Miracle-dz/UniFAR-FTUs huggingface dataset:
Trait and phylogenetic diversity provide insights into community assembly of reef‐associated shrimps (Palaemonidae) at different spatial scales across the Chagos Archipelago

Abstract Coral reefs are the most biodiverse marine ecosystem and one of the most threatened by global climate change impacts. The vast majority of diversity on reefs is comprised of small invertebrates that live within the reef structure, termed the cryptofauna. This component of biodiversity is hugely understudied, and many species remain undescribed. This study represents a rare analysis of assembly processes structuring a distinct group of cryptofauna, the Palaemonidae, in the Chagos Archipelago, a reef ecosystem under minimal direct human impacts in the central Indian Ocean. The Palaemonidae are a diverse group of Caridae (infraorder of shrimps) that inhabit many different niches on coral reefs and are of particular interest because of their varied habitat associations. Phylogenetic and trait diversity and phylogenetic signal were used to infer likely drivers of community structure. The mechanisms driving palaemonid community assembly and maintenance in the Chagos Archipelago showed distinct spatial patterns. At local scales, among coral colonies and among reefs fringing individual atolls, significant trait, and phylogenetic clustering patterns suggest environmental filtering may be a dominant ecological process driving Palaemonidae community structure, although local competition through equalizing mechanisms may also play a role in shaping the local community structure. Importantly, we also tested the robustness of phylogenetic diversity to changes in evolutionary information as multi‐gene phylogenies are resource intensive and for large families, such as the Palaemonidae, are often incomplete. These tests demonstrated a very modest impact on phylogenetic community structure, with only one of the four genes (PEPCK gene) in the phylogeny affecting phylogenetic diversity patterns, which provides useful information for future studies on large families with incomplete phylogenies. These findings contribute to our limited knowledge of this component of biodiversity in a marine locality as close to undisturbed by humans as can be found. It also provides a rare evaluation of phylogenetic diversity methods.
Active Learning for Breast Cancer Identification

Breast cancer is the second most common malignancy among women and has become a major public health problem in current society. Traditional breast cancer identification requires experienced pathologists to carefully read the breast slice, which is laborious and suffers from inter-observer variations. Consequently, an automatic classification framework for breast cancer identification is worthwhile to develop. Recent years witnessed the development of deep learning technique. Increasing number of medical applications start to use deep learning to improve diagnosis accuracy. In this paper, we proposed a novel training strategy, namely reversed active learning (RAL), to train network to automatically classify breast cancer images. Our RAL is applied to the training set of a simple convolutional neural network (CNN) to remove mislabeled images. We evaluate the CNN trained with RAL on publicly available ICIAR 2018 Breast Cancer Dataset (IBCD). The experimental results show that our RAL increases the slice-based accuracy of CNN from 93.75% to 96.25%.
Memory, Decision-Making, and the Ventromedial Prefrontal Cortex (vmPFC): The Roles of Subcallosal and Posterior Orbitofrontal Cortices in Monitoring and Control Processes.

The ventromedial prefrontal cortex (vmPFC) prominently and separately features in neurobiological models of decision-making (e.g., value-encoding) and of memory (e.g., automatic veracity-monitoring). Recent decision-making models propose value judgments that inherently comprise of second-order confidence estimates. These demonstrate quadratic relationships with first-order judgments and are automatically encoded in vmPFC activity. Memory studies use Quantity-Accuracy Profiles to capture similar first-order and second-order meta-mnemonic processes, suggesting convergence across domains. Patients with PFC damage answered general knowledge questionnaires under 2 conditions. During forced report, they chose an answer and rated the probability of it being correct (first-order "monitoring"). During free report, they could choose to volunteer or withhold their previous answers (second-order "control") to maximize performance. We found quadratic relationships between first-order and second-order meta-mnemonic processes; voxel-based lesion-symptom mapping demonstrated that vmPFC damage diminished that relationship. Furthermore, damage to subcallosal vmPFC was specifically associated with impaired monitoring and additional damage to posterior orbitofrontal cortex led to deficient control. In decision-making, these regions typically support valuation and choice, respectively. Persistent spontaneous confabulation (false memory production) confirmed the clinical relevance of these dissociations. Compared with patients with no confabulation history, patients who currently confabulate were impaired on both monitoring and control, whereas former confabulators demonstrated impaired monitoring but intact control.
Development and Functional Organization of the Cranial Nerves in Lampreys

Lampreys, together with hagfishes, are the only extant representatives of the oldest branch of vertebrates, the agnathans, which are the sister group of gnathostomes; therefore, studies on these animals are of great evolutionary significance. Lampreys exhibit a particular life cycle with remarkable changes in their behavior, concomitant, in part, with important modifications in the head and its musculature, which might influence the development of the cranial nerves. In this context, some cranial nerves such as the optic nerve and the ocular motor nerves, which develop slowly during an extremely long larval period lasting more than five years, have been more thoroughly investigated; however, much less experimental information is available about others, such as the facial or the hypoglossal nerves. In addition, the possible existence of a “true” accessory nerve in these animals is still a matter of conjecture. Although growing in last decades, investigations on the physiology of the lamprey cranial nerves is scanty. This review focuses on past and recent findings that have contributed to characterize the anatomical organization of the cranial nerves in lampreys, including their components and nuclei, and their relations in the brain; in addition, comments on their development and functional role are also included. Anat Rec, 302:512–539, 2019. © 2018 Wiley Periodicals, Inc.
Understanding and Predicting Delay in Reciprocal Relations

Reciprocity in directed networks points to user»s willingness to return favors in building mutual interactions. High reciprocity has been widely observed in many directed social media networks such as following relations in Twitter and Tumblr. Therefore, reciprocal relations between users are often regarded as a basic mechanism to create stable social ties and play a crucial role in the formation and evolution of networks. Each reciprocity relation is formed by two parasocial links in a back-and-forth manner with a time delay. Hence, understanding the delay can help us gain better insights into the underlying mechanisms of network dynamics. Meanwhile, the accurate prediction of delay has practical implications in advancing a variety of real-world applications such as friend recommendation and marketing campaign. For example, by knowing when will users follow back, service providers can focus on the users with a potential long reciprocal delay for effective targeted marketing. This paper presents the initial investigation of the time delay in reciprocal relations. Our study is based on a large-scale directed network from Tumblr that consists of 62.8 million users and 3.1 billion user following relations with a timespan of multiple years (from 31 Oct 2007 to 24 Jul 2013). We reveal a number of interesting patterns about the delay that motivate the development of a principled learning model to predict the delay in reciprocal relations. Experimental results on the above mentioned dynamic networks corroborate the effectiveness of the proposed delay prediction model.
Expression dynamics of self-renewal factors for spermatogonial stem cells in the mouse testis

Glial cell line-derived neurotrophic factor (GDNF) and fibroblast growth factor 2 (FGF2) are bona fide self-renewal factors for spermatogonial stem cells (SSCs). Although GDNF is indispensable for the maintenance of SSCs, the role of FGF2 in the testis remains to be elucidated. To clarify this, the expression dynamics and regulatory mechanisms of Fgf2 and Gdnf in the mouse testes were analyzed. It is well known that Sertoli cells express Gdnf, and its receptor is expressed in a subset of undifferentiated spermatogonia, including SSCs. However, we found that Fgf2 was mainly expressed in the germ cells and its receptors were expressed not only in the cultured spermatogonial cell line, but also in testicular somatic cells. Aging, hypophysectomy, retinoic acid treatment, and testicular injury induced distinct Fgf2 and Gdnf expression dynamics, suggesting a difference in the expression mechanism of Fgf2 and Gdnf in the testis. Such differences might cause a dynamic fluctuation of Gdnf/Fgf2 ratio depending on the intrinsic/extrinsic cues. Considering that FGF2-cultured spermatogonia exhibit more differentiated phenotype than those cultured with GDNF, FGF2 might play a role distinct from that of GDNF in the testis, despite the fact that both factors are self-renewal factor for SSC in vitro.
Quantifying Nitrogen Scavenging Benefits of Cover Crops in the Mississippi River Basin

The sandy soils of Muscatine County, Iowa, are prone to erosion and leaching. In the fall, leftover fertilizer applied to the corn and soybean crop is highly susceptible to leaching. Cover crops have been widely acclaimed to mitigate such issues as they prevent erosion and scavenge residual nitrogen. Although these attributes are widely known, adoption of cover crops has been slow. Information on cover crop planting dates, performance, and advantages are available, but few data are available that is applicable to Iowa soils and growing conditions.
Paradigms of Dynamic Control of Thyroid Hormone Signaling.

Thyroid hormone (TH) molecules enter cells via membrane transporters and, depending on the cell type, can be activated, that is thyroxine (T4) to 3,5,3'-tri-iodothyronine (T3) conversion, or inactivated - T3 to 3,3'-diiodo-L-thyronine (T2) or T4 to reverse tri-iodothyronine (rT3) conversion. These reactions are catalyzed by the deiodinases. The biologically active hormone, T3, eventually binds to intracellular TH receptors (TR), TRα and TRβ, and initiate TH signaling, i.e. regulation of target genes and other metabolic pathways. At least three families of transmembrane transporters, MCT, OATP and LAT, facilitate the entry of TH into cells, which follow the gradient of free hormone between the extracellular fluid and the cytoplasm. Inactivation or marked downregulation of TH transporters can dampen TH signaling. At the same time, dynamic modifications in the expression or activity of TRs and transcriptional co-regulators can affect positively or negatively the intensity of TH signaling. However, the deiodinases are the element that provides greatest amplitude in dynamic control of TH signaling. Cells that express the activating deiodinase DIO2 can rapidly enhance TH signaling due to intracellular build-up of T3. In contrast, TH signaling is dampened in cells that express the inactivating deiodinase DIO3. This explains how THs can regulate pathways in development, metabolism and growth, despite rather stable levels in the circulation. As a consequence, TH signaling is unique for each cell (tissue or organ), depending on circulating TH levels and on the exclusive blend of transporters, deiodinases and TRs present in each cell. In this article we explore the key mechanisms underlying customization of TH signaling during development, in health and in disease states.
Hidden truths in dead software paths

Approaches and techniques for statically finding a multitude of issues in source code have been developed in the past. A core property of these approaches is that they are usually targeted towards finding only a very specific kind of issue and that the effort to develop such an analysis is significant. This strictly limits the number of kinds of issues that can be detected. In this paper, we discuss a generic approach based on the detection of infeasible paths in code that can discover a wide range of code smells ranging from useless code that hinders comprehension to real bugs. Code issues are identified by calculating the difference between the control-flow graph that contains all technically possible edges and the corresponding graph recorded while performing a more precise analysis using abstract interpretation. We have evaluated the approach using the Java Development Kit as well as the Qualitas Corpus (a curated collection of over 100 Java Applications) and were able to find thousands of issues across a wide range of categories.
Time Consistent Optimal Fiscal Policy Over the Business Cycle

This paper examines a dynamic stochastic economy with a benevolent government that cannot commit to its future policies. I consider equilibria that are time‐consistent and allow for history‐dependent strategies. A new numerical algorithm is developed to solve for the set of equilibrium payoffs. For a baseline economy calibrated to the U.S. economy, the capital income tax with the highest social welfare is slightly procyclical, while the labor income tax is countercyclical. Compared with the data, this equilibrium provides a better account of the cyclical properties of U.S. tax policy than other solutions that abstract from history dependence. The welfare cost of no commitment is about 0.22% of aggregate consumption as compared to the Ramsey allocation with full commitment.
Study of Normal and Abnormal Prenatal Development Using the Kyoto Collection of Human Embryos

Four topics on normal and abnormal human prenatal development are briefly reviewed. These studies were made possible by using the Kyoto Collection of Human Embryos, the largest collection of human embryo specimens procured after therapeutic abortion. The topics discussed include: (1) variability of human embryo development and implications for clinical teratology, (2) abnormal development in human embryos and intrauterine fate of human conceptuses, (3) holoprosencephaly, and (4) maternal hyperthermia in early pregnancy and birth defects. Anat Rec, 301:955–959, 2018. © 2018 Wiley Periodicals, Inc.
Selenium in global food systems

Food systems need to produce enough of the essential trace element Se to provide regular adult intakes of at least 40 μg/d to support the maximal expression of the Se enzymes, and perhaps as much as 300 μg/d to reduce risks of cancer. Deprivation of Se is associated with impairments in antioxidant protection, redox regulation and energy production as consequences of suboptimal expression of one or more of the Se-containing enzymes. These impairments may not cause deficiency signs in the classical sense, but instead contribute to health problems caused by physiological and environmental oxidative stresses and infections. At the same time, supranutritional intakes of Se, i.e. intakes greater than those required for selenocysteine enzyme expression, appear to reduce cancer risk. The lower, nutritional, level is greater than the typical intakes of many people in several parts of the world, and few populations have intakes approaching the latter, supranutritional, level. Accordingly, low Se status is likely to contribute to morbidity and mortality due to infectious as well as chronic diseases, and increasing Se intakes in all parts of the world can be expected to reduce cancer rates.
Exploring gender differences in sexual and reproductive health literacy among young people from refugee backgrounds

Abstract Young refugees often have limited access to sexual health information and resources in their places of resettlement. However, there is currently little research examining differences in sexual health literacy between young refugee men and women. Consequently, this study employed qualitative research methods to better understand sexual health literacy, sources of information and perceived barriers to access across groups of refugee men and women between the ages of 18 and 24 years old. Three focus groups and 12 interviews were conducted with 25 refugee men and women living in the metropolitan Atlanta area. Both men and women appeared to have limited knowledge about sexual health. School was their primary source of information; women also talked with their parents, whereas men preferred to reach out to teachers, peers and online sources. For both groups, barriers to access included language difficulties and lack of money, insurance and transport. Men also stressed concerns about confidentiality, whereas women focused on shame and embarrassment when discussing sexual health. Overall, study findings emphasise the need for sexual health education as part of resettlement services. Moreover, programmes need to be independently designed for men and women to address gender differences in sexual health literacy and concerns.
High Risk Sexual Behaviors for HIV among the In-School Youth in Swaziland: A Structural Equation Modeling Approach

Background Global efforts in response to the increased prevalence of the human immunodeficiency virus (HIV) are mainly aimed at reducing high risk sexual behaviors among young people. However, knowledge regarding intentions of young people to engage in protective sexual behaviors is still lacking in many countries around the world, especially in Sub-Saharan Africa where prevalence of human immunodeficiency virus is the highest. The objective of this study was to test the theory of planned behavior (TPB) for predicting factors associated with protective sexual behaviors, including sexual abstinence and condom use, among in-school youths aged between 15 and 19 years in Swaziland. Methods This cross-sectional survey was conducted using a anonymous questionnaire. A two-stage stratified and cluster random sampling method was used. Approximately one hundred pupils from each of four schools agreed to participate in the study, providing a total sample size of 403 pupils of which 369 were ultimately included for data analysis. The response rate was 98%. Structural equation modeling was used to analyse hypothesized paths. Results The TPB model used in this study was effective in predicting protective sexual behavior among Swazi in-school youths, as shown by model fit indices. All hypothesized constructs significantly predicted intentions for abstinence and condom use, except perceived abstinence controls. Subjective norms were the strongest predictors of intention for premarital sexual abstinence; however, perceived controls for condom use were the strongest predictors of intention for condom use. Conclusions Our findings support application of the model in predicting determinants of condom use and abstinence intentions among Swazi in-school youths.
Glucocorticoids: Biochemical Group That Play Key Role in Fetal Programming of Adult Disease

Glucocorticoids are subclass from corticosteroids. The other subclass of corticosteroids is mineralocorticoids. Historically, the discovery of glucocorticoids has been commenced during the early of last century. In fact, glucocorticoids have revealed themselves by their absence. In 1849, Thomas Addison, who was a physician at Guy`s Hospital in London, had noticed that certain patients were presenting with a cluster of characteristic clinical picture including anemia, weakness, peculiar dark skin color and eventually death (1). He presented his observation on 11 cases at the South London medical society meeting. In 1855 he published monograph entitled (On the Constitutional and Local Effects of Disease of the Supra-Renal capsules), (2, 3). 100 years later, Dr Philip Hench with a collaborated work with Edward Kendall, Professor of Physiological Chemistry, were both at Mayo Clinic which was first rheumatic disease service, had extracted “substance X” and in 21 September 1948 first injection of substance X was given to 29 years old lady who was suffering from severe, erosive arthropathies and became able to walk out of the hospital after 4 days of treatment. Dr Hench then named substance X Cortisone and shared the Nobel prize with professor Kendall in 1950 (4).
Polyubiquitinylation Profile in Down Syndrome Brain Before and After the Development of Alzheimer Neuropathology.

AIMS Among the putative mechanisms proposed to be common factors in Down syndrome (DS) and Alzheimer's disease (AD) neuropathology, deficits in protein quality control (PQC) have emerged as a unifying mechanism of neurodegeneration. Considering that disturbance of protein degradation systems is present in DS and that oxidized/misfolded proteins require polyubiquitinylation for degradation via the ubiquitin proteasome system, this study investigated if dysregulation of protein polyubiquitinylation is associated with AD neurodegeneration in DS. RESULTS Postmortem brains from DS cases before and after development of AD neuropathology and age-matched controls were analyzed. By selectively isolating polyubiquitinated proteins, we were able to identify specific proteins with an altered pattern of polyubiquitinylation as a function of age. Interestingly, we found that oxidation is coupled with polyubiquitinylation for most proteins mainly involved in PQC and energy metabolism. INNOVATION This is the first study showing alteration of the polyubiquitinylation profile as a function of aging in DS brain compared with healthy controls. Understanding the onset of the altered ubiquitome profile in DS brain may contribute to identification of key molecular regulators of age-associated cognitive decline. CONCLUSIONS Disturbance of the polyubiquitinylation machinery may be a key feature of aging and neurodegeneration. In DS, age-associated deficits of the proteolytic system may further exacerbate the accumulation of oxidized/misfolded/polyubiquitinated proteins, which is not efficiently degraded and may become harmful to neurons and contribute to AD neuropathology. Antioxid. Redox Signal. 26, 280-298.
Fast Miss Ratio Curve Modeling for Storage Cache

The reuse distance (least recently used (LRU) stack distance) is an essential metric for performance prediction and optimization of storage cache. Over the past four decades, there have been steady improvements in the algorithmic efficiency of reuse distance measurement. This progress is accelerating in recent years, both in theory and practical implementation. In this article, we present a kinetic model of LRU cache memory, based on the average eviction time (AET) of the cached data. The AET model enables fast measurement and use of low-cost sampling. It can produce the miss ratio curve in linear time with extremely low space costs. On storage trace benchmarks, AET reduces the time and space costs compared to former techniques. Furthermore, AET is a composable model that can characterize shared cache behavior through sampling and modeling individual programs or traces.