Miracle-dz/UniFAR-FTUs huggingface dataset:
Breeding Dairy Cows to Reduce Greenhouse Gas Emissions

The dairy industry has made large advances in efficiencies over the past 60 years as a result of changes in breeding, nutrition and management practices [1]. To meet the growing demand for dairy products, which is projected to continue out to the year 2050 [2], milk production per cow has increased over the last thirty years primarily by genetic selection and better nutrition. Genetic selection has tended to focus on mostly production traits (kilograms milk, kilograms fat and protein) rather than fitness (lameness, mastitis, fertility and lifespan) traits, although most countries now include fitness traits in addition to production traits in modern breeding goals. The Holstein Friesian is a popular breed due to its high genetic potential to produce milk; however it is characterised by having a lower body condition score, and reduced fertility and survival compared to other breeds [3]. Even with these negative attributes, in tandem with efficiencies in production in recent decades have come reductions in greenhouse gas (GHG) emissions and resource inputs per unit product [1, 4, 5], while emissions per unit area have increased.
Cusp size, sexual dimorphism, and heritability of cusp size in twins.

Overall measures of mandibular molars reflect the combined size contributions of the component cusps and ridges. Until now, the size hierarchy of primary and permanent mandibular molar cusps remained unclear. This paper utilizes the relative plane surface areas (basal area dimensions) of the individual molar cusps, as assays of cusp size to demonstrate cusp size variations within populations, antimere cuspal variations, sexual dimorphism, and, the heritability of cusp size. Duplicate dental casts from 199 pairs of like-sexed twins provide the raw dats. Defined anatomic landmarks on the occlusal surfaces were reduced to X-Y rectangular coordinates prior to the computation of the basal areas dimensions. The results establish a cusp size hierarchy specific for molar type, i.e., five-cusped molars with a distal fovea and distal marginal ridge (5fd), five-cusped molars without a distal fovea and without a distal marginal ridge (5o), and four-cusped molars (4c). Sexual dimorphism in cusp size is apparent in 5fd molar cusped but not in 5o molar cusps. However, males have a significantly higher frequency of 5fd molars. Females have a higher frequency of smaller 5o and 4c molars which have fewer crown components. Moreover, female 5o molars have cusps as large as or larger than 5o male molor cusps. Right-side-left-side differences exist between antimere cusps based on relatively low correlations. The mirroring of molor types occurs infrequently. When observed, most intrapair differences for cusp size, using F-ratios, indicate a low component of hereditary variability.
Modeling spiking activity of in vitro neuronal networks through non linear methods

Neuroscience research is even more exploiting technologies developed for electronic engineering use: this is the case of Micro-Electrode Array (MEA) technology, an instrumentation which is able to acquire in vitro neuron spiking activity from a finite number of channels. In this work we present three models of synaptic neuronal network connections, called “Full-Connected”, “Hierarchical” and “Closed-Path”. Related to each one we implemented an index giving quantitative measures of similarity and of statistical dependence among neuron activities recorded in different MEA channels. They are based on Information Theory techniques as Mutual and Multi Information: the last one extending the pair-wise information to higher-order connections on the entire MEA neuronal network. We calculated indexes for each model in order to test the presence of self-synchronization among neurons evolving in time, in response to external stimuli such as the application of chemical neuron-inhibitors. The availability of such different models helps us to investigate also how much the synaptic connections are spatially sparse or hierarchically structured and finally how much of the information exchanged on the neuronal network is regulated by higher-order correlations.
Polymorphism and expression of insulin-like growth factor 1 (IGF1) gene and its association with growth traits in chicken

Abstract 1. The objectives of the study were to detect polymorphism in the coding region of the IGF1 gene, explore the expression profile and estimate association with growth traits in indigenous and exotic chickens. 2. A total of 12 haplotypes were found in Cornish, control layer and Aseel breeds of chicken in which the h1 haplotype was most frequent. 3. Nucleotide substitutions among haplotypes were found at 21 positions in the IGF1 gene in which 4 substitutions resulted in non-synonymous mutations in the receptor binding domain of the IGF1 protein. 4. The haplogroup showed a significant effect on body weight at 24 and 42 d of age in the control layer line, body weight at 42 d and daily weight gain between 29 and 42 d in the control broiler line, daily weight gain between 29 and 42 d in Cornish, and body weights at 42 d as well as daily weight gain between 29 and 42 d in Aseel birds. 5. IGF1 expression varied among the breeds during embryonic and post-hatch periods. The expression among the haplogroups varied in different chicken tissues. The effect of haplogroup on myofibre number in pectoral muscle was non-significant, although there was significant variation in numbers between d 1 and d 42, and between broiler and layer lines. 6. It was concluded that the coding region of the IGF1 gene was polymorphic, expressed differentially during the pre-hatch and post-hatch periods, and haplogroups showed significant association with growth traits in chicken.
eMiRo: an ontology-based system for clinical data integration and analysis

Biological experiments and bioinformatics analysis are producing large datasets of omics data (e.g. genomics, proteomics, interac-tomics, etc.), stored in diversiﬁed sources and databases. Biological data and bioinformatics results can be related to various information, such as clinical data (e.g. cancer stage) or environment data (e.g. place where a patient lives), but this requires novel data integration mechanisms and analysis algorithms. Novel data structures are needed for data integration, while eﬃcient algorithms are necessary for managing integrated data and to analyze results in order to extract knowledge and underline correlation with environmental factors. In this paper an ontology-based system for clinical data integration and analysis is presented. The sys-tem, called eMiRo (Electronic MedIcal RecOrd), includes geo-reference features for epidemiological analysis based on geographical and clinical information. Using eMiRo, a physician is able to handle and integrate biological data; moreover, the system supports the retrieval of additional information such as ontology terms and information about genes and diseases. When conducting a study, for each gene relevant to the study, biological function and relations with other genes as well as involvement in biological processes is reported.
Topical antimicrobial therapy of chronic wounds healing by secondary intention using iodine products

All open wounds healing by secondary intention are contaminated by bacteria and in chronic wounds this can progress through colonisation to invasive infection. Iodine products reduce bacterial load and are active against most species of micro‐organisms, and certainly those encountered in chronic wound care. This review evaluates the use of iodine products in chronic wound care including povidone‐iodine solutions and cadexomer iodine. Antiseptics containing iodine are relatively cheap, resistance is unknown and concerns about systemic toxicity are probably overstated. More widespread use of these agents as topical anti‐microbials in chronic wound care should be considered to reduce the need for systemic antibiotics when colonisation has progressed to invasive infection with systemic signs.
Pomegranate (Punica granatum L.) seed: A comparative study on biochemical composition and oil physicochemical characteristics

The pomegranate seeds of four Iranian commercial varieties (Abanmahi (AB), Malas (MS), Pust Sefid (PS) and Shahvar (SH)) were evaluated in terms of some quality properties including protein, oil, dietary fiber, mineral contents and fatty acid composition. Physicochemical properties and antioxidant activity of pomegranate seed oils (PSOs) were also determined. The oil antioxidant activity was measured by 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging capacity. Results showed that PS had the highest oil (16.9%) and crude fiber (42.4%), and nutritional value (460.7Kcal/100g) among selected varieties. PS had the highest level of phosphorus (2766.3 mg/kg) and magnesium (2052.0mg/kg), while the highest calcium (675.3mg/kg) and potassium (3724.6mg/kg) were related to SH. The main fatty acid identified by gas chromatography was punicic acid ranged from 72.07% for SH to 73.31% for MS (p<0.05). The ratios of polyunsaturated/saturated and unsaturated/saturated fatty acids of PSOs were found to be between 9.174 and 9.450, and 10.325 and 10.861, respectively (p<0.05). PSOs obtained presented acid (3.78-8.36% punicic acid), peroxide (0.39-0.48meq O2/kg), iodine (216.9-220.3g I2/100g) and saponification (179.3-182.5mg KOH/g) values. Also, refractive index at 25°C, viscosity and density of PSOs varied from 1.461-1.527, 0.036-0.063Pa. s and 0.9202-0.9311g/cm3, respectively. The oil obtained from MS showed the lowest level of ortho-diphenols (ODC) and DPPH radical scavenging capability. The relationship between percentage of remaining DPPH and ODC of PSOs also illustrated high correlation among all varieties (R2 = 0.98, p<0.01).
Structure and stability of a model three‐helix‐bundle protein on tailored surfaces

The interaction of protein molecules with surfaces is important in numerous applications. Theoretical work on protein adsorption has been limited. In particular, it is difficult to obtain quantitative predictions about the structure and stability of proteins on surfaces. In this study, density‐of‐states‐based simulations were performed on a Gō‐like model of a three‐helix‐bundle fragment from protein A (PDB ID: 1bdd). Both mechanical and thermal stability were investigated on neutral and attractive surfaces and compared to that in the absence of a surface. It was found that attaching the peptide to any type of surface decreases its melting temperature by as much as 9 K, depending upon orientation. Calorimetric cooperativity, as measured by van't Hoff to calorimetric enthalpy ratios, similarly decreased. It was also found that the mechanical strength of the peptide attached to surfaces is degraded to varying extents, depending upon the surface type and protein orientation. A comparison of mechanical and thermal stability showed that the two are not synonymous, but occur through different pathways, and that system configurations that are more thermally stable are not always so mechanically. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Activity of urine arylsulfatase A in brain‑dead graft donors is a predictor of early and late graft function.

OBJECTIVE Human lysosomal arylsulfatase A (ASA) is a member of the sulfatase family. Arylsulfatase A is required to degrade sulfatides. Sulfatides occur in the myelin sheets of the central and peripheral nervous system. In this study we evaluated the urine activity of lysosomal enzyme arylsulfatase A in brain‑dead donors as a marker and predictor of short - and long‑term renal allograft function. PATIENTS/METHODS We analyzed data from kidney recipients who received organs from brain‑dead donors. Data from 40 donors and 68 recipients were analyzed. RESULTS Urine activity of arylsulfatase A in graft donors correlated positively with creatinine clearance in graft recipients after transplantation: significantly after 30 days (Rs=0.38, p=0.004) and after 3 years (Rs=0.38, p=0.03), and with borderline significance after 14 days (Rs=0.25, p=0.08) and after one year (Rs=0.23, p=0.07). CONCLUSIONS The results of this study suggest that arylsulfatase A has a protective effect on kidney allograft, and the urine activity of this enzyme in kidney donors correlates positively with graft function.
Symbolic Revolutions and the Australian Archaeological Record

Australia was colonized by at least 40,000 bp and scientists agree that the continent was only ever occupied by anatomically and behaviourally modern humans. Australia thus offers an alternative early record for the archaeological expression of behavioural modernity. This review finds that the pattern of change in the Australian archaeological sequence bears remarkable similarity to the pattern from the Lower to Upper Palaeolithic in the Old World, a finding that is inconsistent with the ‘symbolic revolution’ model of the origin of modern behaviour. This highlights the need for archaeologists to rethink the implications of the various criteria and scales of analysis used to identify modern human behaviour.
Biodynamic understanding of mercury accumulation in marine and freshwater fish

Mercury (Hg) is a global environmental pollutant that has been the cause of many public concerns. One particular concern about Hg in aquatic systems is its trophic transfer and biomagnification in food chains. For example, the Hg concentration increases with the increase of food chain level. Fish at the top of food chain can accumulate high concentrations of Hg (especially the toxic form, methylmercury, MeHg), which is then transferred to humans through seafood consumption. Various biological and physiochemical conditions can significantly affect the bioaccumulation of Hgincluding both its inorganic (Hg(II)) and organic (MeHg) formsin fish. There have been numerous measurements of Hg concentrations in marine and freshwater fish worldwide. Many of these studies have attempted to identify the processes leading to variations of Hg concentrations in fish species from different habitats. The development of a biokinetic model over the past decade has helped improve our understanding of the mechanisms underlying the bioaccumulation processes of Hg in aquatic animals. In this review, I will discuss how the biokinetic modeling approach can be used to reveal the interesting biodynamics of Hg in fish, such as the trophic transfer and exposure route of Hg(II) and MeHg, as well as growth enrichment (the increases in Hg concentration with fish size) and biomass dilution (the decreases in Hg concentration with increasing phytoplankton biomass). I will also discuss the relevance of studying the subcellular fates of Hg to predict the Hg bioaccessibility and detoxification in fish. Future challenges will be to understand the inter- and intra-species differences in Hg accumulation and the management/mitigation of Hg pollution in both marine and freshwater fish based on our knowledge of Hg biodynamics.
Nuclear cysteine‐protease involved in male chromatin remodeling after fertilization is ubiquitously distributed during sea urchin development

Previously we have identified a cysteine‐protease involved in male chromatin remodeling which segregates into the nuclei of the two blastomeres at the first cleavage division. Here we have investigated the fate of this protease during early embryogenesis by immunodetecting this protein with antibodies elicited against its N‐terminal sequence. As shown in this report, the major 60 kDa active form of this protease was found to be present in the extracts of chromosomal proteins obtained from all developmental stages analyzed. In morula and gastrula the 70 kDa inactive precursor, which corresponds to the major form of the zymogen found in unfertilized eggs, was detected. In plutei larvas, the major 60 kDa form of this enzyme was found together with a higher molecular weight precursor (90 kDa) which is consistent with the less abundant zymogen primarily detected in unfertilized eggs. As reported here, either the active protease or its zymogens were visualized in most of the embryonic territories indicating that this enzyme lacks a specific pattern of spatial‐temporal developmental segregation. Taken together our results indicate that this protease persists in the embryo and is ubiquitously distributed up to larval stages of development, either as an active enzyme and/or as an inactive precursor. These results suggest that this enzyme may display yet unknown functions during embryonic development that complement its role in male chromatin remodeling after fertilization. J. Cell. Biochem. 101: 1–8, 2007. © 2007 Wiley‐Liss, Inc.
Reference values for respiratory system impedance by using impulse oscillometry in children aged 2–11 years

The forced oscillation technique makes it possible to evaluate the mechanical properties of the respiratory system with a minimum of cooperation. The method is therefore especially useful in children. Impulse oscillometry (IOS) is a commercially available version of this technique. There is, as yet, limited information on reference values for IOS in children. The aim of this study was to extend the reference values for IOS variables and to study their correlation with height, weight and age in healthy children. A sample (n = 360) of children (age 2·1–11·1 years) was measured by using impulse oscillometry (IOS; Jaeger, Würzburg, Germany). The sample was based on children attending kindergarten in Finland and children attending primary school in Sweden. Measurements of respiratory resistance (Rrs) and reactance (Xrs) at 5, 10, 15 and 20 Hz, total respiratory impedance (Zrs) and the resonance frequency (Fr) were made. All variables were related to body height. Most of them were also weakly related to weight. Reference equations for children (height 90–160 cm) are presented.
Effect of health education intervention on the awareness and use of personal protective equipments among small scale electric arc welders in Ilorin, Nigeria

Introduction: Welding is associated with workplace hazards that can affect the health of those who engaged in it as they are exposed to harmful dust. Subjects and Methods: This was a health education intervention study carried out among self-employed electric arc welder. Data were collected using an interviewer administered questionnaire and health education intervention was carried out between the preintervention and postintervention stages. Epi-info version 3.5. 1 software package was used for data analysis and Chi-square analysis was used to determine the statistical significance of observed differences between the study and control groups before the intervention and after intervention. Level of significance was set at a P < 0.05. Results: At the preintervention phase, 285 respondents were interviewed in each of the study and control groups, while 280 study respondents and 275 control respondents were available for the postintervention phase of the study. Before the intervention, 279 (97.9%) of the respondents in the study group were aware of eye goggles as a means of protection, 20 (7%) were aware of welding helmet, 206 (72.3%) were aware of hand gloves and 4 (1.4%) were aware of face mask. All showed a significant increase in awareness postintervention (P < 0.05) while there was no significant increase in awareness in the control group. Conclusion: Health education brought about a significant increase in awareness and use of personal protective equipment among the welders. There is a need for proper education of welders on workplace hazards, the types and use of different protective devices in other to safeguard their health.
Investigation of Racial Disparities in Early Supportive Medication Use and End-of-Life Care Among Medicare Beneficiaries With Stage IV Breast Cancer.

PURPOSE Early supportive care may improve quality of life and end-of-life care among patients with cancer. We assessed racial disparities in early use of medications for common cancer symptoms (depression, anxiety, insomnia) and whether these potential disparities modify end-of-life care. METHODS We used 2007 to 2012 SEER-Medicare data to evaluate use of supportive medications (opioid pain medications and nonopioid psychotropics, including antidepressants/anxiolytics and sleep aids) in the 90 days postdiagnosis among black and white women with stage IV breast cancer who died between 2007 and 2012. We used modified Poisson regression to assess the relationship between race and supportive treatment use and end-of-life care (hospice, intensive care unit, more than one emergency department visit or hospitalization 30 days before death, in-hospital death). RESULTS The study included 752 white and 131 black women. We observed disparities in nonopioid psychotropic use between black and white women (adjusted risk ratio [aRR], 0.51; 95% CI, 0.35 to 0.74) but not in opioid pain medication use. There were also disparities in hospice use (aRR, 0.86; 95% CI, 0.74 to 0.99), intensive care unit admission or more than one emergency department visit or hospitalization 30 days before death (aRR, 1.28; 95% CI, 1.01 to 1.63), and risk of dying in the hospital (aRR, 1.59; 95% CI, 1.22 to 2.09). Supportive medication use did not attenuate end-of-life care disparities. CONCLUSION We observed racial disparities in early supportive medication use among patients with stage IV breast cancer. Although they did not clearly attenuate end-of-life care disparities, medication use disparities may be of concern if they point to disparities in adequacy of symptom management given the potential implications for quality of life.
Gene expression profiling in the mammary gland of rats treated with 7,12‐dimethylbenz[a]anthracene

Identification of molecular markers of early‐stage breast cancer development is important for the diagnosis and prevention of the disease. In the present study, we used microarray analysis to examine the differential expression of genes in the rat mammary gland soon after treatment with a known chemical carcinogen, 7,12‐dimethylbenz[a]anthracene (DMBA), and prior to tumor development. Six weeks after DMBA, differential expression of multiple genes involved in cell growth, differentiation and microtubule dynamics were observed. Gene expression changes were further validated by a combination of techniques, including real‐time PCR, RT‐PCR, Western blotting and immunohistochemistry. An inhibition of differentiation in this early stage was suggested by the lower expression of β‐casein and transferrin and higher expression of hsp27 in glands from DMBA‐treated rats. Possible cell cycle deregulation was indicated by an increased expression of cyclin D1 and hsp86, a heat shock protein associated with cyclin D1. Prior to tumor development, DMBA increased cellular proliferation as detected by Ki‐67 and stathmin immunostaining in histologically normal mammary gland. Genes regulating microtubule function, including stathmin, Ran, α‐tubulin and hsp27, were all overexpressed in the mammary gland of DMBA‐treated rats, raising the possibility that disruption of microtubule dynamics and abnormal mitosis may be critical events preceding breast cancer development. Several of the altered proteins, including hsp27, hsp86 and stathmin, may ultimately serve as markers of early breast cancer development. Published 2005 Wiley‐Liss, Inc.