bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Native Grass Substitution with Jengkol (Archidendron jiringa) Peel on Sheep Performance
Authors: Hidayah N , Lubis R , Wiryawan K G , Suharti S , Rita W , Nurhaita
Published: May 2020

The effect of substitution native grass with jengkol (A. jiringa) peel on sheep performance was investigated. Three treatments substitution of jengkol peel (0, 15, 22.5%) were five replications in a randomized block design. This research used 15 sheep with body weight around 15-27 kg. The jengkol peel and concentrate were given in pellet form to reducing the strong odor from jengkol peel. Substitution of jengkol peel at 22.5% increased feed intake (746,74 g/h/d) but did not affect on every daily gain and feed efficiency. The more substitution of jengkol peel change the texture of pellets become more compact and solid so increased the palatability and lead to the feed intake increased. It is concluded that native grass can be substituted with jengkol peel until 22.5% to increase feed consumption of sheep
Complete Dried Ration for Ruminant Based on Pennisetum purpureum cv. Mott Enriched Phyto-Protein of Tree Legumes Leaf
Authors: Anis S.D , Telleng M.M , Kaligis D.A. , Najoan M , Waleleng P.O.V , Dalie S
Published: May 2020

Indonesia is a country with a big human population in the world, still import red meat, since the price of this commodity is higher than those import. The problem is supply of forages is insufficient due to limitation of space for forage production. Especially during the dry season the forages almost disappears and farmers face on shortage supply of forage followed decrease beef production. This research aimed to study the effects of enriched protein of tree legume leaf on complete dry ration based on tropical grass. The treatments were: T-0 = P.purpureum (control); T-1 = PP + GS+Crt; T-2 = PP + LL + Crt; T-3 = PP + IZ + Crt. Treatments were arranged on Completely Randomized Design, with 5 replications. Twenty male goats with average body weight +15 Kg has been used. The results of this research showed that treatment T-3 with I. zolingeriana (IZ) as a source of phyto-protein in complete rations has the best results on all variables measured. It could be concluded that leaves of this tree legumes prospective to support the application of technology complete ration based on local resources to resolve the problem of shortages of feeds supply to ruminant in the tropic region.
The Effect of Cutting Age and Ratooning on Growth, Production, and Nutrient Content of Brown Midrib Resistance Sorghum
Authors: Suhartanto Bambang , Widodo Slamet , Umami Nafiatul , Prasadita Rauufa , Utomo Ristianto
Published: May 2020

This research aimed to determine the effect of cutting age and ratooning on growth, production, and nutrient contentof the Brown Midrib Resistance(BMR) sorghum. This research used a split-plot design with the main plot was ratoon (ratoon 1 and 2), and the subplot was the cutting age (6 and 8 weeks). Each treatment was replicated three times. Sorghum was planted with planting space 75 × 25 cm. The variables observed were growth (plant height, plant length, and leaf width), production (dry matter and organic matter), nutrient content (dry matter content, organic matter, crude protein, extract ether, crude fiber, nitrogen-free extract, and calculation of the total digestible nutrient). The result showed that the ratooning treatment significantly affected (P<0.05) the plant height, plant length, leaf width, dry matter production, organic matter production, and crude fiber content. Dry matter production from ratoon 1 was higher than ratoon 2. The cutting age significantly affected (P<0.05) on plant height, plant length, leaf width, extract ether, crude fiber, crude protein, and total digestible nutrient. Crude protein content at the 6-week cutting age was higher (P <0.05) than the 8-week cutting age. Based on the research, it can be concluded that the growth and production of sorghum will decrease during the second ratoon. The older the plants, the growth, and crude fiber content increased, but the crude protein and total digestible nutrient decreased.
Determination of Minimum Effective Concentration of Cashew Nut Shell (CNS) Pyrolysis Products for Antibacterial Escherichia coli Using Kinetics Approach
Authors: Musta R , Nurliana L , Afil A , Damhuri
Published: May 2020

Determination of minimum effective concentration of cashew nut shell (CNS) pyrolysis products as an antibacterial Escherichia coli using kinetics approach has been done. The purpose of this study is to determine minimum concentration of CNS pyrolysis products which are effective as antibacterial E. coli using chemical kinetics and determine reaction order (n) and rate constant (k), equipped with the rate of reaction equation. And it also determine the relation of initial concentration [A]o, concentration in time [A]t and time variable (t). The results showed that the CNS pyrolysis products consist of two groups: phenolic compounds and alkane compounds. GCMS results also showed that main constituent of the compound is m-octyl-phenol (13.86%). Inhibitory zone on variation in concentration of 100%, 75%, 50%, 25% and 12.5% was 1.47; 1.20; 1.19; 0.87; and 0.75 cm respectively. Reaction order (n) = 0.3 and rate constants (k) = 3.3 so reaction rate equations is r = 3.3 [A]0.3. Relations of initial concentration [A]o and concentration in time [A]t and time variable (t) obtained [A]t = [A]o-0.05t. Minimum concentration making the CNS pyrolysis products effective as an antibacterial E. coli is 24.06%.
Study on the impact of environmental pollution: Parasitic infestation and conditions factor of fish living in amalgamation ponds
Authors: Nur I , Yusnaini  , Idris M , Sari A I
Published: May 2020

Artisanal and small-scale gold mining activities often leave pools. During rainy seasons, they form lakes where various species of fish live. Fish that live in amalgamation lakes or near streams may obtain contaminated water from mercury. Therefore, the aims of this research was to investigate the species of parasites as well as the condition of tilapia that live in the former pool of gold mining in Bombana Regency, Southeast Sulawesi, Indonesia. The samples that were used were tilapia fish (Oreochromis niloticus) with a total sample size of 40 fish. Fish condition factor was evaluated on the basis of body weight and length data. Examination of ectoparasites and endoparasites were performed on fish for prevalence and intensity parameters, while the measurements of heavy metals Hg were carried out on water and sediment and sampled four times. Based on the research results, three species of parasites attacking on external body of fish (ectoparasites) were found, namely Dactylogyrus sp., Ergasilus sp., and Microsporidia (Glugea sp.). Prevalence of those three parasites ranged from 10-90%, while intensity ranged from 1.7-3.5 parasite/fish. Condition factor of tilapia was between 2.70-3.81. Moreover, an average of Hg concentration was higher in sediment (0.167 ppm) than in water (0.039 ppm). Although it seems that the presence of parasites in fish is still relatively low and fish shows normal growth, people should not consume fish live in ex-mining ponds often for the health of the local community.
Sexual behaviors of Ongole Crossbred bulls and cows with colony housing system
Authors: Baliarti E , Panjono  , Ali M H , Widi T S M , Yulianto D E , Atmoko B A , Maulana H , Effendhy J , Prihandini P W , Pamungkas D
Published: May 2020

This study was conducted to determine the sexual behaviors of Ongole crossbreed bulls and cows with colony housing systems. Bull sexual behaviors was observed, including Oro-Nasal Contact (ONC), Flehmen, Mounts Orientation Response (MOR), Mounts, and Services. Cows sexual behaviors were: Mounting, Standing-to-be-mounted (STBM), and vulvar appearance (color, swelling, secretion of mucus). Sexual behaviors were observed in 24 hours, with the estrous cycle stage was determined by changes in the character of the vaginal epithelial cells. The data was analyzed by using statistic varian one-way method. The result showed that Ongole crossbreed bulls had sexual behaviors (ONC, Flehmen, MOR, Mounts, and Services) significantly higher than cows with estrous phase (P<0.01). The intensity of bull sexual behaviors had been influenced by the phase of estrous of the cows. At the time of estrus, the cows had the response of mounting (25%), STBM (100%), reddening vulva (75%), swelling vulva (75%), and mucus secretion (100%) that could be a factor of high sexual behavior intensity of the bulls. The conclusion of this study was bulls and cows that kept with the colony housing system had increased sexual behaviors when the cows at the estrous phase.
The Effect of Soybean Oil Calcium Soap (SOCS) and Cashew Fruit Flour (CFF) on Spermatozoa Motility of Bali Cattle Stored at 5°C
Authors: Putranti Oktora Dwi , Bain Ali , Muhsafaat La Ode
Published: May 2020

This research was conducted to evaluate the motility of Bali cattle spermatozoa stored at 5°C. Bali cattle was given three different types of ration, those are PI: 40% field grass (RL) + 60% concentrate, P2: 40% RL + 60% concentrate supplemented by 5% soybean calcium oil soap, and P3: 40% RL + 60% of the concentrate which was supplemented by 5% COS + 10% cashew fruit flour (CFF). The variables measured were the motility of spermatozoa stored with Egg Yolk Tris diluent at 5°C and observed for 3 (three) days. This study used a completely randomized design (CRD) with 3 treatments and 3 replications. The data of the percentage of motility analyzed using one-way analysis of variance (ANOVA). If there are significant differences (P <0.05) or very significant (P <0.01), then the Tukey-W-Procedure test with SPSS is continued. Bali cattle consuming P3 rations had higher motility (P <0.05) than P1 and P2. Feeding of 5% soybean oil calcium soap (SOCS) and 10% cashew fruit flour CFF had a significant influence on the motility of Bali cattle.
Quality of Garut Ram’s Sperm in Tris Extender Supplemented with Ethylene Diamine Tetraacetic Acid Preserved at Low Temperature (3–5°C)
Authors: Herdis  , Anwar R.I. , Saili T. , Rizal M. , Arifiantini R.I.
Published: May 2020

Ethylenediaminetetraacetic acid (EDTA) is a chemical substance that can bind the heavy metal and other toxic compounds so it is suitable to use for protecting sperm during preservation at 3-5°C. The research aimed to evaluate the role of EDTA to maintain the quality of Garut ram sperm in low-temperature preservation. Semen was collected by an artificial vagina. Fresh semen was evaluated and divided into 3 tubes and diluted with tris extender contain 20% egg yolk (TEY) without EDTA (T1), TEY+0.01% EDTA (T2) and TEY+0.02% EDTA (T 3). Semen was evaluated both macroscopically and microscopically before preserved in a refrigerator at 3-5°C. During storage, semen was also evaluated on daily basis (four consecutive days) that included variables relate to sperm motility (SM), sperm viability (SV), sperm membrane integrity (SMI) and sperm acrosome intact (SAI). The research design used was Completely Randomized Design with three treatments and five replications. Differences between treatments were tested with the least significant difference test. The results showed that the average of each variable gained of fresh semen was 0.88mL for volume, cream for color, thick for consistency and 7 for pH. While the mass movement of sperm was +++ and sperm concentration was 3,962 million cells/mL. The average percentages of SM, SV, abnormality, SMI, and SAI were 75.00%, 86.60%, 4.80%, 84.40%, and 84.80%, respectively. On the day-4 of storage, percentages of SM, SV, SMI, and SAI in control (T1) decreased to 48.75%, 66.25%, 64.75%, and 63.5%, respectively, but still met the requirement of sperm quality for artificial insemination purposes. Moreover, there was no significant difference between T2 (45.00%, 65.00%, 63.25% and 65.25%) and T3 (40.00%, 65.67%, 60.75% and 62.50%) of those variables measured. Finally, it was concluded that the addition of EDTA in Tris extender could maintain the quality of Garut ram sperm.
Evaluation of Implementation Good Dairy Farming Practices (GDFP) at Ambopi Smallholder Dairy Farm, Southeast Sulawesi
Authors: Asminaya Nur Santy , Bain Ali , Sandiah Natsir , Muhsafaat Laode , Irawan Fanny Yulia , Indi Amiludin , Sulfitrana Andini
Published: May 2020

Generally, Dairy cows maintenance traditionally by the farmer on a small scale and did not use Standard Operating Procedures (SOP). This study was done to evaluate the application of Good Dairy Farming Practice (GDFP) at a smallholder dairy farm in Ambopi village. The methods used were a survey and distribution of questionnaires, observations and direct measurements. Data were analyzed descriptively and presented in tabulated frequencies form to illustrate the characteristics of each aspect of raising dairy cows. Assessment of technical aspects of maintenance include: 1) Genetic and Reproduction; 2) Feeding; 3) Management; 4) Enclosures and equipment; 5) Animal health and 6) Animal welfare. The results showed the value of GDFP in unfavorable categories (C) i.e 1.67. Feeding, enclosure and equipment and also animal welfare are in a bad category (D) i.e 0.85; 0.75 and 0.60 respectively while the other technical aspects are in the quite good category (B). D value indicates the poor management of dairy cattle maintenance in Ambopi Village so it needs special attention to optimized milk production and dairy cows productivity.
Profit and Financial Feasibility Analysis of Broiler Chicken Livestock in South Konawe District, Indonesia
Authors: Geo Laode , Saediman H. , Ariani Wa Ode Rachmasari
Published: May 2020

This study is to find out: 1) the cost structure of broiler chicken farming; 2) the level of profitability of broiler chickens; 3) financial feasibility of broiler chicken farms. This research was conducted in Konawe Selatan Regency. To answer the research objectives, the type of data used is primary data obtained by interviews and observations. The analytical tool is descriptive analysis. The results showed that: 1) the types of costs in the chicken farming business were dominated by feed costs and DOC; 2) The profit of broiler chickens farming is quite large at an average of Rp. 28,778,493 per harvest season in which the largest amount of income is Rp. 61,239,900 and the smallest income is Rp. 4,934,250 per harvest season; 3) calculation of R-C Ratio is 1.55 on average or more than 1, so it is feasible to keep it running.
The Profiling of the Farmers with Semi-Intensive and Intensive Cattle Production Systems in South Konawe District, Southeast Sulawesi Province
Authors: Sulfiar A. E. T. , Atmoko B A , Guntoro B. , Budisatria I. G. S.
Published: May 2020

The study aimed at determining the profile of the beef cattle farmers with semi-intensive and intensive production systems in South Konawe district. It was expected that the results of the study could be information source for stakeholders and policymakers in developing farming resources. It was conducted in July-August 2019 using participatory rural appraisal method and involved 105 farmers selected using purposive sampling and considering production system and minimum cattle ownership. Data were quantitatively described and analyzed using independent T-test. The mean age, the cattle farming experience, the number of family members, and the cattle ownership of the farmers were not significantly different. The cattle farming motivations as savings and insurance were higher among the farmers with semi-intensive production system (P<0.05), which were 2.98±0.13 vs. 2.72±0.45, but those as primary livelihood and manure producer were higher (P<0.05) among the farmers with intensive production system, which were 2.28±0.45 and 1.46±0.50 vs. 1.62±0.53 and 1.09±0.29. The participation of the family members of the farmers in the cattle farming activity was not significantly different. It was concluded that the cattle production system related to farming motivation. The farmers with the semi-intensive production systems used cattle more as saving and insurance, while those with the intensive production system used cattle as primary source of income and manure producer.
Acceleration of Laying Chicken Business Development in Response to Egg Demand in Southeast Sulawesi Province
Authors: Salam Idrus , Nafiu Laode
Published: May 2020

The high demand for broiler eggs in Southeast Sulawesi at this time requires efforts from all parties to jointly think about how to fulfill them. The average egg production by farmers in Southeast Sulawesi only reaches 13,021 tons annually, which means that 60% of local farmers’ needs are met and the rest (40%) is supplied from South Sulawesi and East Java. The average increase in egg production per year in the region reached 157,787-kilograms or 12.57 percent. This can have an impact on the scarcity of stock and soaring egg prices in certain seasons that cause inflation. The solution that has been made to anticipate this condition, the government has played an active role together and the community. Hope in the future is to release dependence on egg supply from outside the region. In the last few years, there has been an increase in business in the field of animal husbandry, especially in laying hens. The participation that has been carried out by the government, among others, is to provide skills training on laying hens, including business management. The government has also facilitated the procurement of capital from banks. must be accompanied by the availability of funds as capital for business development. Likewise, the breeders have tried to develop their businesses, which has been proven to have increased production by 13.23% one year.
Priority of Risk (But Not Perceived Magnitude of Risk) Predicts Improved Sun-Protection Behavior Following Genetic Counseling for Familial Melanoma
Authors: Taber Jennifer M , Aspinwall Lisa G , Drummond Danielle M , Stump Tammy K , Kohlmann Wendy , Champine Marjan , Cassidy Pamela , Leachman Sancy A
Published: May 2020

Background

Understanding multiple components of risk perceptions is important because perceived risk predicts engagement in prevention behaviors.

Purpose

To examine how multiple components of risk perceptions (perceived magnitude of and worry about risk, prioritization of the management of one’s risk) changed following genetic counseling with or without test reporting, and to examine which of these components prospectively predicted improvements in sun-protection behavior 1 year later.

Methods

A prospective, nonrandomized study design was used. Participants were 114 unaffected members of melanoma-prone families who (i) underwent genetic testing for a CDKN2A/p16 mutation (n = 69) or (ii) were at comparably elevated risk based on family history and underwent genetic counseling but not testing (no-test controls, n = 45). Participants reported risk perception components and sun-protection behavior at baseline, immediately following counseling, and 1 month and 1 year after counseling.

Results

Factor analysis indicated three risk components. Carriers reported increased perceived magnitude and priority of risk, but not cancer worry. No-test controls showed no changes in any risk perception. Among noncarriers, priority of risk remained high at all assessments, whereas magnitude of risk and cancer worry decreased. Of the three risk components, greater priority of risk uniquely predicted improved self-reported sun protection 1 year post-counseling.

Conclusions

Priority of risk (i) seems to be a component of risk perceptions distinguishable from magnitude of risk and cancer worry, (ii) may be an important predictor of daily prevention behavior, and (iii) remained elevated 1 year following genetic counseling only for participants who received a positive melanoma genetic test result.
Experiences of Discrimination and Urinary Catecholamine Concentrations: Longitudinal Associations in a College Student Sample
Authors: Homandberg Lydia K , Fuller-Rowell Thomas E
Published: May 2020

Background

Experiences of discrimination are a risk factor for subsequent cardiovascular disease. However, there is a lack of longitudinal research examining associations between discrimination and urinary catecholamines. This is surprising given the likely mediating role of sympathetic nervous system dysregulation in the association between psychosocial stress and cardiovascular morbidity.

Purpose

The current study examined the 3 year longitudinal association between experiences of discrimination and urinary catecholamines.

Methods

The sample included 149 college students (mean age at baseline = 18.8, standard deviation = 0.96; 45% Black/African American; 55% White/European American). Concentrations of epinephrine and norepinephrine—urinary catecholamines with established links to psychosocial stress exposure and subsequent morbidity—were determined from 12 hr overnight samples.

Results

Results indicated that experiences of discrimination were associated with increases in both epinephrine (β = .284, standard error [SE] = .117, p = .015) and norepinephrine (β = .306, SE = .114, p = .001). These longitudinal associations persisted after adjusting for negative affect, depression, and rejection sensitivity and did not vary as a function of race/ethnicity.

Conclusions

Results suggest that examination of overnight urinary catecholamines as a biological mediator of associations between experiences of discrimination and cardiovascular morbidity is warranted.
Placental Pathology in COVID-19
Authors: Shanes Elisheva D , Mithal Leena B , Otero Sebastian , Azad Hooman A , Miller Emily S , Goldstein Jeffery A
Published: May 2020

Objectives

To describe histopathologic findings in the placentas of women with coronavirus disease 2019 (COVID-19) during pregnancy.

Methods

Pregnant women with COVID-19 delivering between March 18, 2020, and May 5, 2020, were identified. Placentas were examined and compared to historical controls and women with placental evaluation for a history of melanoma.

Results

Sixteen placentas from patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were examined (15 with live birth in the third trimester, 1 delivered in the second trimester after intrauterine fetal demise). Compared to controls, third trimester placentas were significantly more likely to show at least one feature of maternal vascular malperfusion (MVM), particularly abnormal or injured maternal vessels, and intervillous thrombi. Rates of acute and chronic inflammation were not increased.

The placenta from the patient with intrauterine fetal demise showed villous edema and a retroplacental hematoma.

Conclusions

Relative to controls, COVID-19 placentas show increased prevalence of decidual arteriopathy and other features of MVM, a pattern of placental injury reflecting abnormalities in oxygenation within the intervillous space associated with adverse perinatal outcomes. Only 1 COVID-19 patient was hypertensive despite the association of MVM with hypertensive disorders and preeclampsia. These changes may reflect a systemic inflammatory or hypercoagulable state influencing placental physiology.
Breeding performance of Common Terns (Sterna hirundo) does not decline among older age classes
Authors: Nisbet Ian C T , Iles David , Kaneb Andrew , Mostello Carolyn S , Jenouvrier Stéphanie
Published: May 2020

Declines in reproductive performance among older age classes have been reported in many bird and mammal species, and are commonly presented as demonstrating reproductive senescence. However, no declines in performance could be demonstrated in studies of several bird species. We measured reproductive performance in Common Terns (Sterna hirundo) of known age (2–28 yr) during a 19-yr period at a site in Buzzards Bay, Massachusetts, USA. We measured 6 components of reproductive performance and used generalized additive mixed models (GAMMs) in a Bayesian framework to analyze dependence of each measure on parental age, while controlling for variations among years and indices of individual quality. Four measures of performance improved (earlier laying date, higher values of clutch size, fledging success, and productivity) with age, most rapidly between ages 2 and 10 yr; egg mass and hatching success varied only slightly with age. No measure of performance showed reversals among the older age classes; fledging success and productivity continued to increase through at least age 22 yr. These findings are consistent with results from an earlier study of the same species. Continued increase in reproductive performance through the oldest age classes is not incompatible with “reproductive senescence” (decline in physiological or other functions required for successful reproduction) if either reproductive effort or efficiency continue to increase. Studies within our population have yielded no evidence for age-related increase in reproductive effort, but 3 studies have suggested that older Common Terns can raise chicks more successfully than younger birds without increasing reproductive effort, probably by more efficient foraging and chick provisioning. Our findings suggest that Common Terns offset reproductive senescence by continuing to improve efficiency through at least age 22 yr. Age-related changes in efficiency should be investigated in other species with similar life-history traits.
Combining phenome-driven drug-target interaction prediction with patients’ electronic health records-based clinical corroboration toward drug discovery
Authors: Zhou Mengshi , Zheng Chunlei , Xu Rong
Published: May 2020

Motivation

Predicting drug–target interactions (DTIs) using human phenotypic data have the potential in eliminating the translational gap between animal experiments and clinical outcomes in humans. One challenge in human phenome-driven DTI predictions is integrating and modeling diverse drug and disease phenotypic relationships. Leveraging large amounts of clinical observed phenotypes of drugs and diseases and electronic health records (EHRs) of 72 million patients, we developed a novel integrated computational drug discovery approach by seamlessly combining DTI prediction and clinical corroboration.

Results

We developed a network-based DTI prediction system (TargetPredict) by modeling 855 904 phenotypic and genetic relationships among 1430 drugs, 4251 side effects, 1059 diseases and 17 860 genes. We systematically evaluated TargetPredict in de novo cross-validation and compared it to a state-of-the-art phenome-driven DTI prediction approach. We applied TargetPredict in identifying novel repositioned candidate drugs for Alzheimer’s disease (AD), a disease affecting over 5.8 million people in the United States. We evaluated the clinical efficiency of top repositioned drug candidates using EHRs of over 72 million patients. The area under the receiver operating characteristic (ROC) curve was 0.97 in the de novo cross-validation when evaluated using 910 drugs. TargetPredict outperformed a state-of-the-art phenome-driven DTI prediction system as measured by precision–recall curves [measured by average precision (MAP): 0.28 versus 0.23, P-value < 0.0001]. The EHR-based case–control studies identified that the prescriptions top-ranked repositioned drugs are significantly associated with lower odds of AD diagnosis. For example, we showed that the prescription of liraglutide, a type 2 diabetes drug, is significantly associated with decreased risk of AD diagnosis [adjusted odds ratios (AORs): 0.76; 95% confidence intervals (CI) (0.70, 0.82), P-value < 0.0001]. In summary, our integrated approach that seamlessly combines computational DTI prediction and large-scale patients’ EHRs-based clinical corroboration has high potential in rapidly identifying novel drug targets and drug candidates for complex diseases.

Availability and implementation

nlp.case.edu/public/data/TargetPredict.
SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction
Authors: Uddin Mostofa Rafid , Mahbub Sazan , Rahman M Saifur , Bayzid Md Shamsuzzoha
Published: May 2020

Motivation

Protein structures provide basic insight into how they can interact with other proteins, their functions and biological roles in an organism. Experimental methods (e.g. X-ray crystallography and nuclear magnetic resonance spectroscopy) for predicting the secondary structure (SS) of proteins are very expensive and time consuming. Therefore, developing efficient computational approaches for predicting the SS of protein is of utmost importance. Advances in developing highly accurate SS prediction methods have mostly been focused on 3-class (Q3) structure prediction. However, 8-class (Q8) resolution of SS contains more useful information and is much more challenging than the Q3 prediction.

Results

We present SAINT, a highly accurate method for Q8 structure prediction, which incorporates self-attention mechanism (a concept from natural language processing) with the Deep Inception-Inside-Inception network in order to effectively capture both the short- and long-range interactions among the amino acid residues. SAINT offers a more interpretable framework than the typical black-box deep neural network methods. Through an extensive evaluation study, we report the performance of SAINT in comparison with the existing best methods on a collection of benchmark datasets, namely, TEST2016, TEST2018, CASP12 and CASP13. Our results suggest that self-attention mechanism improves the prediction accuracy and outperforms the existing best alternate methods. SAINT is the first of its kind and offers the best known Q8 accuracy. Thus, we believe SAINT represents a major step toward the accurate and reliable prediction of SSs of proteins.

Availability and implementation

SAINT is freely available as an open-source project at https://github.com/SAINTProtein/SAINT.
18F-MK-6240 PET for early and late detection of neurofibrillary tangles
Authors: Pascoal Tharick A , Therriault Joseph , Benedet Andrea L , Savard Melissa , Lussier Firoza Z , Chamoun Mira , Tissot Cécile , Qureshi Muhammad Naveed Iqbal , Kang Min Su , Mathotaarachchi Sulantha , Stevenson Jenna , Hopewell Robert , Massarweh Gassan , Soucy Jean-Paul , Gauthier Serge , Rosa-Neto Pedro
Published: May 2020

Braak stages of tau neurofibrillary tangle accumulation have been incorporated in the criteria for the neuropathological diagnosis of Alzheimer’s disease. It is expected that Braak staging using brain imaging can stratify living individuals according to their individual patterns of tau deposition, which may prove crucial for clinical trials and practice. However, previous studies using the first-generation tau PET agents have shown a low sensitivity to detect tau pathology in areas corresponding to early Braak histopathological stages (∼20% of cognitively unimpaired elderly with tau deposition in regions corresponding to Braak I–II), in contrast to ∼80–90% reported in post-mortem cohorts. Here, we tested whether the novel high affinity tau tangles tracer 18F-MK-6240 can better identify individuals in the early stages of tau accumulation. To this end, we studied 301 individuals (30 cognitively unimpaired young, 138 cognitively unimpaired elderly, 67 with mild cognitive impairment, 54 with Alzheimer’s disease dementia, and 12 with frontotemporal dementia) with amyloid-β 18F-NAV4694, tau 18F-MK-6240, MRI, and clinical assessments. 18F-MK-6240 standardized uptake value ratio images were acquired at 90–110 min after the tracer injection. 18F-MK-6240 discriminated Alzheimer’s disease dementia from mild cognitive impairment and frontotemporal dementia with high accuracy (∼85–100%). 18F-MK-6240 recapitulated topographical patterns consistent with the six hierarchical stages proposed by Braak in 98% of our population. Cognition and amyloid-β status explained most of the Braak stages variance (P < 0.0001, R2 = 0.75). No single region of interest standardized uptake value ratio accurately segregated individuals into the six topographic Braak stages. Sixty-eight per cent of the cognitively unimpaired elderly amyloid-β-positive and 37% of the cognitively unimpaired elderly amyloid-β-negative subjects displayed tau deposition, at least in the transentorhinal cortex (Braak I). Tau deposition solely in the transentorhinal cortex was associated with an elevated prevalence of amyloid-β, neurodegeneration, and cognitive impairment (P < 0.0001). 18F-MK-6240 deposition in regions corresponding to Braak IV–VI was associated with the highest prevalence of neurodegeneration, whereas in Braak V–VI regions with the highest prevalence of cognitive impairment. Our results suggest that the hierarchical six-stage Braak model using 18F-MK-6240 imaging provides an index of early and late tau accumulation as well as disease stage in preclinical and symptomatic individuals. Tau PET Braak staging using high affinity tracers has the potential to be incorporated in the diagnosis of living patients with Alzheimer’s disease in the near future.
Salience Network Atrophy Links Neuron Type-Specific Pathobiology to Loss of Empathy in Frontotemporal Dementia
Authors: Pasquini Lorenzo , Nana Alissa L , Toller Gianina , Brown Jesse A , Deng Jersey , Staffaroni Adam , Kim Eun-Joo , Hwang Ji-Hye L , Li Libo , Park Youngsoon , Gaus Stephanie E , Allen Isabel , Sturm Virginia E , Spina Salvatore , Grinberg Lea T , Rankin Katherine P , Kramer Joel H , Rosen Howard J , Miller Bruce L , Seeley William W
Published: May 2020

Each neurodegenerative syndrome reflects a stereotyped pattern of cellular, regional, and large-scale brain network degeneration. In behavioral variant of frontotemporal dementia (bvFTD), a disorder of social-emotional function, von Economo neurons (VENs), and fork cells are among the initial neuronal targets. These large layer 5 projection neurons are concentrated in the anterior cingulate and frontoinsular (FI) cortices, regions that anchor the salience network, a large-scale system linked to social-emotional function. Here, we studied patients with bvFTD, amyotrophic lateral sclerosis (ALS), or both, given that these syndromes share common pathobiological and genetic factors. Our goal was to determine how neuron type-specific TAR DNA-binding protein of 43 kDa (TDP-43) pathobiology relates to atrophy in specific brain structures and to loss of emotional empathy, a cardinal feature of bvFTD. We combined questionnaire-based empathy assessments, in vivo structural MR imaging, and quantitative histopathological data from 16 patients across the bvFTD/ALS spectrum. We show that TDP-43 pathobiology within right FI VENs and fork cells is associated with salience network atrophy spanning insular, medial frontal, and thalamic regions. Gray matter degeneration within these structures mediated loss of emotional empathy, suggesting a chain of influence linking the cellular, regional/network, and behavioral levels in producing signature bvFTD clinical features.
Atrial pacing and administration of nifekalant hydrochloride for unstable atrial fibrillation: a case report
Authors: Yakabe Daisuke , Araki Masahiro , Furukawa Kojiro , Nakamura Toshihiro
Published: May 2020

Background

Atrial fibrillation (AF) is a common arrhythmia in patients with hypertrophic cardiomyopathy (HCM) and can deteriorate haemodynamic status.

Case summary

We report a case of a 77-year-old woman with cardiogenic shock due to paroxysmal AF, complicated with HCM and aortic stenosis. Atrial fibrillation was successfully managed with temporary atrial pacing and administration of nifekalant hydrochloride without invasive mechanical circulatory support until surgery. Septal myectomy, aortic valve replacement, and pulmonary vein isolation were performed.

Discussion

This case suggests that atrial pacing and nifekalant may be safe and effective for rhythm control.
Primary extraskeletal chondroblastic osteosarcoma of the pericardium: a case report and literature review
Authors: Wang Qianqian , Wang Xiaojie , Zhu Qing , Gu Xinghua , Gao Peng , Chen Yuguo , Wu Xiaojuan , Li Chuanbao
Published: May 2020

Background

Primary extraskeletal chondroblastic osteosarcoma has very poor prognosis, especially in the elderly. The pericardium is an extremely rare site for this tumour.

Case summary

A 67-year-old man presented with a large pericardial effusion and an intrapericardial mass. His past medical history of pulmonary tuberculosis led us to initially suspect tuberculous pericarditis. Primary extraskeletal chondroblastic osteosarcoma arising from the pericardium was diagnosed by the pathologist after surgery. The patient suffered severe intraoperative blood loss and surgical trauma. He went into shock and died a few hours after surgery.

Discussion

Extraskeletal chondroblastic osteosarcoma is a very rare tumour with a grim prognosis. Clinical manifestations frequently are not specific and can be explained by associated pathology. In this report, we describe an unusual case of primary extraskeletal chondroblastic osteosarcoma located in the pericardium and present a review of the literature.
Pathogenesis of Influenza A(H7N9) Virus in Aged Nonhuman Primates
Authors: Fukuyama Satoshi , Iwatsuki-Horimoto Kiyoko , Kiso Maki , Nakajima Noriko , Gregg Robert W , Katsura Hiroaki , Tomita Yuriko , Maemura Tadashi , da Silva Lopes Tiago Jose , Watanabe Tokiko , Shoemaker Jason E , Hasegawa Hideki , Yamayoshi Seiya , Kawaoka Yoshihiro
Published: May 2020

The avian influenza A(H7N9) virus has caused high mortality rates in humans, especially in the elderly; however, little is known about the mechanistic basis for this. In the current study, we used nonhuman primates to evaluate the effect of aging on the pathogenicity of A(H7N9) virus. We observed that A(H7N9) virus infection of aged animals (defined as age 20–26 years) caused more severe symptoms than infection of young animals (defined as age 2–3 years). In aged animals, lung inflammation was weak and virus infection was sustained. Although cytokine and chemokine expression in the lungs of most aged animals was lower than that in the lungs of young animals, 1 aged animal showed severe symptoms and dysregulated proinflammatory cytokine and chemokine production. These results suggest that attenuated or dysregulated immune responses in aged animals are responsible for the severe symptoms observed among elderly patients infected with A(H7N9) virus.
Influence of Storage Conditions on SARS-CoV-2 Nucleic Acid Detection in Throat Swabs
Authors: Li Lin , Li Xiao , Guo Zhendong , Wang Zhongyi , Zhang Ke , Li Chao , Wang Changjun , Zhang Shoufeng
Published: May 2020

The detection of SARS-CoV-2 infection is the premise of quarantine. In many countries or areas, samples need to be shipped or inactivated before SARS-CoV-2 testing. In this study, we checked the influence of sample storage conditions on SARS-CoV-2 nucleic acid testing results, including sample inactivation time, storage temperature, and storage time. All of these conditions caused an increase in the cycle threshold values of the nucleic acid tests and led to the misclassification of at least 10.2% of positive cases as negative or suspected. The results highlight the importance of immediate testing of samples for SARS-CoV-2 nucleic acid detection.
Binary evolution leading to the formation of the very massive neutron star in the J0740+6620 binary system
Authors: Echeveste M , Novarino M L , Benvenuto O G , De Vito M A
Published: May 2020

We study the evolution of close binary systems in order to account for the existence of the recently observed binary system containing the most massive millisecond pulsar ever detected, PSR J0740+6620, and its ultra-cool helium white dwarf companion. In order to find a progenitor for this object we compute the evolution of several binary systems composed by a neutron star and a normal donor star employing our stellar code. We assume conservative mass transfer. We also explore the effects of irradiation feedback on the system. We find that irradiated models also provide adequate models for the millisecond pulsar and its companion, so both irradiated and non irradiated systems are good progenitors for PSR J0740+6620. Finally, we obtain a binary system that evolves and accounts for the observational data of the system composed by PSR J0740+6620 (i.e. orbital period, mass, effective temperature and inferred metallicity of the companion, and mass of the neutron star) in a time scale smaller than the age of the Universe. In order to reach an effective temperature as low as observed, the donor star should have an helium envelope as demanded by observations.
Structure of two G-quadruplexes in equilibrium in the KRAS promoter
Authors: Marquevielle Julien , Robert Coralie , Lagrabette Olivier , Wahid Mona , Bourdoncle Anne , Xodo Luigi E , Mergny Jean-Louis , Salgado Gilmar F
Published: May 2020

KRAS is one of the most mutated oncogenes and still considered an undruggable target. An alternative strategy would consist in targeting its gene rather than the protein, specifically the formation of G-quadruplexes (G4) in its promoter. G4 are secondary structures implicated in biological processes, which can be formed among G-rich DNA (or RNA) sequences. Here we have studied the major conformations of the commonly known KRAS 32R, or simply 32R, a 32 residue sequence within the KRAS Nuclease Hypersensitive Element (NHE) region. We have determined the structure of the two major stable conformers that 32R can adopt and which display slow equilibrium (>ms) with each other. By using different biophysical methods, we found that the nucleotides G9, G25, G28 and G32 are particularly implicated in the exchange between these two conformations. We also showed that a triad at the 3′ end further stabilizes one of the G4 conformations, while the second conformer remains more flexible and less stable.
A powder method for the high-efficacy evaluation of electro-optic crystals
Authors: Xu Feng , Zhang Ge , Luo Min , Peng Guang , Chen Yu , Yan Tao , Ye Ning
Published: May 2020

The electro-optic crystal holds great promise for extensive applications in optoelectronics and optical communication. However, the discovery of novel electro-optic crystals is sporadic due to the difficulties of large-sized crystal growth for electro-optic coefficient measurement. Herein, to address this issue, a high-efficacy evaluation method using accessible powder samples is proposed in which the second-harmonic-generation effect, infrared reflectance spectrum and Raman spectrum are introduced to predict the magnitude of the electro-optic coefficient. The calculated electro-optic coefficients of numerous reported electro-optic crystals through this approach give universal agreement to the experimental values, evidencing the validity of the strategy. Based on this method, CsLiMoO4 is screened as a novel potential electro-optic crystal and a high-quality crystal is grown by the Czochralski technique for electro-optic coefficient measurement using the half-wave voltage method, the result of which is also comparable to the calculated value. Consequently, the evaluation strategy presented here will pave a new way to explore promising electro-optic crystals efficiently.
Correlation Between Chest CT Findings and Clinical Features of 211 COVID-19 Suspected Patients in Wuhan, China
Authors: Song Songlin , Wu Feihong , Liu Yiming , Jiang Hongwei , Xiong Fu , Guo Xiaopeng , Zhang Hongsen , Zheng Chuansheng , Yang Fan
Published: May 2020

Background

Chest computed tomography (CT) has been widely used to assess pulmonary involvement in COVID-19. We aimed to investigate the correlation between chest CT and clinical features in COVID-19 suspected patients with or without fever.

Methods

We retrospectively enrolled 211 COVID-19 suspected patients who underwent both chest CT and reverse transcription polymerase chain reaction in Wuhan, China. The performance of CT in patients with relevant onset of symptoms, with fever (n = 141) and without fever (n = 70), was assessed respectively.

Results

The sensitivity of CT for COVID-19 was 97.3%, with area under the curve (AUC) of 0.71 (95% confidence interval [CI], 0.66–0.76). There were 141 suspected patients with fever and 70 without fever. In the fever group, 4 variables were screened to establish the basic model: age, monocyte, red blood cell, and hypertension. The AUC of the basic model was 0.72 (95% CI, 0.63–0.81), while the AUC of the CT-aided model was 0.77 (95% CI, 0.68–0.85), a significant difference (P < .05). In the nonfever group, only dry cough was screened out to establish the basic model. The AUC was 0.76 (95% CI, 0.64–0.88), which was not significantly different than the CT-aided model (P = .08).

Conclusions

Chest CT has a high sensitivity in patients with COVID-19, and it can improve diagnostic accuracy for COVID-19 suspected patients with fever during the initial screen, whereas its value for nonfever patients remains questionable.
Life Stressors: Elevations and Disparities Among Older Adults with Pain
Authors: Brennan Penny L
Published: May 2020

Objective

To examine stressor elevations among older adults with pain, and gender and race disparities in the dual burdens of late-life pain and stressors.

Design

Cross-sectional.

Setting

Community.

Subjects

Participants in the Longitudinal Late-Life Health study (LLLH; N = 1,884) and the Health and Retirement Study (HRS; N = 7,704).

Methods

Pain and stressor measures were harmonized across the LLLH and HRS samples. Analyses of covariance were conducted to determine the effects of older adults’ pain, gender, race, and interactions between these factors, on their stressors in nine separate life domains, and in stressors overall.

Results

In both the LLLH and HRS samples, older adults with painful conditions (joint, back, headache, chest pain), more numerous painful conditions, more severe pain, and more pain interference had elevated stressors in all life domains, compared with older adults without or with less serious pain. Pain was more prevalent among women and nonwhites than men and whites. Stressor exposure was higher for men than women in most life domains; it was higher for nonwhites than whites in all life domains. For certain types of pain and life domains, pain and gender, as well as pain and race, interacted to predict stressor elevations.

Conclusions

Late-life pain is associated with elevations in stressors, and there are gender and race disparities in the dual burdens of heightened pain and elevated stressors in later life. Pain and stressors are not consistently more strongly linked among older women than older men, or among older nonwhite than older white persons.
The effects of phenanthrene exposure on Treg and Th17 cells related cytokines in female rats
Authors: Ma Haitao , Guo Huizhen , Zhang Wenwen , Hu Fengjing , Huang Yushan , Zeng Yong , Liu Yang , Li Chengyun , Wang Junling
Published: May 2020

Phenanthrene (Phe) female rat model was established to explore the mechanism of Phe on immune impairment. The rats were randomly divided into three groups, including control (C), low (L), and high (H) groups. Phe was supplied to L and H groups at the dose of 180 and 900 mg/kg orally at first day and with the dose of 90 and 450 mg/kg by intraperitoneal injection at the last 2 days. The C group was enriched with the same volume of corn oil. The liver tissue was collected. Then, the protein and mRNA expressions of interleukin (IL)-35 and the concentration IL-17 were detected to evaluate the function of regulatory T cells (Treg cells) and T helper 17 cells (Th17 cells). In addition, IL-1β and interferon-γ (IFN-γ) were analyzed to evaluate the immune impairment. The results showed that the protein and mRNA expressions of IL-35 decreased significantly in H groups (P < 0.05). Meanwhile, there were significant increases in IL-17, IFN-γ and IL-1β in the liver of H group (P < 0.05). This study demonstrated that Phe exposure might be associated with the immune impairment via changing inflammatory mediators including IL-35 and IL-17 in female rats.