Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of seed storage periods, conditions and materials on seed quality of some soybean cultivars.

- In order to examine the effect of storage period, storage conditions and storage materials on seed quality of some soybean cultivars. A Laboratory experiment was conducted in Agronomy Department, Fac. of Agric. , Mansoura Univ., Egypt during 2011 and 2012. The results showed that acid number, peroxide number and electrical conductivity (dSm-1)were increased with the period of ageingwere increased. The obtained results indicated that Giza 22cultivar exceeded other cultivars in electrical conductivity and moisture percentage. Giza 35 cultivar exceeded the other cultivars in acid number and peroxide number. Crawford cultivar exceeded the other cultivars in oil percentage. Storage under refrigerator conditions at 10°C ± 1 exceeded storage under ambient conditions in oil percentage and moisture percentage. Storage under ambient conditions exceeded storage under refrigerator conditions at 10°C ± 1 in acid number, peroxide number and electrical conductivity. Acid number and peroxide number significantly affected by storage material. Storage soybean cultivars as seeds or pods in plastic bags recorded lowest values of peroxide and acid number compared with other package materials. Results clearly showed that oil percentage, moisture percentage, acid number, peroxide number and electrical conductivity significantly affected by the varies interactions.
Higher Order Oligomerization of the Licensing ORC4 Protein Is Required for Polar Body Extrusion in Murine Meiosis

We have previously shown that the DNA replication licensing factor ORC4 forms a cage around the chromosomes that are extruded in both polar bodies during murine oogenesis, but not around the chromosomes that are retained in the oocyte or around the sperm chromatin. We termed this structure the ORC4 cage. Here, we tested whether the formation of the ORC4 cage is necessary for polar body extrusion (PBE). We first experimentally forced oocytes to extrude sperm chromatin as a pseudo‐polar body and found that under these conditions the sperm chromatin did become enclosed in an ORC4 cage. Next, we attempted to prevent the formation of the ORC4 cage by injecting peptides that contained sequences of different domains of the ORC4 protein into metaphase II (MII) oocytes just before the cage normally forms. Our rationale was that the ORC4 peptides would block protein‐protein interactions required for cage formation. Two out of six tested peptides prevented the ORC4 cage formation and simultaneously inhibited PBE, resulting in the formation of two pronuclei (2 PN) that were retained in the oocyte. Together, these data demonstrate that ORC4 oligomerization is required to form the ORC4 cage and that it is required for PBE. J. Cell. Biochem. 118: 2941–2949, 2017. © 2017 Wiley Periodicals, Inc.
A Bayesian Approach to Multistate Hidden Markov Models: Application to Dementia Progression

Abstract People are living longer than ever before, and with this arises new complications and challenges for humanity. Among the most pressing of these challenges is of understanding the role of aging in the development of dementia. This article is motivated by the Mayo Clinic Study of Aging data for 4742 subjects since 2004, and how it can be used to draw inference on the role of aging in the development of dementia. We construct a hidden Markov model (HMM) to represent progression of dementia from states associated with the buildup of amyloid plaque in the brain, and the loss of cortical thickness. A hierarchical Bayesian approach is taken to estimate the parameters of the HMM with a truly time-inhomogeneous infinitesimal generator matrix, and response functions of the continuous-valued biomarker measurements are cut-point agnostic. A Bayesian approach with these features could be useful in many disease progression models. Additionally, an approach is illustrated for correcting a common bias in delayed enrollment studies, in which some or all subjects are not observed at baseline. Standard software is incapable of accounting for this critical feature, so code to perform the estimation of the model described below is made available online. Code submitted with this article was checked by an Associate Editor for Reproducibility and is available as an online supplement.
Antithrombotic therapy in obesity

summary Clinical management of obese subjects to reduce their risk of suffering cardiovascular events is complex. Obese patients typically require preventive strategies, life-style modifications, and multi-drug therapy to address obesity-induced co-morbidities. Data regarding the effects of excess weight on the pharmacokinetics of most drugs is scarce as these individuals are often excluded from clinical trials. However, the physiological alterations observed in obese patients and their lower response to some antiplatelet agents and anticoagulants have suggested that dosage regimes need to be adjusted for these subjects. In this review we will briefly discuss platelet alterations that can contributeto increased thrombotic risk, analyse existing data regarding the effects of obesity on drug pharmacokinetics focusing on antiplatelet agents and anticoagulants, and we will describe the beneficial effects of weight loss on thrombosis.
Primary surgery with or without postoperative radiotherapy in early stage squamous cell carcinoma in the anal canal and anal margin

Abstract Background Standard treatment of localized squamous cell carcinoma of the anus (SCCA) is radiotherapy (RT) combined with chemotherapy, that is, chemoradiation (CRT). Primary surgery has a limited role, but is a recommended treatment for small well differentiated SCCA localized in the anal margin, with re-excision or postoperative RT/CRT in case of involved surgical margins. The evidence supporting these strategies is limited. Aim To study the recurrence patterns and survival outcomes in patients treated with surgery alone compared with surgery followed by postoperative RT/CRT. Material and methods From a large Nordic database we identified 93 patients with stage TxT1–2N0M0 SCCA treated with surgery alone (n = 59) or surgery followed by RT/CRT (n = 34). Surgery consisted of local excision in 86 patients and abdominoperineal resection in seven patients, all of them in the surgery alone group. In 38 (41%) of the patients, the tumor was localized merely in the anal margin and in all remaining cases the anal canal was involved. Median RT dose to the tumor bed was 54 (range 46–66) Gy. Adjuvant RT to lymph nodes was given in 75% of the patients. Half of the patients received concomitant chemotherapy, usually 5-fluorouracil and mitomycin C. Results The locoregional recurrence (LRR) rate was significantly higher after surgery alone compared to surgery followed by adjuvant RT/CRT (36% vs. 9%, p = .006). The 3-year recurrence free survival (RFS) and overall survival (OS) were significantly better in patients who received postoperative RT/CRT than in patients who did not (3-year RFS 84.2% vs. 52.7%, p < .001 and 3-year OS 87.2% vs. 70%, p = .026). Conclusions Surgery alone of SCCA was associated with a high LRR rate and poor survival. The addition of postoperative RT/CRT lead to significantly improved locoregional control and survival.
The influence of various calcium and phosphorus levels on tibia strength and eggshell quality of pullets during peak production.

One thousand and eighty DeKalb XL pullets were randomly allocated to nine treatments and arranged in a 3 x 3 factorial to determine the effects of three levels of dietary calcium (2.75, 3.75, and 4.25%) and three levels of dietary available phosphorus (.30, .40, and .50%) on eggshell quality and tibia weight, tibia breaking strength, tibia ash, and bone mineral content of pullets during peak production. Feed consumption increased as dietary calcium or phosphorus increased. Increasing dietary calcium caused a significant linear increase in egg specific gravity, but dietary phosphorus had no significant effect on egg specific gravity. Calcium and phosphorus levels did not significantly affect egg production, body weight, plasma chloride, or phosphorus. Ionized calcium increased significantly as dietary calcium increased. Tibia breaking strength, tibia weight, tibia ash, and bone mineral content increased significantly with increasing dietary calcium. Dietary phosphorus had no significant effect on these parameters. However, when 2.75% calcium was fed, reducing dietary phosphorus significantly decreased tibia weight, tibia ash, and bone mineral content.
Carcass composition and yield of 1991 vs 1957 broilers when fed "typical" 1957 and 1991 broiler diets.

Whole carcass yield and the yield of parts (i.e., wings, saddle and legs, Pectoralis major, Pectoralis minor, breast skin, rack, abdominal fat pad, heart, and lungs), as well as whole carcass analysis for fat, moisture, and ash, were measured in the 1957 Athens-Canadian Randombred Control (ACRBC) and in the 1991 Arbor Acres (AA) feather-sexable strain, when fed "typical" 1957 and 1991 diets. Using the average of both sexes, the carcass weights of the 1991 birds on the 1991 diets were 4.4, 3.9, and 3.5 times heavier than those from the 1957 ACRBC on the 1957 diet at 43, 71, and 84 d of age, respectively. Birds fed the 1991 diets had significantly heavier carcass weights than those fed the 1957 diets. Hot carcass yield of the AA broiler (mean of both sexes) was approximately 6 to 7% higher at the same age than for the ACRBC. Water uptake in the carcass (following a 60-min immersion in ice water) was approximately 2 to 2.5% higher in the ACRBC than in the AA broiler. Yield of saddle and legs as a percentage of live BW was about 4% higher in the AA than in the ACRBC. Dietary regimen did not affect the yield of saddle and legs. Males had 2 to 3% more saddle and legs than the females. The yield of total breast meat for the AA was approximately 3% higher (mean = 16.9%) than for the ACRBC over both sexes and all ages. Breast yield on the 1991 diets was approximately 1.2% higher for the AA than for the ACRBC. Females had slightly higher breast yield (1%) than males. The AA broiler had consistently heavier fat pads and higher percentage carcass fat at the same age and on the same diet than did the ACRBC. The percentage carcass fat was significantly higher on the 1991 vs the 1957 diet and in females vs males. The male-female difference in percentage carcass fat increased with age. Heart and lung size as a percentage of live BW were lower in the AA than in the ACRBC.
ComPAS: Community Preserving Sampling for Streaming Graphs

In the era of big data, graph sampling is indispensable in many settings. Existing sampling methods are mostly designed for static graphs, and aim to preserve basic structural properties of the original graph (such as degree distribution, clustering coefficient etc.) in the sample. We argue that for any sampling method it is impossible to produce an universal representative sample which can preserve all the properties of the original graph; rather sampling should be application specific (such as preserving hubs - needed for information diffusion). Here we consider community detection as an application scenario. We propose ComPAS, a novel sampling strategy that unlike previous methods, is not only designed for streaming graphs (which is a more realistic representation of a real-world scenario) but also preserves the community structure of the original graph in the sample. Empirical results on both synthetic and different real-world graphs show that ComPAS is the best to preserve the underlying community structure with average performance reaching 73.2% of the most informed algorithm for static graphs.
Female hormonal factors and osteoarthritis of the knee, hip and hand: a narrative review

Abstract Osteoarthritis is a leading cause of disability with no cure. The incidence of osteoarthritis is sexually dimorphic: women have a higher rate of osteoarthritis than men after the age of 50. Research has investigated the contribution of sex hormones, reproductive factors and hormone supplementation to osteoarthritis. It has been recognized that different joints are susceptible to different risk factors for osteoarthritis. We reviewed the evidence for the effect of endogenous sex hormones, reproductive factors and hormone supplementation on joint-specific osteoarthritis of the knee, hip and hand. Although the role of these hormonal factors in the pathogenesis of osteoarthritis is complex, data suggest that endogenous hormones and reproductive factors have a role in the pathogenesis of osteoarthritis, especially knee osteoarthritis, with uncertainty for the effect of exogenous hormones. From the available data, it is hard to conclude whether this is a direct effect of hormonal factors, or whether other factors related to these hormonal factors, i.e. obesity and inflammation, have a role in this association. Further studies should consider the mediation effect of body weight and inflammation, change in body weight throughout life, circulatory levels of all endogenous hormones and circulatory levels of hormones after hormone supplementation in this complex relationship.
Validated Predictions of Metabolic Energy Consumption for Submaximal Effort Movement

Physical performance emerges from complex interactions among many physiological systems that are largely driven by the metabolic energy demanded. Quantifying metabolic demand is an essential step for revealing the many mechanisms of physical performance decrement, but accurate predictive models do not exist. The goal of this study was to investigate if a recently developed model of muscle energetics and force could be extended to reproduce the kinematics, kinetics, and metabolic demand of submaximal effort movement. Upright dynamic knee extension against various levels of ergometer load was simulated. Task energetics were estimated by combining the model of muscle contraction with validated models of lower limb musculotendon paths and segment dynamics. A genetic algorithm was used to compute the muscle excitations that reproduced the movement with the lowest energetic cost, which was determined to be an appropriate criterion for this task. Model predictions of oxygen uptake rate (VO2) were well within experimental variability for the range over which the model parameters were confidently known. The model's accurate estimates of metabolic demand make it useful for assessing the likelihood and severity of physical performance decrement for a given task as well as investigating underlying physiologic mechanisms.
Clinical Features of Pulmonary Sarcoidosis Complicated by Lung Cancer

Objective For lung cancer complicated with sarcoidosis, there are no exact features that indicate whether lymphadenopathy is metastatic. This makes the validity of surgery uncertain for clinicians. The aim of this study was to clarify the clinical features of pulmonary sarcoidosis complicated by lung cancer, especially from the viewpoint of evaluating lymphadenopathy. Methods We retrospectively reviewed medical records from 2004 to 2013 at our institution, and 18 patients who were diagnosed with sarcoidosis and lung cancer were thus found to be eligible. We investigated the relationship between the clinical and pathological findings of their swollen lymph nodes. Results Of 18 patients, 11 conducted surgery, and the postoperative pathological evaluation of swollen lymph nodes was done in 8 of the patients. Postoperative N factor in all these patients was 0, even though lymphatic metastasis had been suspected preoperatively because of the unbalanced distribution of lymphadenopathy or the accumulation of fluorodeoxyglucose. Conclusion In patients with lung cancer complicated by sarcoidosis, the clinical assessment of the state of lymphadenopathy is difficult to make. However, as many of them tend to be benign, we suggest that surgical resection should be considered for a complete cure in the absence of any remote metastasis.
Director: A User Interface Designed for Robot Operation with Shared Autonomy

Operating a high degree of freedom mobile manipulator, such as a humanoid, in a field scenario requires constant situational awareness, capable perception modules, and effective mechanisms for interactive motion planning and control. A well‐designed operator interface presents the operator with enough context to quickly carry out a mission and the flexibility to handle unforeseen operating scenarios robustly. By contrast, an unintuitive user interface can increase the risk of catastrophic operator error by overwhelming the user with unnecessary information. With these principles in mind, we present the philosophy and design decisions behind Director—the open‐source user interface developed by Team MIT to pilot the Atlas robot in the DARPA Robotics Challenge (DRC). At the heart of Director is an integrated task execution system that specifies sequences of actions needed to achieve a substantive task, such as drilling a wall or climbing a staircase. These task sequences, developed a priori, make online queries to automated perception and planning algorithms with outputs that can be reviewed by the operator and executed by our whole‐body controller. Our use of Director at the DRC resulted in efficient high‐level task operation while being fully competitive with approaches focusing on teleoperation by highly trained operators. We discuss the primary interface elements that comprise Director, and we provide an analysis of its successful use at the DRC.
Assessment of Early Evidence of Multiple Sclerosis in a Prospective Study of Asymptomatic High-Risk Family Members

Importance Subclinical inflammatory demyelination and neurodegeneration often precede symptom onset in multiple sclerosis (MS). Objective To investigate the prevalence of brain magnetic resonance imaging (MRI) and subclinical abnormalities among asymptomatic individuals at risk for MS. Design, Setting, and Participants The Genes and Environment in Multiple Sclerosis (GEMS) project is a prospective cohort study of first-degree relatives of people with MS. Each participant’s risk for MS was assessed using a weighted score (Genetic and Environmental Risk Score for Multiple Sclerosis Susceptibility [GERSMS]) comprising an individual’s genetic burden and environmental exposures. The study dates were August 2012 to July 2015. Main Outcomes and Measures Participants in the top and bottom 10% of the risk distribution underwent standard and quantitative neurological examination, including disability status, visual, cognitive, motor, and sensory testing, as well as qualitative and quantitative neuroimaging with 3-T brain MRI and optical coherence tomography. Results This study included 100 participants at risk for MS, with 41 at higher risk (40 women [98%]) and 59 at lower risk (25 women [42%]), at a mean (SD) age of 35.1 (8.7) years. Given the unequal sex distribution between the 2 groups, the analyses were restricted to women (n = 65). When considering all measured outcomes, higher-risk women differed from lower-risk women (P = .01 by omnibus test). Detailed testing with a vibration sensitivity testing device in a subgroup of 47 women showed that higher-risk women exhibited significantly poorer vibration perception in the distal lower extremities (P = .008, adjusting for age, height, and testing date). Furthermore, 5 of 65 women (8%) (4 at higher risk and 1 at lower risk) met the primary neuroimaging outcome of having T2-weighted hyperintense brain lesions consistent with the 2010 McDonald MRI criteria for dissemination in space. A subset of participants harbor many different neuroimaging features associated with MS, including perivenous T2-weighted hyperintense lesions and focal leptomeningeal enhancement, consistent with the hypothesis that these individuals are at higher risk of developing clinical symptoms of MS than the general population. Conclusions and Relevance Higher-risk asymptomatic family members of patients with MS are more likely to have early subclinical manifestations of MS. These findings underscore the importance of early detection in high-risk individuals. Trial Registration clinicaltrials.gov Identifier: NCT01353547
Early articular cartilage MRI T2 changes after anterior cruciate ligament reconstruction correlate with later changes in T2 and cartilage thickness

Anterior cruciate ligament (ACL) injury is a known risk factor for future development of osteoarthritis (OA). This human clinical study seeks to determine if early changes to cartilage MRI T2 maps between baseline and 6 months following ACL reconstruction (ACLR) are associated with changes to cartilage T2 and cartilage thickness between baseline and 2 years after ACLR. Changes to T2 texture metrics and T2 mean values in medial knee cartilage of 17 human subjects 6 months after ACLR were compared to 2‐year changes in T2 and in cartilage thickness of the same areas. T2 texture and mean assessments were also compared to that of 11 uninjured controls. In ACLR subjects, six‐month changes in mean T2 correlated to 2‐year changes in mean T2 (R = 0.80, p = 0.0001), and 6‐month changes to T2 texture metrics, but not T2 mean, correlated with 2‐year changes in medial femoral cartilage thickness in 9 of the 20 texture features assessed (R = 0.48–0.72, p ≤ 0.05). Both mean T2 and texture differed (p < 0.05) between ALCR subjects and uninjured controls. Clinical Significance: These results show that short‐term longitudinal evaluation of T2 map and textural changes may provide early warning of cartilage at risk for progressive degeneration after ACL injury and reconstruction. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:699–706, 2017.
Psychometric Analysis of the Heart Failure Somatic Perception Scale as a Measure of Patient Symptom Perception

Background: Symptoms are known to predict survival among patients with heart failure (HF), but discrepancies exist between patients’ and health providers’ perceptions of HF symptom burden. Objective: The purpose of this study is to quantify the internal consistency, validity, and prognostic value of patient perception of a broad range of HF symptoms using an HF-specific physical symptom measure, the 18-item HF Somatic Perception Scale v. 3. Methods: Factor analysis of the HF Somatic Perception Scale was conducted in a convenience sample of 378 patients with chronic HF. Convergent validity was examined using the Physical Limitation subscale of the Kansas City Cardiomyopathy Questionnaire. Divergent validity was examined using the Self-care of HF Index self-care management score. One-year survival based on HF Somatic Perception Scale scores was quantified using Cox regression controlling for Seattle HF Model scores to account for clinical status, therapeutics, and lab values. Results: The sample was 63% male, 85% white, 67% functionally compromised (New York Heart Association class III–IV) with a mean (SD) age of 63 (12.8) years. Internal consistency of the HF Somatic Perception Scale was &agr; = . 90. Convergent (r = −0.54, P < .0001) and divergent (r = 0.18, P > .05) validities were supported. Controlling for Seattle HF scores, HF Somatic Perception Scale was a significant predictor of 1-year survival, with those most symptomatic having worse survival (hazard ratio, 1.012; 95% confidence interval, 1.001–1.024; P = .038). Conclusions: Perception of HF symptom burden as measured by the HF Somatic Perception Scale is a significant predictor of survival, contributing additional prognostic value over and above objective Seattle HF Risk Model scores. This analysis suggests that assessment of a broad range of HF symptoms, or those related to dyspnea or early and subtle symptoms, may be useful in evaluating therapeutic outcomes and predicting event-free survival.