Miracle-dz/UniFAR-FTUs huggingface dataset:
G-SGD: Optimizing ReLU Neural Networks in its Positively Scale-Invariant Space

It is well known that neural networks with rectified linear units (ReLU) activation functions are positively scale-invariant. Conventional algorithms like stochastic gradient descent optimize the neural networks in the vector space of weights, which is, however, not positively scale-invariant. This mismatch may lead to problems during the optimization process. Then, a natural question is: can we construct a new vector space that is positively scale-invariant and sufficient to represent ReLU neural networks so as to better facilitate the optimization process? In this paper, we provide our positive answer to this question. First, we conduct a formal study on the positive scaling operators which forms a transformation group, denoted as G. We prove that the value of a path (i.e. the product of the weights along the path) in the neural network is invariant to positive scaling and the value vector of all the paths is sufficient to represent the neural networks under mild conditions. Second, we show that one can identify some basis paths out of all the paths and prove that the linear span of their value vectors (denoted as G-space) is an invariant space with lower dimension under the positive scaling group. Finally, we design stochastic gradient descent algorithm in G-space (abbreviated as G-SGD) to optimize the value vector of the basis paths of neural networks with little extra cost by leveraging back-propagation. Our experiments show that G-SGD significantly outperforms the conventional SGD algorithm in optimizing ReLU networks on benchmark datasets.
Metatranscriptome Profiling Indicates Size-Dependent Differentiation in Plastic and Conserved Community Traits and Functional Diversification in Dinoflagellate Communities

Communities of microscopic dinoflagellates are omnipresent in aquatic ecosystems. Consequently, their traits drive community processes with profound effects on global biogeochemistry. Species traits are, however, not necessarily static but respond to environmental changes in order to maintain fitness and may differ with cell size that scales physiological rates. Comprehending such trait characteristics is necessary for a mechanistic understanding of plankton community dynamics and resulting biogeochemical impacts. Here, we used information theory to analyze metatranscriptomes of micro- and nano-dinoflagellate communities in three ecosystems. Measures of gene expression variations were set as a proxy to determine conserved and plastic community traits and the environmental influence on trait changes. Using metabarcoding, we further investigated if communities with a more similar taxon composition also express more similar traits. Our results indicate that plastic community traits mainly arise from membrane vesicle associated processes in all the environments we investigated. A specific environmental influence on trait plasticity was observed to arise from nitrogen availability in both size classes. Species interactions also appeared to be responsible for trait plasticity in the smaller-sized dinoflagellates. Additionally, the smaller-sized dinoflagellate communities are characterized by the expression of a large pool of habitat specific genes despite being taxonomically more similar across the habitats, in contrast to the microplanktonic assemblages that adapted to their environments by changing species composition. Our data highlight the functional diversification on the gene level as a signature of smaller sized dinoflagellates, nitrogen availability and species interactions as drivers of trait plasticity, and traits most likely linked to fitness and community performance.
Thesiumnautimontanum, a new species of Thesiaceae (Santalales) from South Africa

Abstract Thesiumnautimontanum M.A. García, Nickrent & Mucina, a new species from the Matroosberg Mt. of Western Cape Province of South Africa, is described and illustrated. This species shows several morphological features unusual for the genus including stem sympodial branching, indeterminate spicate inflorescences subtended by numerous bracts and fleshy, non-trichome tissue lining the inside of the corolla lobes. Molecular phylogenetic analyses using nuclear ribosomal internal transcribed spacer sequences place this taxon as sister to all African, Madagascan and South American Thesium species. Given that only two proximal populations are known, this species is of conservation concern.
Examining the relationship between performance-based and questionnaire assessments of executive function in young preterm children: Implications for clinical practice

ABSTRACT The aim of this study was to determine whether specific performance-based executive function assessment tools were associated with executive functioning in everyday life as reported by parents and teachers of four- to five-year-old preterm and term children. At the age of 4 years, 141 preterm children born <33 weeks’ gestation and 77 term children were assessed using performance-based intelligence (WPPSI-III) and executive function (EF) assessment tools (NEPSY-II, Day-Night and Shape School tasks). The assessment results were compared with the parent and teacher completed questionnaires of EF (BRIEF-P) when the children started kindergarten at the age of 4 to 5 years. The performance-based intelligence and EF assessment results were not consistently associated with the parent and teacher reports of EF in everyday life for either preterm or term groups. Clinical implications of using and interpreting performance-based EF assessment tools and EF questionnaires are discussed with a particular focus on young preterm children at the commencement of formal schooling.
Climate communication for biologists: When a picture can tell a thousand words

Pictures often tell a story better than the proverbial 1,000 words. However, in connection with climate change, many pictures can be highly misleading, for example, when a snowball is used to ridicule the notion of global warming or when a picture of a dead crop is supposed to alert people to climate change. We differentiate between such inappropriate pictures and those that can be used legitimately because they capture long-term trends. For example, photos of a glacier’s retreat are legitimate indicators of the long-term mass balance loss that is observed for the vast majority of glaciers around the world.
High moisture extrusion of lupin protein: influence of extrusion parameters on extruder responses and product properties.

BACKGROUND High moisture extrusion (HME) of lupin protein concentrate and isolate (50:50) mixture was performed by varying the extrusion parameters, such as barrel temperature (138-180 °C), water feed (40-68%) and screw speed (400-1800 rpm). The effect of extrusion parameters on extruder responses [die pressure, product temperature, torque and specific mechanical energy (SME)] and product properties [colour, cutting force, cooking yield, microstructure and in vitro protein digestibility (IVPD)] was evaluated. RESULTS The multiple regression analysis of the results revealed that the water feed had a significant negative linear effect on the extruder responses considered, as well as on colour difference and cutting force of extrudates. Screw speed had a positive linear effect on product temperature, SME and cooking yield. Barrel temperature affected extruder responses and product properties to a lesser extent. Scanning electron microscopy showed that denser microstructure and higher number of fibre layers were created by increasing temperature and screw speed along with decreasing water feed. The results of IVPD of selected extrudates showed that the increase in barrel temperature decreased the IVPD, whereas the increase in water feed resulted in higher IVPD. The screw speed had no significant effect on IVPD. CONCLUSION The study demonstrates that the use of lupin protein is feasible to produce meat analogues with HME which could enhance the possibilities to meet the growing protein demands for human consumption. © 2018 Society of Chemical Industry.
An analysis of the survival impact of dexmedetomidine in children undergoing cytoreductive surgery with hyperthermic intraperitoneal chemotherapy

Abstract Objective: Recent evidence suggests the α2-adrenoreceptor agonist dexmedetomidine may promote metastasis of cancer cells. In this study we sought to evaluate the impact of dexmedetomidine administration on the survival of children and adolescents with cancer. Design: Retrospective chart review. Setting: Comprehensive cancer center. Patients: Children and adolescents who had undergone cytoreductive surgery with hyperthermic intraperitoneal chemotherapy for peritoneal carcinomatosis. Intervention: Intraoperative and/or early postoperative (within 24 hours of surgery) administration of dexmedetomidine. Measurements: Multivariable cox proportional hazard models were used to assess the association between dexmedetomidine administration and progression free survival (PFS) or overall survival (OS). Main results: Ninety-three patients were identified. The median age was 12 years, 42% were female, and 35% received dexmedetomidine. There were no significant differences between the baseline and perioperative characteristics of patients who received dexmedetomidine and those who did not. In the multivariable analysis, the administration of dexmedetomidine was not associated with PFS (HR = 1.20, 95% CI [0.60–2.41], p = .606) or OS (HR = 0.81, 95% CI [0.35–1.85], p = .611). Conclusion: In this retrospective study of children and adolescents who had undergone a major oncologic surgery, the intraoperative and/or early postoperative administration of dexmedetomidine was not associated with survival.
Personality links with lifespan in chimpanzees

Life history strategies for optimizing individual fitness fall on a spectrum between maximizing reproductive efforts and maintaining physical health over time. Strategies across this spectrum are viable and different suites of personality traits evolved to support these strategies. Using data from 538 captive chimpanzees (Pan troglodytes) we tested whether any of the dimensions of chimpanzee personality – agreeableness, conscientiousness, dominance, extraversion, neuroticism, and openness – were associated with longevity, an attribute of slow life history strategies that is especially important in primates given their relatively long lives. We found that higher agreeableness was related to longevity in males, with weaker evidence suggesting that higher openness is related to longer life in females. Our results link the literature on human and nonhuman primate survival and suggest that, for males, evolution has favored the protective effects of low aggression and high quality social bonds.
MDA-MB-231 Breast Cancer Cells and Their CSC Population Migrate Towards Low Oxygen in a Microfluidic Gradient Device

Most cancer deaths are caused by secondary tumors formed through metastasis, yet due to our limited understanding of this process, prevention remains a major challenge. Recently, cancer stem cells (CSCs) have been proposed as the source of metastases, but only little is known about their migratory behavior. Oxygen gradients in the tumor have been linked to directional migration of breast cancer cells. Here, we present a method to study the effect of oxygen gradients on the migratory behavior of breast CSCs using a microfluidic device. Our chip contains a chamber in which an oxygen gradient can be generated between hypoxic (<1%) and ambient (21%) conditions. We tracked the migration of CSCs obtained from MDA-MB-231 breast cancer cells, and found that their migration patterns do not differ from the average MDA-MB-231 population. Surprisingly, we found that the cells migrate towards low oxygen levels, in contrast with an earlier study. We hypothesize that in our device, migration is exclusively due to the pure oxygen gradient, whereas the effects of oxygen in earlier work were obscured by additional cues from the tumor microenvironment (e.g., nutrients and metabolites). These results open new research directions into the role of oxygen in directing cancer and CSC migration.
Predictors of Antiretroviral Adherence Self-efficacy Among People Living With HIV/AIDS in a Canadian Setting

Background: Suboptimal adherence to antiretroviral therapy (ART) among people living with HIV/AIDS (PLWHA) who use illicit drugs remains an ongoing health concern. Although health outcomes associated with adherence self-efficacy have been well-documented, there is dearth research exploring the predictors of this construct. This study sought to identify possible determinants of adherence self-efficacy among a cohort of PLWHA who use illicit drugs. Methods: From December 2004 to May 2014, we collected data from the AIDS Care Cohort to evaluate Exposure to Survival Services, a prospective cohort of adult PLWHA who use illicit drugs in Vancouver, Canada. We used multivariate generalized estimating equation analyses to identify longitudinal factors independently associated with higher adherence self-efficacy. Results: Among 742 participants, 493 (66.4%) identified as male and 406 (54.7%) reported white ancestry. In multivariate generalized estimating equation analysis, older age at ART initiation (adjusted odds ratio [AOR] = 1.02, 95% confidence interval [CI]: 1.00 to 1.03) and recent year of baseline interview (AOR = 1.08, 95% CI: 1.05 to 1.11) were independently associated with higher adherence self-efficacy, whereas homelessness (AOR = 0.78, 95% CI: 0.65 to 0.94), ≥daily crack smoking (AOR = 0.81, 95% CI: 0.68 to 0.96), experienced violence (AOR = 0.82, 95% CI: 0.69 to 0.98), and childhood abuse (AOR = 0.75, 95% CI: 0.60 to 0.92) were negatively associated. Conclusions: These findings highlight the potential role that personal and contextual factors can play in predicting levels of ART adherence self-efficacy. Future research should seek to identify and validate strategies to optimize adherence self-efficacy.
An overview about the impact of hinge region towards the anticancer binding affinity of the Ck2 ligands: a quantum chemical analysis

Abstract Casein kinase 2 (CK2) is extremely preserved and universally uttered serine/threonine kinase, vital for cellular feasibility. The present study aimed to analyse the binding strength of CK2 ligands specifically in the hinge region, as it is aware that most of the existing drugs are targeted to bind the hinge of the corresponding protein. The analysis will give a clear picture about the role of hinge region with ligand, which will be useful for scientist community in drug designing. To predict the binding strength of CK2 ligands, the role of halogen bond, hydrogen bond interaction at the hinge region was depicted in detail through interaction energy calculations at M062Z/def2-QZVP level of theory. Highest occupied molecular orbital (HOMO) map plotted for CK2 ligands gives a clear pictorial representation of orbitals, which induce for interaction. Ligand properties discussed in detail through Lipinski’s five rules predict that almost all the ligands satisfy the rule, except 3KXG, which violates Lipinski’s two rules, i.e. molecular mass exceeds 500 Da, i.e. 512.61 Da, and Log P value is high of 5.09. The natural bond orbital analysis deliberates that the hydrogen/halogen bonds figuring out within the complexes are observed to have moderate stabilization energy, but those hydrogen/halogen bonds that exist with close contacts have high stabilization energy. Overall, this computational work will give an understandable depiction for modelling anticancer ligands along the hinge region in CK2 protein; also, it will give a new path for the choice of side chains on the ligand. Communicated by Ramaswamy H. Sarma
Executive Functioning Mediates Predictions of Youth Academic and Social Development from Parenting Behavior

ABSTRACT Using multiple mediation with bootstrapping, dimensions of executive functioning (i.e., inhibitory control, working memory, set shifting) were tested as mediators of predictions of academic and social outcomes from observed positive and negative parenting in 131 children followed prospectively into early adolescence. Inhibitory control and working memory mediated predictions of academic achievement, whereas inhibitory control meditated predictions of school competence from positive parenting. Additionally, working memory mediated predictions of negative social preference, but not social competence, from positive parenting. Executive functioning did not mediate predictions from negative parenting. The role of parenting in shaping youth outcomes through executive functioning is considered.
Measuring the Impact of Research Using Conventional and Alternative Metrics

Abstract Bibliometrics use statistical methods to measure the scholarly impact of publications. Bibliometrics are categorized as conventional metrics or alternative metrics. Conventional metrics have often been considered the standard to measure the impact of publication-related scholarship. With the growing popularity of social media and ease of instantaneous distribution of information globally, alternative metrics have become an important complementary measure of scholarly activity. Bibliometrics may provide a standard performance measurement that may be used for tenure and/or promotion among academic institutions. The alternative metric industry has shown considerable growth with increasingly improved algorithms working towards standardization. Together, conventional metrics and alternative metrics may synergistically complement each other to provide an accelerated translation from research to clinical care that may lead to tremendous benefits in patients. All physicians and other healthcare professionals should receive training in bibliometrics and understand the potential impact of professional social media use.
Acylated ghrelin protects aorta damage post-MI via activation of eNOS and inhibition of angiotensin-converting enzyme induced activation of NAD(P)H-dependent oxidase

ABSTRACT NAD(P)H dependent oxidase derived-reactive oxygen species (ROS) due to activation of the renin-angiotensin-aldosterone system (RAAS) in blood vessels postmyocardial infarction MI or during the HF leads to endothelium dysfunction and enhanced apoptosis. Acylated ghrelin (AG) is a well-reported cardioprotective and antiapoptotic agent for the heart. AG receptors are widely distributed in most of blood vessels, suggesting a role in the regulation of endothelial function and survival. This study investigated if AG can protect aorta of rats’ postmyocardial infarction (MI)-induced damage and endothelial dysfunction. Adult male rats were divided into four groups of (1) Sham, (2) Sham + AG, (3) MI, and (4) MI + AG. Vehicle (normal saline) or AG (100 µ/kg) was administered to rats for 21 consecutive days, after which, numerous biochemical markers were detected by blot. Both histological and electron microscope studies were carried on aortic samples from MI-induced rats. AG increased protein levels of both total and phosphorylated forms of endothelial nitric oxide synthase (eNOS and p-eNOS, respectively). Only in MI-treated rats, AG prevented the decreases in the levels of reduced glutathione (GSH) and superoxide dismutase (SOD) and lowered levels of malondialdehyde (MDA) and glutathione disulfide (GSSG). Concomitantly, it lowered the increased protein levels of angiotensin-converting enzyme (ACE), p22phox and cleaved caspase-3 and prevented the aorta histological and ultrustructural abnormalities induced by MI.
Scapula Dyskinesis: A Review of Current Concepts and Evaluation of Assessment Tools

Scapula dyskinesis is prevalent in athletes conducting forceful overhead movements. This review summarizes our current understanding of the condition and evaluates the different options for assessing dyskinesis. Current methods for assessing scapula dyskinesis involve clinical observations, three-dimensional kinematics and three-dimensional wing computer tomography. Clinical observation is the most pragmatic method for assessing dyskinesis yielding inter-rater agreement of 79% and sensitivity of 76%. Similar sensitivities have been recorded using three-dimensional kinematics. Three-dimensional wing computer tomography has yielded a near-perfect interclass correlation coefficient of 0.972 when used to assess dyskinesis. Three-dimensional wing computer tomography, given its expense, low availability, and levels of irradiation, should be reserved for high-performance athletes where detailed assessments need to be made to aid rehabilitation. Observational assessments should remain the main modality used for general assessment.
Multiple antenna placement in microwave ablation assisted by a three-dimensional fusion image navigation system for hepatocellular carcinoma

Abstract Purpose: This study was conducted to compare a three-dimensional (3D) fusion image navigation system (FINS) with ultrasound (US) for guiding percutaneous microwave ablation (PMWA) for treatment of hepatocellular carcinoma (HCC). Materials and methods: This is a retrospective, non-randomized, comparative study. Our team developed a 3D FINS and used it to guide PMWAs for HCCs in 19 patients (3D group) and compared the results to those of 24 PMWAs guided by US (US group). The complete ablation rate of the first session, the local tumor progression (LTP), intrahepatic recurrence and disease-free survival were compared between the groups. Results: The 3D FINS was successfully applied in all 19 patients. The mean size of HCCs was 4.14 cm ±0.95 in 3D the group and 4.07 cm ±0.91 in the US group. Major complications were identified at 5.3% in the 3D group and 4.2% in the US group (p = .865). Average time of image fusion was 404.53 ± 161.84 s. There were more antenna insertions in the 3D group (3.68 ± 1.57) than in the US group (2.71 ± 1.12) (p = .02). The complete ablation rate of the first session was higher in the 3D group (94.7%) than in the US group (62.5%) (p = .034). The mean follow-up period was 11.4 months ±4.9 in the 3D group and 9.8 months ±5.5 in the US group. There were no significant differences in technique efficacy rate and LTP rate between the two groups. Conclusions: The 3D FINS could be a safe, feasible and effective technique for guiding PMWA of HCC, which could help an operator improve the complete ablation rate of the first session.
An ultrastructural study of byssus stem formation in Mytilus californianus

In Mytilus californianus, root lamellae of the byssus stem are formed by two morphologically distinct exocrine cell types. Type 1 cells contain large ellipsoid granules which are ultrastructurally identical to those of the collagen gland associated with byssus thread formation: these granules are secreted only at the base of the stem generator. Type 2 cells contain small cylindroid granules which are secreted only from the lateral surfaces of generator septa. The resultant matrix is biphasic because the two secretions are incompletely mixed. Lamellar sheets of matrix are propelled outward by the action of cilia and are molded into a cylinder at the neck region of the stem. However, the stem retains a lamellar pattern.