Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk factors involved in retained placenta of dairy cows from family agriculture herds

Objective: The aim of this paper was to assess the risk factors in the occurrence of retained placenta in cows from family agriculture herds in four cities in southwest Paraná. Methods: A total of 607 calving’s in 25 herds were studied, considering as a diagnosis if the placenta was retained 12 hours after calving. A semi-structured questionnaire was applied to the producer in order to evaluate the risk factors involved concerning the cow, its pre-partum supplementation, its parturition, its calf, its clinical sanitary conditions and its seropositivity for reproductive diseases. Results: A total of 89 retained placenta cases were studied during a year, being the average prevalence of 16.8%. Among those cows, 50.6% had received mineral salt pre-partum, 18% had received mineral salt for lactating cows and 31.5% had not receive any supplementation. Among the calving’s observed in the cows involved, 21.3% were premature, 19.1% had dystocia and 4.5% twin births. 55.9% of the calves were male, 20.43% were large, 53.76% medium and 22.5% small in size. Among the affected cows, 44.9% presented hyperthermia, 41.6% decreased appetite, 27.0% concomitant disorders, 47.19% were seronegative for brucellosis, leptospirosis and neosporosis, 32.58% were seropositive for leptospirosis, 10.11% were seropositive for neosporosis and 4.49% were seropositive for both diseases. Conclusions: It can be concluded that under the study conditions, there were no decisive factors for the occurrence of retained placenta, reaffirming the multifactorial nature of this disease. Palavras-chave: Doenças reprodutivas; Fêmea bovina; Multifatorial; Suplementação Mineral; Escore
A deep learning framework for improving protein interaction prediction using sequence properties

Motivation Almost all critical functions and processes in cells are sustained by the cellular networks of protein-protein interactions (PPIs), understanding these is therefore crucial in the investigation of biological systems. Despite all past efforts, we still lack high-quality PPI data for constructing the networks, which makes it challenging to study the functions of association of proteins. High-throughput experimental techniques have produced abundant data for systematically studying the cellular networks of a biological system and the development of computational method for PPI identification. Results We have developed a deep learning-based framework, named iPPI, for accurately predicting PPI on a proteome-wide scale depended only on sequence information. iPPI integrates the amino acid properties and compositions of protein sequence into a unified prediction framework using a hybrid deep neural network. Extensive tests demonstrated that iPPI can greatly outperform the state-of-the-art prediction methods in identifying PPIs. In addition, the iPPI prediction score can be related to the strength of protein-protein binding affinity and further showed the biological relevance of our deep learning framework to identify PPIs. Availability and Implementation iPPI is available as an open-source software and can be downloaded from https://github.com/model-lab/deeplearning.ppi Contact xiang-chen@zju.edu. cn
Pengaruh Ekstrak Etanol Daun Jambu Biji (Psidium Guajava Linn) Konsentrasi 7% Terhadap Proses Penyembuhan Stomatitis Pada Tikus Putih Jantan

Background: Stomatitis can be caused by trauma, infection, gastrointestinal disorders, blood disorders, infection with HIV (Human Immunodeficiency Virus), emotional disorders, immunological disorders, nutritional deficiencies and hormonal disorders. Stomatitis patients with symptomatic treatment aimed at reducing inflammation, pain in the area of the lesion and accelerate the healing process. To produce an effective wound healing, the body has to supply material and nutrients to the damaged area. Guava leaf is one of medicinal plants that can be used as an alternative medicine community. Seeing the current economic conditions needed alternatives that are cheaper and more easily available and have a fairly good efficacy in treating inflammation. Ministry of Health of the Republic of Indonesia recommends encouraging the use of natural medicinal plant material a treatment alternative in alleviating and curing the pain at a relatively affordable by the community, easily available and quite practical. Methods: This study is a randomized experimental nature Pre-post only Control Group Design. Test in this study using 24 male rats aged 2-3 months and weighing 180-200 grams. Materials guava leaf extract (Psidium Guajava Linn) 7%. This study using One Way ANOVA Results: The One Way ANOVA test of significance contained in the healing influence stomatitis variable value less than 0,05. It can be concluded that there are significant effect of the treatment given. Conclusion: The extract of guava leaves 7% concentration effect on the healing process stomatitis on white male rats.
Primary human macrophages are polarized towards pro-inflammatory phenotypes in alginate hydrogels

Dysregulated macrophage function is implicated in a wide range of disorders. In vitro hydrogel culture systems are often used as matrices to model and explore the effect of various external stimuli on macrophage polarization and behaviour. Here, we show that 3D alginate hydrogels are not “macrophage inert” and instead help to direct the maturation of primary human macrophages towards specific phenotypes. We compared polarization of M1-like and M2-like cells activated on planar substrates or in 3D alginate hydrogels (with or without adhesion motifs (RGD)). We show that culture in 3D alginate systems selectively alters M2 polarisation following activation; cells show a 2.6-fold increase in CD86 expression compared to cells matured on planar controls, and increase IL1β cytokine secretion even in response to an M2-like stimulus (LPS alone in the absence of IFNγ). Our results suggest that alginate materials may intrinsically stimulate M2 macrophages to acquire a unique polarization state (resembling M2b), characterized by enhanced expression of CD86 and IL1β secretion while retaining low IL12 and high IL10 secretion typical for M2 macrophages. This has important implications for researchers using alginate hydrogels to study macrophage behavior in culture and co-culture systems, as alginate itself may induce direct phenotypic changes independently or in conjunction with other stimuli.
Effects of iron fertilizers on iron content of parsley.

Objective: In this study, the effect of iron fertilizers on the amount of iron uptake in parsley vegetation was determined in bicarbonate and bicarbonate-free conditions. Material and Methods: The experiment was carried out in 6 different applications (Control, Fe-EDTA, FeSO4.7H2O, Control+HCO3-, Fe-EDTA+HCO3-, FeSO4.7H2O+HCO3-), 4 replicates, using two different iron fertilizer and Giant of Italy parsley variety. A total of 3 harvests occurred during the experiment. Results: According to research results, Fe-EDTA showed considerable effect in bicarbonate-containing applications and positively affected plant iron content. Fe-EDTA shows the highest iron and active iron results in foliar and stem on the bicarbonate and bicarbonate-free conditions. Highest yield was detected in FeSO4.7H2O applications (147.7g/pot) in bicarbonate-free conditions, Fe-EDTA applications (133.1g/pot) in bicarbonate conditions. Conclusion: As a result, the positive effect of chelated iron fertilizers in bicarbonate rich environments has been determined once again. In the use of iron fertilizers, the use of chelated fertilizers will increase quality and yield.
Reanalysis of Alzheimer’s Brain Sequencing Data Reveals Absence of Purported HHV6A and HHV7

Readhead et al. recently reported in Neuron the detection and association of Human Herpesviruses 6A (HHV6A) and 7 (HHV7) with Alzheimer’s disease by shotgun sequencing. I was skeptical of the specificity of their modified Viromescan bioinformatics method and subsequent analysis for numerous reasons. In their supplementary data, they report the detection of Variola virus, the etiological agent of the eradicated disease smallpox, in 97.5% of their Mount Sinai Brain Bank dataset. I reanlyzed Readhead et al’s data using highly sensitive and specific alternative methods and find no HHV7 reads in their samples; HHV6A reads were found in only 2 out of their top 15 samples sorted by reported HHV6A abundance. Finally, I recreate Readhead et al’s modified Viromescan method and identify reasons for its low specificity.
Repetitive Movements in Melon Cultivation Workers under Greenhouses

Musculoskeletal disorders cause serious problems that affect workers in many sectors. The objective of this study is the ergonomic analysis of melon cultivation farmers in Almeria-type greenhouses. For this, the rapid upper limb assessment (RULA) method has been applied after carrying out a detailed process of observing the farmers’ tasks. The study shows that 65% of the postures have a very-high-risk level, 26% high, 9% average, and no posture is found with a low risk. They also show that in 69.57% of the postures, the upper limbs are less affected than the others such as the neck, trunk, and lower limbs. Measures are proposed to improve the working conditions for workers.
Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome

Methylation of histone H3K4 is a hallmark of actively transcribed genes that depends on mono-ubiquitination of histone H2B (H2B-Ub). H3K4 methylation in yeast is catalyzed by Set1, the methyltransferase subunit of COMPASS. We report here the cryo-EM structure of a six-protein core COMPASS subcomplex, which can methylate H3K4 and be stimulated by H2B-Ub, bound to a ubiquitinated nucleosome. Our structure shows that COMPASS spans the face of the nucleosome, recognizing ubiquitin on one face of the nucleosome and methylating H3 on the opposing face. As compared to the structure of the isolated core complex, Set1 undergoes multiple structural rearrangements to cement interactions with the nucleosome and with ubiquitin. The critical Set1 RxR motif adopts a helix that mediates bridging contacts between the nucleosome, ubiquitin and COMPASS. The structure provides a framework for understanding mechanisms of trans-histone cross-talk and the dynamic role of H2B ubiquitination in stimulating histone methylation.
Effect of Feed Restriction and Photoperiod on Reproduction and LEPR, MELR mRNA Expression of Layers

Photoperiod and nutrition are major factors that affect the reproductive efficiency particularly in female animals. In this study we examined the interaction of photoperiod and food restriction on growth, sexual maturation and receptor mRNA expressions of leptin, melatonin, and estrogen in abdominal fat and the ovary of pullets. There were no interaction effects between photoperiod and feeding level on body weight, abdominal fat weight, ovary weight at both 14 wk and 18 wk. Abdominal fat weight of feed restriction group was significantly lower compared with the control group at the age of 14 wk, 18 wk, and age of the first egg (AFE) (p<0.05). Ovary LEPR (Leptin receptor) gene expression showed an interaction effect of the first egg. Restricted feeding significantly inhibited ovary ER (Estrogen receptor), LEPR and MELR1B (Melatonin 1B receptor) gene expression at 14 wk, 18 wk and the first egg. At 14-week-old, abdominal fat LEPR gene expression was significantly lower in long photoperiod group compared with the short photoperiod group. At the first egg, short photoperiod and feed restriction group reduced abdominal fat LEPR gene expression. The results indicated that the reproductive activity of pullets is sensitive to feed intake and photoperiod. Feed restriction down regulated the ER, LEPR, MELR1A (Melatonin 1A receptor) and MELR1B mRNA expression of the ovary at 14 wk, 18wk and AFE. Long photoperiod enhanced the LEPR, MELR1A and MELR1B mRNA expression of abdominal fat at AFE.
Influence of Seed Inoculation with Commercial Bacterial Inoculants (Bradyrhizobium Japonicum) on Growth and Yield of Soybean

A field experiment was carried out with three bacterial inoculants: HiStick® Soy, Nitragina, Nitrazon and the control. Number and dry weight of nodules were significantly higher with inoculation of bacterial inoculants compared to the control. In 2017, the most pods per plant were obtained after the use of Nitrazon or HiStick® Soy, while in 2018, after the use of HiStick® Soy or Nitragina. In 2018, the highest 1000 seed weight was obtained after the use of Nitragina. In 2017, the seed yield was the most favourably affected by the inoculants HiStick®Soy (3.31 t ha-1) and Nitrazon (3.37 t ha-1) and in 2018, by HiStick® Soy (3.92 t ha-1) and Nitragina (3.87 t ha-1). High Soil Plant Analysis Development (SPAD) and Leaf Area Index (LAI) readings, were observed with HiStick® Soy.
Comparative Efficacy of Newer Insecticides against Plutella xylostella and Spodoptera litura on Cauliflower under Laboratory Conditions

Cabbages and cauliflowers are the most important winter vegetables cultivated mainly in tropical and temperate areas of the globe. Armyworm, Spodoptera litura and Diamondback moth (DBM), Plutella xylostella are the most economic and destructive insect pest for cabbage and cauliflower. The current study was conducted to investigate three new insecticides such as emamectin benzoate, lufenuron and profenofos against two lepidopteran insect pests; Spodoptera litura and Plutella xylostella at different larval instars during 2018 under laboratory conditions. For this purpose, randomized complete design and leaf dip method was used. The current study was resulted that Emamectin benzoate proved to be effective one with significantly higher level of morality followed by profenofos and lufenuron after 48 and 72 hours respectively. Emamectin benzoate can be recommended as the most toxic insecticides against both Spodoptera litura and Plutella xylostella populations along with profenofos.
Diagnosis Value of Detecting Plasm Pyruvate Kinase M2 (M2-PK) in Patients with Gastric Cancer

Objectve To explore the relationship between the change of M2-PK level in plasm with the occurrence of gastric cancer and the diagnostic value for gastric cancer.Methods Plasm M2-PK and serum CA19-9 level were determined by using ELISA method in 55 normal persons,50 patients with gastric cancer,45 patients with acute gastritis or chronic gastritis and 42 patients with gastric benign tumors.Result The plasm M2-PK and serumCA19-9 level and positive rate in gastric cancer group were significantly higher than that in normal control group、acute gastritis or chronic gastritis group and gastric benign tumor group(P0.01). Significant difference of plasm M2-PK and serum CA19-9 level in gastric cancer group did not exist(P0.05),but the comparison of positive rate showed obvious difference(P0.01). The comparison of plasm M2-PK and serum CA19-9 level and positive rate among normal control group、acute gastritis or chronic gastritis group and gastric benign tumor group did not show maked difference(P0.05). Conclusion M2-PK has significantly higher sensitivity than CA19-9.It is considered to be better sensitive tumor marker,and has widespread clinical practice value.
The antinociceptive effect of intrathecal administration of fluorocitrate in a rat model of inflammatory pain

Aim To investigate the effect of intrathecal injection of fluorocitrate(Fc)on mechanical and thermal hyperalgesia induced by complete Freund's adjuvant(CFA)injection in rats.Methods The mechanical withdrawal threshold(MWT)and thermal withdrawal latency(TWL)were measured before and after CFA or Fc treatment.The changes of glial fibrillary acidic protein(GFAP)and OX-42(a microglial marker)expression in the spinal cord dorsal horn were evaluated by immunohistochemistry analysis.Results Rats with CFA-induced arthritis showed mechanical allodynia and thermal hyperalgesia,which was correlated with the increased GFAP and OX-42 expression in the spinal cord dorsal horn.Intrathecal injection of Fc markedly suppressed CFA-induced thermal hyperalgesia and mechanical allodynia.Fc significantly attenuated the activation of GFAP and OX-42 in the spinal cord dorsal horn.Conclusions The glia activation in spinal cord is closely related to the progress of CFA-induced peripheral hyperalgesia.Fc may exert antihyperalgesic effect by inhibiting the activation of astrocyte and microglia.
Aufreinigung und Charakterisierung des Apoptose auslösenden Faktors aus Helicobacter pylori

Helicobacter pylori-infection is accompanied by gastric epithelial cell death and plays an important role in the pathogenesis of peptic ulcer diseases. The responsible factors for the induction of apoptosis are unknown. In this study the apoptosis inducing protein from H. pylori was purified 400fold by ammoniumsulphateand heatprecipitation and further by hydroxylapatiteand hydrophobic interactionchromatography. The aminoterminal sequence of the protein migrating as a band at 60 kDa by SDS-gelelectrophoresis corresponded to the heat shock protein HSP60. The apoptosis-inducing activity of Helicobacter pylori measured by Histon Elisa was inhibited up to 60 % by a monoclonal antibody. ATPase-activity in purified H. pylori-sonicate was stimulated by monovalent kations in the following order NH4 = Na << K and was inhibited up to 50 % by the selective Na/Kand H/K-ATPaseinhibitors Ouabain und Schering 28080, indicating a chimeric ATPase which was sensitive to both ATPase-inhibitors. Furthermore H. p.-induced apoptosis in gastric epithelial cells could be inhibited by both ATPase-inhibitors. Ouabain completely abolished apoptosis whereas Schering 28080 inhibited cell death up to 70 % regarded to the sonicate. These results indicate that the ATPase-domain of HSP60 is involved in Helicobacter pylori-induced apoptosis and therefore plays an impotant role in peptic ulcer diseases.
Isolation, genotyping and antimicrobial susceptibility of pathogenic Escherichia coli serotypes in ready to eat foods

In this study, pathogenic Escherichia coli serotypes (E. coli O157:H7, O26, O111) and their molecular proximity and antimicrobial susceptibility were investigated in RTE foods. A total of 240 samples; consist of 105 stuffed mussel, 56 meatless cig kofte, 54 Russian salad, 25 cheese halva, were analyzed. The conventional culture and serotyping methods for determination of the organisms were performed and further confirmation by PCR was carried out. Confirmed E. coli O157 isolates were genotyped by the enterobacterial repetitive intergenic consensus(ERIC)-PCR. Antibacterial susceptibility testing of the isolates was performed by disc diffusion method. E. coli was detected in 7 (2.9 %) of 240 samples, including 3 (5.5%) Russian salad, 3 (2.8%) stuffed mussel, 1 (4 %) cheese halva. Two isolates from Russian salad, 1 from stuffed mussel and 1 from cheese halva were identified as E. coli O157 . In addition, stuffed mussel isolate was found to carry stx1 ve hlyA genes whereas one Russian salad isolate carried the stx1 gene. E. coli isolates were found to be resistant to amoxycillin/clavulonic acid, gentamicin and ciprofloxacin, at the rate of 29%, 14% and 29 %, respectively. Only one (14 %) isolate from stuffed mussel was classified as multidrug resistant to three antimicrobials. Furthermore, the isolates, related to O157 and O157:H7, presented different ribotypes in this study. The results provide useful data for the development of public health policy concerning the potential presence of pathogenic antimicrobial resistant E. coli serotypes in RTE foods. Strict surveillance of RTE foods at retail points for emerging pathogens, their antimicrobial resistance patterns and the potential likelihood of cross-contamination is required.
Evaluación de los mecanismos de eliminación de Pb2+ en sistemas de fitorremediación en lotes operados con Salvinia biloba raddi (acordeón de agua)

Phytoremediation is an environmentally sound technology that has been shown to be very efficient for wastewater remediation. Treatment systems using aquatic plants have proved to be efficient to remove several contaminants including metals. Previous research has suggested that superficial adsorption and intracellular accumulation are the main mechanisms involved in heavy metals removal from polluted waters in Salvinia species. However, no studies have been done on the phytoremediation potential of Salvinia biloba Raddi, a prolific aquatic plant frequently encountered in many Argentinian coasts. Although, other Salvinia species showed to be lead (Pb2+) hyperaccumulator more information is required to understand the basic mechanisms involved in heavy metal bioremediation in other plants of this type. This work is a contribution to understand some factors and mechanisms involved in Pb2+ removal by Salvinia biloba Raddi, which will be very useful for the optimization of phytotechnologies using hyperaccumulating plants.
Mapping polyclonal antibody responses in non-human primates vaccinated with HIV Env trimer subunit vaccines

Rational immunogen design aims to focus antibody responses to vulnerable sites on the primary antigens. Given the size of these antigens there is however potential for eliciting unwanted, off-target responses. Here, we used our electron microscopy polyclonal epitope mapping approach to describe the antibody specificities elicited by immunization of non-human primates with soluble HIV envelope trimers and subsequent repeated viral challenge. An increased diversity of epitopes recognized, and the approach angle by which these antibodies bound, constituted a hallmark of the humoral response in most protected animals. We also show that fusion peptide-specific antibodies are responsible for some neutralization breadth. Moreover, cryoEM analysis of a fully-protected animal revealed a high degree of clonality within a subset of putatively neutralizing antibodies, enabling a detailed molecular description of the antibody paratope. Our results provide important insights into the immune response against a vaccine candidate that entered into clinical trials earlier this year.
Land management by bird community analysis: comparison among mapping methods for the zonation of a mediterranean habitat

Management algorithms of protected areas are widely used to identify potential networks of natural reserves that meet pre-established ecological requirements, such as a specific habitat percentage or a specific number of populations, while minimizing the related costs. Here we present a comparison of priority conservation maps of a protected area in central Italy, generated using different methods (i.e., Marxan, Marxan with Zones, Zonation, and directly overlapping the bird data with the vegetation type in the study area), based on an eight-year data set describing bird communities in the Circeo National Park. The generated maps can be used as a starting point when working with stakeholders involved in the management of this area. Our cartographic comparison illustrated that in the majority of the cases priority areas overlapped (the proportion of overlap was greater than 80% of the area size), affirming that the methods are equivalent. However, there were also divergent cases (the proportion of overlap was 0% of the area size), suggesting differential sensitivities of the four compared methods.