Miracle-dz/UniFAR-FTUs huggingface dataset:
Milk Yield, Milk Composition, and the Nutritive Value of Feed Accessed Varies with Milking Order for Pasture-Based Dairy Cattle

Simple Summary In pasture-based dairy systems, dairy cattle that voluntarily walk back to pasture immediately after milking access greater feed nutritive value than those cattle milked last. Dairy cattle that were milked first in our work produced more milk and tended to have a greater yield of milk solids than cattle milked last. This work highlights the opportunity to improve nutrient use efficiency on dairy farms through strategic pasture allowance and supplementation. Abstract (1) Background: Pasture varies in its chemical composition from the top of the sward to the base and cattle prefer to eat the leaf fraction. In pasture-based dairy systems, cattle predominantly walk back to pasture voluntarily after each milking, with the first cattle arriving to pasture hours before the last. Here we study the impact of pasture composition according to milking order on milk yield and milk composition for dairy cattle offered grazed ryegrass pasture. (2) Methods: In the first experiment, individual cow milk yield data were recorded on six farms over 8 months. The herd was divided into groups of 50 cows for analysis according to milking order. In the second experiment, the impact of milking order on milk composition and pasture composition accessed was determined in addition to milk yield on three farms. (3) Results: After accounting for age and stage of lactation effects, cattle milked first in experiment 1 produced, on average, 4.5 L/cow/day (+18%; range 14 to 29%) more than cattle milked last. In experiment 2, dairy cattle milked first (first 50 cows) in farm 1 had greater milk, protein, and solids non-fat (SNF) yield; and less lactose content than those milked last (last 50 cows). In farm 2, dairy cattle milked first had greater milk yield, SNF yield, lactose yield, and fat yield; but less protein and SNF content than cattle milked last. In farm 3, cattle milked first produced milk with greater fat and protein content than cattle milked last. In line with these differences in milk yield and composition, the composition of pasture across vertical strata differed, particularly for crude protein (CP) and acid detergent fiber (ADF) content. Conclusion: This work highlights the opportunity to increase herd nutrient use efficiency for improved milk production through strategic pasture allowance and supplementation strategies.
Spatio-temporal regulation of nuclear division by Aurora B kinase Ipl1 in Cryptococcus neoformans

The nuclear division takes place in the daughter cell in the basidiomycetous budding yeast Cryptococcus neoformans. Unclustered kinetochores gradually cluster and the nucleus moves to the daughter bud as cells enter mitosis. Here, we show that the evolutionarily conserved Aurora B kinase Ipl1 localizes to the nucleus upon the breakdown of the nuclear envelope during mitosis in C. neoformans. Ipl1 is shown to be required for timely breakdown of the nuclear envelope as well. Ipl1 is essential for viability and regulates structural integrity of microtubules. The compromised stability of cytoplasmic microtubules upon Ipl1 depletion results in a significant delay in kinetochore clustering and nuclear migration. By generating an in silico model of mitosis, we previously proposed that cytoplasmic microtubules and cortical dyneins promote atypical nuclear division in C. neoformans. Improving the previous in silico model by introducing additional parameters, here we predict that an effective cortical bias generated by cytosolic Bim1 and dynein regulates dynamics of kinetochore clustering and nuclear migration. Indeed, in vivo alterations of Bim1 or dynein cellular levels delay nuclear migration. Results from in silico model and localization dynamics by live cell imaging suggests that Ipl1 spatio-temporally influences Bim1 or/and dynein activity along with microtubule stability to ensure timely onset of nuclear division. Together, we propose that the timely breakdown of the nuclear envelope by Ipl1 allows its own nuclear entry that helps in spatio-temporal regulation of nuclear division during semi-open mitosis in C. neoformans.
Indirect Influence of African Swine Fever Outbreak on the Raven (Corvus corax) Population

Simple Summary The persecution of ravens ceased in the middle of the 20th century, and consequently their abundance started to rise in most European countries. Ravens are food opportunists that can eat plants, prey on animals, and feed on garbage dumps. However, carrion plays a crucial role in their diet. In Central Poland, the carrion of farm animals (disposed of illegally) was thought to be the main food source for ravens. This changed radically in February 2014, after the first case of African swine fever (ASF) in Poland, and the introduction of strict procedures for the utilization of pig and wild boar carcasses to stop the spread of the virus. This decrease in carrion availability influenced the raven population; ravens changed their diet, i.e., instead of feeding on the carrion of pigs (previously their main dietary component), they ate (among others) the carrion of domestic dogs and cats, and also preyed on small vertebrates. Consequently, the number of breeding raven pairs decreased, and birds produced fewer fledglings. This research showed how certain human activities influence wildlife. The illegal disposal of dead animals, motivated by the desire to save money, resulted in abundant food sources for ravens and an increase in population size. Abstract Carrion plays a crucial role in the raven’s diet. In the past, domestic pig carrion was widely available in Poland. This changed with an African swine fever (ASF) outbreak and the introduction of strict procedures aimed at stopping the virus from spreading. We compared data from Central Poland (field and forest mosaic, study area of 105 km2) for two periods, i.e., before (2011–2014) and after the ASF outbreak (2015–2018). In breeding seasons, nests of ravens were found, juveniles were counted, and the time when juveniles left their nests was recorded. Diet composition data were based on pellet analysis and direct observations of feeding birds. The number of breeding pairs dropped from 12.3 to 7.5 in the second period. Breeding parameters were similar. However, birds in the second period had fewer fledglings per successful pair. Domestic pig carrion was found to be an important food item, and with its limited supply, ravens changed their diet, i.e., they fed on the carrion of dogs and cats or preyed on small vertebrates more often. Overall, our study points to a crucial role of the availability of the carrion of big farm animals (i.e., domestic pig) in maintaining the high density of breeding raven populations.
Companion planting with French marigolds protects tomato plants from glasshouse whiteflies through the emission of airborne limonene

Horticulturalists and gardeners in temperate regions often claim that planting marigolds next to tomato plants protects the tomatoes from the glasshouse whitefly (Trialeurodes vaporariorum Westwood). If shown to hold true, this technique could be used in larger-scale tomato production, protecting the crop and helping to introduce greater plant diversity into these agro-ecosystems. Here we present two large-scale glasshouse trials corresponding to the two main ways growers are likely to use marigolds to control whiteflies. In the first, marigolds are grown next to tomato throughout the growing period and we quantify whitefly population growth from the seedling stage over a 48 day infestation period. Here we show that association with marigolds significantly slows whitefly population development. Introducing additional whitefly-attractive ‘pull’ plants around the perimeter of plots has little effect, but reducing the proportion of marigolds and introducing other non-hosts of whiteflies (basil, nasturtium and Chinese cabbage) also reduces whitefly populations on tomato. The second experiment assesses the efficacy of marigolds when used as an ‘emergency’ measure. Here we allow whitefly populations to build to a high density on unprotected tomatoes then introduce marigolds and assess whitefly population over a further period. Following laboratory work showing limonene to be a major chemical component of French marigolds and a negative behaviour response of whiteflies to this compound, limonene dispensers are added as an additional treatment to this experiment. “Emergency” marigold companion planting yielded minimal reductions in whitefly performance, but the use of limonene dispensers was more effective. Our work indicates that companion planting short vine tomatoes with French marigolds throughout the growing season will slow development of whitefly populations. Introducing marigolds to unprotected tomatoes after significant whitefly build-up will be less effective. The use of limonene dispensers placed near to tomato plants also shows promise. It is argued that this work supports the possibility of the development of a mixture of tomato companion plants that infer ‘associational resistance’ against many major invertebrate pests of tomato. Such a mixture, if comprising edible or ornamental plants, would be economically viable, would reduce the need for additional chemical and biological control, and, if used outdoors, would generate plant-diverse agro-ecosystems that are better able to harbour invertebrate wildlife.
Mps1 is associated with the BRAFV600E mutation and predicts poor outcome in patients with colorectal cancer

Colorectal cancer (CRC) with the V600E mutation of B-Raf proto-oncogene serine/threonine kinase (BRAFV600E) mutation is insensitive to chemotherapy and is indicative of a poor patient prognosis. Although BRAF inhibitors have a marked effect on malignant melanoma harboring the BRAFV600E mutation, they have a limited effect on patients with CRC with the same BRAF mutation. A previous study identified a novel gene, monopolar spindle protein kinase 1 (Mps1), a downstream target of BRAFV600E only, rather than of wild-type BRAF as well, which contributes to tumorigenesis in melanoma. In the present study, the incidence of BRAFV600E in patients with CRC was identified and the correlation of Mps1, phospho-extracellular-signal-regulated kinase (p-ERK) and BRAFV600E was investigated. The results indicated that the mutation rate of BRAFV600E was 5.2% in CRC. Poorly differentiated tumors and mucinous tumors have a significantly higher incidence of BRAFV600E compared with well-differentiated tumors and non-mucinous tumors (P<0.05). Kaplan-Meier survival analysis indicated that the survival rate was markedly lower in patients with BRAFV600E compared with in patients with wild-type BRAF (BRAFWT). The expression of p-ERK and Mps1 in CRC with BRAFV600E was significantly higher compared with in CRC with BRAFWT (P<0.05), and their expression is associated with cancer classification, degree of differentiation and lymph node transfusion (P<0.05). In addition p-ERK expression was positively correlated with Mps1 expression, with a contingency coefficient of 0.679 (P=0.002). In conclusion, the results of the present study indicated that Mps1 was significantly associated with BRAFV600E/p-ERK and may serve a crucial function in the development of CRC. The results of the present study raise the possibility that targeting the oncogenic BRAF and Mps1, particularly when in conjunction, could provide promising therapeutic opportunities for the treatment of CRC.
Fraud Detection Protocol for Web-Based Research Among Men Who Have Sex With Men: Development and Descriptive Evaluation

Background Internet is becoming an increasingly common tool for survey research, particularly among “hidden” or vulnerable populations, such as men who have sex with men (MSM). Web-based research has many advantages for participants and researchers, but fraud can present a significant threat to data integrity. Objective The purpose of this analysis was to evaluate fraud detection strategies in a Web-based survey of young MSM and describe new protocols to improve fraud detection in Web-based survey research. Methods This study involved a cross-sectional Web-based survey that examined individual- and network-level risk factors for HIV transmission and substance use among young MSM residing in 15 counties in Central Kentucky. Each survey entry, which was at least 50% complete, was evaluated by the study staff for fraud using an algorithm involving 8 criteria based on a combination of geolocation data, survey data, and personal information. Entries were classified as fraudulent, potentially fraudulent, or valid. Descriptive analyses were performed to describe each fraud detection criterion among entries. Results Of the 414 survey entries, the final categorization resulted in 119 (28.7%) entries identified as fraud, 42 (10.1%) as potential fraud, and 253 (61.1%) as valid. Geolocation outside of the study area (164/414, 39.6%) was the most frequently violated criterion. However, 33.3% (82/246) of the entries that had ineligible geolocations belonged to participants who were in eligible locations (as verified by their request to mail payment to an address within the study area or participation at a local event). The second most frequently violated criterion was an invalid phone number (94/414, 22.7%), followed by mismatching names within an entry (43/414, 10.4%) and unusual email addresses (37/414, 8.9%). Less than 5% (18/414) of the entries had some combination of personal information items matching that of a previous entry. Conclusions This study suggests that researchers conducting Web-based surveys of MSM should be vigilant about the potential for fraud. Researchers should have a fraud detection algorithm in place prior to data collection and should not rely on the Internet Protocol (IP) address or geolocation alone, but should rather use a combination of indicators.
Patterns of biomarkers for three phenotype profiles of persisting specific learning disabilities during middle childhood and early adolescence: A preliminary study

Students without specific learning disabilities [SLDs] [n=18] and with one of three persisting SLDs in written language despite early and current specialized instruction—Dysgraphia [n=21], Dyslexia [n=40], or oral and written language learning disability OWL LD [n=14]— in grades 4 to 9 [N=56 boys, 38 girls] completed behavioral phenotyping assessment and gave a small blood or saliva sample. Molecular analyses informed by current cross-site research on gene candidates for learning disabilities identified associations between molecular genetic markers and the two defining behavioral phenotypes for each SLDs-WL; dysgraphia [impaired writing alphabet from memory for rs3743204 and sentence copying in best handwriting for rs79382 both in DYX1C1], dyslexia [impaired silent word reading/decoding rate for rs4535189 in DCDC2 and impaired spelling/encoding for rs374205 in DYX1C1], and OWL LD [impaired aural syntax comprehension for rs807701 and oral syntax construction for rs807701 both in DYX1C1]. Implications of these identified associations between molecular markers for alleles for different sites within two gene candidates [and mostly one] and hallmark phenotypes are discussed for translation science [application to practice] and neuroimaging that has identified contrasting brain bases for each of the three SLDs.
Meals with Similar Fat Content from Different Dairy Products Induce Different Postprandial Triglyceride Responses in Healthy Adults: A Randomized Controlled Cross-Over Trial

ABSTRACT Background Postprandial lipemia is a risk factor for cardiovascular disease. Dairy products differ in nutrient content and food matrix, and little is known about how different dairy products affect postprandial triglyceride (TG) concentrations. Objective We investigated the effect of meals with similar amounts of fat from different dairy products on postprandial TG concentrations over 6 h in healthy adults. Methods A randomized controlled cross-over study was performed on 47 subjects (30% men), with median (25th–75th percentile) age of 32 (25–46) y and body mass index of 23.6 (21.0–25.8) kg/m2. Meals included 1 of butter, cheese, whipped cream, or sour cream, corresponding to 45 g of fat (approximately 60 energy%). Serum concentrations of TGs (primary outcome), and total cholesterol (TC), low density lipoprotein cholesterol (LDL cholesterol), high density lipoprotein cholesterol (HDL cholesterol), insulin, glucose, non-esterified fatty acids, and plasma glucose-dependent insulinotropic polypeptide (secondary outcomes) were measured before the meal and 2, 4, and 6 h postprandially. Incremental AUC (iAUC) was calculated for the responses, and data were analyzed using a linear mixed model. Results Sour cream induced a 61% larger TG-iAUC0–6 h compared to whipped cream (P < 0.001), a 53% larger TG-iAUC0–6 h compared to butter (P < 0.001), and a 23% larger TG-iAUC0–6 h compared to cheese (P = 0.05). No differences in TG-iAUC0–6 h between the other meals were observed. Intake of sour cream induced a larger HDL cholesterol-iAUC0–6 h compared to cheese (P = 0.01). Intake of cheese induced a 124% larger insulin iAUC0–6 h compared to butter (P = 0.006). No other meal effects were observed. Conclusions High-fat meals containing similar amount of fat from different dairy products induce different postprandial effects on serum TGs, HDL cholesterol, and insulin in healthy adults. The potential mechanisms and clinical impact of our findings remain to be further elucidated. The study was registered at www.clinicaltrials. gov as NCT02836106.
Eosinophil peroxidase over-expression predicts the clinical outcome of patients with primary lung adenocarcinoma

Eosinophil peroxidase (EPO), a heme protein abundantly expressed in eosinophils, involves in the catalysis of cytotoxic oxidants associated with the pathogenesis of cancer, asthma, and allergic inflammatory disorders. To date, its roles in the pathogenesis of lung cancer are still not known. We determined the expression of EPO in the lung adenocarcinoma tissues and the normal adjacent lung tissues using Real-time PCR and Western blotting analysis, respectively. Also, EPO protein expression in 90 lung adenocarcinoma (AD) samples were confirmed with immunohistochemistry (IHC) using tissue microarrays. Meanwhile, we investigated the association between EPO and the clinicopathological characteristics and disease prognosis in the pulmonary adenocarcinoma patients, which demonstrated that EPO mRNA and protein were significantly higher in lung AD tissues that those of the adjacent normal lung tissues (P<0.05). EPO overexpression was significantly correlated with pathologic-tumour nodes metastasen stage (p-TNM stage, P=0.017) and lymph node metastasis (P=0.027). Patients with EPO overexpression showed shorter survival time than those with low EPO levels (P=0.017), according to the Kaplan-Meier survival curve. Furthermore, a multivariate Cox regression model was utilized to analyze the prognostic factors, which indicated that N stage (HR=0.965, 95% CI=0.328-1.359, P=0.008), p-TNM Stage (HR=3.127, 95% CI =2.463-5.015, P=0.021) and high EPO protein expression (HR=3.145, 95% CI=2.016-5.519, P=0.018) were independent factors for the prognosis of lung AD. In conclusion, increased EPO expression could be used as a biomarker for lung AD patients with poor prognosis.
Action Recognition with deep network features and dimension reduction

Action recognition has been studied in computer vision field for years. We present an effective approach to recognize actions using a dimension reduction method, which is applied as a crucial step to reduce the dimensionality of feature descriptors after extracting features. We propose to use sparse matrix and randomized kd-tree to modify it and then propose modified Local Fisher Discriminant Analysis (mLFDA) method which greatly reduces the required memory and accelerate the standard Local Fisher Discriminant Analysis. For feature encoding, we propose a useful encoding method called mix encoding which combines Fisher vector encoding and locality-constrained linear coding to get the final video representations. In order to add more meaningful features to the process of action recognition, the convolutional neural network is utilized and combined with mix encoding to produce the deep network feature. Experimental results show that our algorithm is a competitive method on KTH dataset, HMDB51 dataset and UCF101 dataset when combining all these methods.
Sequential Aggregate MACs from Any MACs: Aggregation and Detecting Functionality

The aggregate message authentication code (aggregate MAC) is a cryptographic primitive which can compress MAC tags on multiple messages into a short aggregate MAC tag. Furthermore, the sequential aggregate MAC can check not only the validity of multiple messages but also the (sequential) order of messages. In this paper, we introduce a new model of sequential aggregate MACs (SAMACs) where an aggregation algorithm generates a sequential aggregate tag depending only on any multiple and independent MAC tags with no secret-key, and we formally define security in this model. We also propose a generic construction of sequential aggregate MACs starting from any MACs without changing the structure of the MACs. This property is useful to make the existing networks more efficient by combining the aggregation algorithm with various MAC schemes already existing in the networks. Furthermore, by extending the results of SAMAC, we also introduce a sequential aggregate MAC which has detecting functionality (SAMD). The SAMD enables us to specify an invalid message or an invalid order of a certain message. We formalize the security of SAMD and provide a generic construction of SAMD in the random oracle model from any MACs and non-adaptive group testing protocols with formal security proofs.
Sea ice variability in the southern Norwegian Sea during glacial Dansgaard-Oeschger climate cycles

New biomarker sea ice reconstructions document that sea ice changes shaped past abrupt climate change. The last glacial period was marked by pronounced millennial-scale variability in ocean circulation and global climate. Shifts in sea ice cover within the Nordic Seas are believed to have amplified the glacial climate variability in northern high latitudes and contributed to abrupt, high-amplitude temperature changes over Greenland. We present unprecedented empirical evidence that resolves the nature, timing, and role of sea ice fluctuations for abrupt ocean and climate change 32 to 40 thousand years ago, using biomarker sea ice reconstructions from the southern Norwegian Sea. Our results document that initial sea ice reductions at the core site preceded the major reinvigoration of convective deep-water formation in the Nordic Seas and abrupt Greenland warming; sea ice expansions preceded the buildup of a deep oceanic heat reservoir. Our findings suggest that the sea ice variability shaped regime shifts between surface stratification and deep convection in the Nordic Seas during abrupt climate changes.