
Formation of Axon‐dendrite polarity in situ: Initiation of axons from polarized and non‐polarized cells

Neurons are polarized cells that extend a single axon and several dendrites. Historically, how neurons establish their axon‐dendrite polarity has been extensively studied using dissociated hippocampal cells in culture. Although such studies have identified the cellular and molecular mechanisms underlying axon‐dendrite polarization, the conclusions have been limited to in vitro conditions. Recent progress using live imaging has enabled us to directly observe axon formation in situ, revealing distinct cellular mechanisms that regulate axon‐dendrite polarization in vivo. In this review, we compare the cellular events during axon formation studied in various systems both in vivo and in vitro and discuss possible common mechanisms underlying the axon‐dendrite polarization.
α‐lipoic acid inhibits high glucose‐induced apoptosis in HIT‐T15 cells

High blood glucose plays an important role in the pathogenesis of diabetes. α‐lipoic acid (LA) has been used to prevent and treat diabetes, and is thought to act by increasing insulin sensitivity in many tissues. However, whether LA also has a cytoprotective effect on pancreatic islet beta cells remains unclear. In this study, we assessed whether LA could inhibit apoptosis in beta cells exposed to high glucose concentrations. HIT‐T15 pancreatic beta cells were treated with 30 mmol/L glucose in the presence or absence of 0.5 mmol/L LA for 8 days. LA significantly reduced the numbers of apoptotic HIT‐T15 cells and inhibited the cell overgrowth normally induced by high glucose treatment. Additionally, LA inhibited insulin expression and secretion in HIT‐T15 cells induced by high glucose. Further study demonstrated that LA upregulated Pdx1 and Bcl2 gene expression, reduced Bax gene expression, and promoted phosphorylation of Akt in HIT‐T15 cells treated with high glucose. Intriguingly, knockdown of Pdx1 expression partially offset the anti‐apoptotic effect of LA. However, inhibition of Akt by PI3K/AKT antagonist LY294002 only slightly reversed the anti‐apoptosis effect of LA and mildly decreased the gene expression level of Pdx1 (P > 0.05). Moreover, LA only slightly attenuated reactive oxygen species (ROS) production and augmented mitochondrial membrane potential. Therefore, our data suggest that α‐lipoic acid can effectively attenuate high glucose‐induced HIT‐T15 cell apoptosis probably by increasing Pdx1 expression. These findings provide a new interpretation on the role of LA in the treatment of diabetes.
Effects of Spontaneous Breathing During Airway Pressure Release Ventilation on Cerebral and Spinal Cord Perfusion in Experimental Acute Lung Injury

Background Systemic-blood flow, cerebral-blood flow, and spinal cord blood flow can be affected by mechanical ventilation. We investigated the effect of spontaneous breathing on cerebral and spinal blood flow during airway pressure release ventilation (APRV) with and without spontaneous breathing. Methods Twelve pigs with oleic-acid-induced lung injury were ventilated with APRV with or without spontaneous breathing in random order. Without spontaneous breathing, either the upper airway pressure limit of mechanical ventilation or the ventilator rate was increased to maintain pH and PaCO2 constant. Systemic hemodynamic parameters were determined by the double indicator dilution method, cerebral and spinal cord blood flow was measured with colored microspheres. Statistics: ANOVA+Newmann-Keuls-test. Results As compared with APRV without spontaneous breathing and high tidal volume (VT) spontaneous breathing during APRV showed higher systemic blood flow and perfusion of the basal ganglia, frontal lobe, hippocampus, brain stem, temporal lobe, thalamus (all P<0.001), cerebellum, spinal cord (all P<0.01), and the central cortical region (P<0.05). During APRV without spontaneous breathing and low VT blood flow was lower in the basal ganglia, frontal lobe, hippocampus (all P<0.01), and temporal lobe (P<0.05) whereas perfusion of the thalamus, central cortical region, brain stem, cerebellum, and spinal cord were not different compared with APRV with spontaneous breathing. Conclusions In parallel with higher systemic blood flow regional cerebral and spinal cord blood flow were also higher when spontaneous breathing was maintained during APRV. The higher regional blood flow by maintaining spontaneous breathing was more pronounced when compared with full ventilatory support using high VT.
University of Birmingham Three-dimensional Gabor feature extraction for hyperspectral imagery classification using a memetic framework

Feature extraction based on three-dimensional (3D) wavelet transform is capable of improving the classiﬁcation accuracy of hyperspectral imagery data by simultaneously capturing the geometrical and statistical spectral-spatial structure of the data. Nevertheless, the design of wavelets are always proceeded with empirical parameters, which tends to involve a large number of irrelevant and redundant spectral-spatial features and results in suboptimal conﬁguration. This paper proposes a 3D Gabor wavelet feature extraction in a memetic framework, named M3DGFE, for hyper-spectral imagery classiﬁcation. Particularly, the parameter setting of 3D Gabor wavelet feature extraction is optimized using memetic algorithm so that discriminative and parsimonious feature set is acquired for accurate classiﬁcation. M3DGFE is characterized by an e ﬃ cient ﬁtness evaluation function and a pruning local search. In the ﬁtness evaluation function, a new concept of redundancy-free relevance based on conditional mutual information is proposed to measure the goodness of the extracted candidate features. The pruning local search is specially designed to eliminate both irrelevant and redundant features without sacriﬁcing the discriminability of the obtained feature subset. M3DGFE is tested on both pixel-level and image-level classiﬁcation using real-world hyperspectral remote sensing data and hyperspectral face data, respectively. The experimental results show that M3DGFE achieves promising classiﬁcation accuracy with parsimonious feature subset.
A cross-sectional survey on wounds in horses in New Zealand

Abstract AIM: To determine the frequency and type of skin wounds encountered by New Zealand veterinarians in their equine patients, the duration and estimated costs of treatment as well as the expected outcomes for these wounds. METHODS: An online survey was sent to all veterinarians registered with the New Zealand Equine Veterinary Association. The survey comprised questions on the location and experience of respondents, the number of wound-related cases in relation to the total equine caseload, the type and anatomical location of wounds treated, the frequency, duration and costs of treatments, the outcome of wound treatment and an estimate of the most common causes of death or euthanasia in their equine patients. RESULTS: The survey response rate was 110/262 (41.9%). The median number of equine cases seen by respondents was 20 (interquartile range (IQR) 6–60) per month; of these, five (IQR 2–10) were wound related. Wounds ranked third after lameness and respiratory disease for the relative frequency with which respondents encountered them. Of 102 respondents 59 (58%) reported that their clients frequently treated wounds incurred by their horse without consulting a veterinarian. Wounds on the distal limb, whether involving only the skin or also deeper structures, were reported by 86/101 (85%) respondents as the most frequently encountered. Wounds in this location also incurred the longest treatment period and were the most prone to develop complications. Finally, wounds ranked second, after colic, as the most common cause of death/euthanasia in the veterinary respondents’ equine patients. CONCLUSIONS: The data obtained via the survey indicate that skin wounds, particularly on the distal limb, are a common occurrence in horses in New Zealand and, when they involve structures underlying the skin, are costly and time-consuming to manage and may lead to decreased performance, retirement or euthanasia. Consequently, we recommend that more effort be devoted to the education of equine veterinarians and owners, and that appropriate research funds be allocated to help improve patient outcomes.
Rudimentary claws and pigmented nail-like structures on the distal tips of the digits of Wnt7a mutant mice: Wnt7A suppresses nail-like structure development in mice.

BACKGROUND As Wnt7a mutant mice exhibit double ventral structures in the digits of autopods, it has been accepted that dorsal-ventral identity in limb development is regulated by the Wnt7a signal. The most important evidence for this was the presence of surface pads, typical characteristics of ventral structures, on the dorsal side of digital tips and at the base of digits and their pigmentation. METHODS The morphologic features of the appendages on the distal tips of digits were inspected in the fore- and hindlimbs of mice having a different Wnt7a mutation. The digital structures were examined macroscopically and histologically. RESULTS The Wnt7a homozygous mutant mice with defects in postaxial digits had rudimentary claws or claws and pigmented nail-like structures, instead of dorsal pads, on the distal digital tips and hairs on the dorsal surface of the digits of fore- and hindlimbs. Furthermore, pigmented ectopic nail-like structures but not pads were also present on the dorsal surface of the base of digits. Double ventral structures were observed in the bones and tendons, excluding pads in digital areas. CONCLUSIONS These findings suggest that Wnt7a is not necessarily an exclusive dorsalizing signal to the dorsal ectoderm of the digital areas of autopods. Rather, the Wnt7a signal may participate in suppression of the development of pigmented nail-like structures in normal limb development. This means that even rodents, a species lower than primates in the evolution from claws to nails, have molecular potential to develop cutaneous appendages similar to nails at their location.
&bgr;2 Adrenergic-mediated Reduction of Blood Glutamate Levels and Improved Neurological Outcome After Traumatic Brain Injury in Rats

Background: Isoflurane-anesthetized rats subjected to traumatic brain injury (TBI) show a transient reduction in blood L-glutamate levels. Having previously observed that isoproterenol produces a sustained decrease in blood glutamate levels in naive rats, we investigated the possible effects of nonselective and selective &bgr;1 and &bgr;2 adrenergic agonists and antagonists both on blood glutamate levels and on the neurological outcomes of rats subjected to TBI. Methods: Rats received either 10 mL/kg of isotonic saline 1 hour after TBI, 50 µg/kg of isoproterenol pretreatment 30 minutes before TBI, 10 mg/kg of propranolol pretreatment 60 minutes before TBI, 10 mg/kg of metoprolol pretreatment 60 minutes before TBI, or 10 mg/kg of butaxamine pretreatment 40 minutes before TBI and 10 minutes before pretreatment with 50 µg/kg isoproterenol or 10 mg/kg of propranolol 60 minutes after TBI. A neurological severity score (NSS) was measured at 1, 24, and 48 hours after TBI. Blood glutamate, blood glucose, mean arterial blood pressure, and heart rate were measured at the time of drug injection, at the time of TBI, 60 minutes after TBI, and 90 minutes after TBI. Results: Blood glutamate levels decreased spontaneously by 60 minutes after TBI in the control group (P<0.05), reverting to baseline levels by 90 minutes after TBI. A pretreatment with either 10 mg/kg of metoprolol 60 minutes before TBI or with 50 µg/kg of isoproterenol 30 minutes before TBI also reduced blood glutamate levels (P<0.05) both at 90 minutes after TBI and improved the NSS measured 24 and 48 hours after TBI in comparison with the control saline-treated group. However, a 10-mg/kg butoxamine pretreatment 40 minutes before TBI and 10 minutes before pretreatment with 50 µg/kg of isoproterenol or 10 mg/kg of propranolol 60 minutes before TBI neither affected blood glutamate levels across time after TBI nor caused any significant change in the NSS measured 24 and 48 hours after TBI in comparison with the control saline-treated group. A strong correlation (r2=0.73) was demonstrated between the percent decrease in blood glutamate levels at 90 minutes after TBI and the percent improvement of NSS measured 24 hours after TBI. Conclusions: The results suggest that the transient blood glutamate reduction seen after TBI is the result of a stress response and of the activation of the sympathetic nervous system through the &bgr;2 adrenergic receptors, causing an increase of the brain-to-blood efflux of glutamate observed with excess brain glutamate levels after a brain insult. This strongly correlates with the neurological improvement observed 24 hours after TBI.
Retrospective evaluation of milk production and culling risk following either surgical, toggle-pin suture or conservative treatment of left displaced abomasum in Chilean dairy cows

Abstract AIMS To describe milk yield and culling risk in cows diagnosed with left displacement of abomasum (LDA) treated either conservatively, by right flank pyloric omentopexy, or rolling and toggling, compared with normal herdmates from four Chilean dairy herds. METHODS Historical records were obtained from four commercial dairy farms located in Central Chile for cows with a history of LDA between 2010 and 2012, and healthy herdmates. Cows with LDA were categorised into three groups: cows treated with right omentopexy (ST, n=58), cows treated by toggle suturing (TT, n=15) and cows treated conservatively (CT, n=56). Control cows (n=129) were selected from unaffected cows, matched by days in milk (DIM), parity and herd with affected cows. Groups were compared for risk of culling up to 300 DIM and for milk production up to 5 months of lactation using survival and Cox proportional hazard models and mixed models for repeated measures, respectively. RESULTS Compared with cows in the Control group, the risk of being culled up to 300 DIM was 9.1 (SE 0.62) times greater in ST cows, 10.4 (SE 0.68) times greater in TT cows, and 37.3 (SE 0.61) times greater in CT cows (p<0.01). In the first 5 months of lactation, compared with cows in the Control group, mean daily milk production was 23.3 (SE 1.5) kg less in ST cows, 15.3 (SE 1.6) kg less in TT cows, and 30.1 (SE 1.3) kg less in CT cows (p<0.001). CONCLUSIONS AND CLINICAL RELEVANCE Cows in four dairy herds in central Chile diagnosed and treated for LDA produced significantly less milk and had a higher risk of culling than healthy herdmates. Although cows treated surgically or with toggle suture never recovered to the extent of healthy cows, they produced more milk than cows treated conservatively. However, the retrospective nature of the data, the inclusion of only four herds and the non-random allocation to treatments means that these conclusions cannot be extrapolated to the overall dairy cattle population in Chile.
Fetal genetic risk of isolated cleft lip only versus isolated cleft lip and palate: a subphenotype analysis using two population-based studies of orofacial clefts in Scandinavia.

BACKGROUND: Cleft lip only (CLO) and cleft lip and palate (CLP) are commonly regarded as variants of the same defect and are traditionally combined to form the single group of cleft lip with or without cleft palate (CL/P) prior to analysis. However, recent data have suggested that at least a subgroup of isolated CLO may be etiologically distinct from isolated CLP. METHODS: To explore fetal genetic risk of isolated CLO separately from isolated CLP, we performed a subphenotype analysis using two population-based studies of clefts in Scandinavia. One hundred twenty-one isolated CLO, 190 isolated CLP, and 592 control triads were available from Norway (1996–2001), and a further 76 isolated CLO and 107 isolated CLP triads were available from Denmark (1991–2001). Genotypes for 1315 SNPs in 334 autosomal cleft candidate genes were analyzed using two complementary statistical methods, Triad Multi-Marker (TRIMM; Shi et al., 2007)) and HAPLIN (Gjessing and Lie, 2006), to look for genetic associations across the two national samples. RESULTS: Both TRIMM and HAPLIN identified strong associations between FGF12 and isolated CLO in both populations. In addition, only TRIMM identified associations with IRF6 and VCL, and only HAPLIN found an association with CX43. When analyses were repeated on the larger sample of isolated CLP, no significant associations were found with FGF12, IRF6, VCL, or CX43. CONCLUSIONS: Despite some inconsistency in the pattern of associations across the two populations, the associations themselves were phenotype-specific. While both IRF6 and FGF12 have previously shown strong associations with isolated CL/P, the associations with VCL and CX43 are novel and warrant further investigation in other isolated CLO samples. Birth Defects Research (Part A), 2010. © 2010 Wiley-Liss, Inc.