jimnoneill/paper-to-field-training huggingface dataset:
Improving 3D convolutional neural network comprehensibility via interactive visualization of relevance maps: evaluation in Alzheimer's disease.

Field: Computer Science (Physical Sciences)

Background!#!Although convolutional neural networks (CNNs) achieve high diagnostic accuracy for detecting Alzheimer's disease (AD) dementia based on magnetic resonance imaging (MRI) scans, they are not yet applied in clinical routine. One important reason for this is a lack of model comprehensibility. Recently developed visualization methods for deriving CNN relevance maps may help to fill this gap as they allow the visualization of key input image features that drive the decision of the model. We investigated whether models with higher accuracy also rely more on discriminative brain regions predefined by prior knowledge.!##!Methods!#!We trained a CNN for the detection of AD in N = 663 T1-weighted MRI scans of patients with dementia and amnestic mild cognitive impairment (MCI) and verified the accuracy of the models via cross-validation and in three independent samples including in total N = 1655 cases. We evaluated the association of relevance scores and hippocampus volume to validate the clinical utility of this approach. To improve model comprehensibility, we implemented an interactive visualization of 3D CNN relevance maps, thereby allowing intuitive model inspection.!##!Results!#!Across the three independent datasets, group separation showed high accuracy for AD dementia versus controls (AUC ≥ 0.91) and moderate accuracy for amnestic MCI versus controls (AUC ≈ 0.74). Relevance maps indicated that hippocampal atrophy was considered the most informative factor for AD detection, with additional contributions from atrophy in other cortical and subcortical regions. Relevance scores within the hippocampus were highly correlated with hippocampal volumes (Pearson's r ≈ -0.86, p &lt; 0.001).!##!Conclusion!#!The relevance maps highlighted atrophy in regions that we had hypothesized a priori. This strengthens the comprehensibility of the CNN models, which were trained in a purely data-driven manner based on the scans and diagnosis labels. The high hippocampus relevance scores as well as the high performance achieved in independent samples support the validity of the CNN models in the detection of AD-related MRI abnormalities. The presented data-driven and hypothesis-free CNN modeling approach might provide a useful tool to automatically derive discriminative features for complex diagnostic tasks where clear clinical criteria are still missing, for instance for the differential diagnosis between various types of dementia.
Dramatic effects of COVID-19 public health measures and mass reverse migration on youth sexual and reproductive health in rural Uganda

Field: Health Professions (Health Sciences)

Abstract Introduction Youth (aged 10 to 24 years) comprise nearly one-third of Uganda’s population and often face challenges accessing sexual and reproductive health (SRH) services, with a disproportionately high incidence of negative SRH outcomes. Responding to COVID-19, Uganda implemented strict public health measures including broad public transportation, schooling, and business shut-downs, causing mass reverse-migration of youth from urban schools and workplaces back to rural home villages. Our study aimed to qualitatively describe the perceived unintended impacts of COVID-19 health measures on youth SRH in two rural districts. Methods Semi-structured focus group discussions (FGD) and key informant interviews (KII) with purposively selected youth, parents, community leaders, community health worker (CHW) coordinators and supervisors, health providers, facility and district health managers, and district health officers were conducted to explore lived experiences and impressions of the impacts of COVID-19 measures on youth SRH. Interviews were recorded, transcribed, and coded using deductive thematic analysis. Results Four COVID-19-related themes and three subthemes resulted from 15 FGDs and 2 KIIs (n=94). Public transportation shutdown and mandatory mask-wearing were barriers to youth SRH care-seeking. School/workplace closures and subsequent urban youth migration back to rural homes increased demand at ill-prepared, rural health facilities, further impeding care-seeking. Youth reported fear of discovery by parents, which deterred SRH service seeking. Lockdown led to family financial hardship, isolation, and overcrowding; youth mistreatment, gender-based violence, and forced marriage ensued with some youth reportedly entering partnerships as a means of escape. Idleness and increased social contact were perceived to lead to increased and earlier sexual activity. Reported SRH impacts included increased severity of infection and complications due to delayed care seeking, and surges in youth sexually transmitted infections, pregnancy, and abortion. Conclusion COVID-19 public health measures reportedly reduced youth care seeking while increasing risky behaviours and negative SRH outcomes. Investment in youth SRH programming is critical to reverse unintended pandemic effects and regain momentum toward youth SRH targets. Future pandemic management must consider social and health disparities, and mitigate unintended risks of public health measures to youth SRH.
Malignant lymphoma of the adrenal gland: its possible correlation with the Epstein-Barr virus.

Field: Medicine (Health Sciences)

Initial manifestation of malignant lymphoma in the adrenal gland is a rare event, and clinical and pathologic features are not fully understood. We conducted a nationwide study in Japan, and 20 patients with malignant lymphoma that showed initial and main manifestation in the adrenal gland were identified. Clinical and pathologic findings were summarized. In addition, the presence of the Epstein-Barr virus (EBV) genome in the tumor cells was examined by using polymerase chain reaction (PCR) and in situ hybridization (ISH), together with the immunohistochemical evaluation of the expression of latent membrane protein-1 (LMP-1). There were 13 men and seven women; their ages at admission ranged from 40 to 87 years (median, 65 yr). Fever, anemia, and elevation of lactic dehydrogenase levels were the common presenting findings. One patient had acquired immunodeficiency syndrome. Adrenal tumors were bilateral in 15 patients and unilateral (all in the left site) in five. Prognosis was very poor; all but two patients died within 1 year after admission. Histologically diffuse large cell type was the commonest type (14 specimens). Immunohistologically, 16 specimens were B-cell type, and one was T-cell type. Another three specimens showing no positive reaction for any antibodies were also judged as B-cell type on purely morphologic grounds. Prominent intravascular proliferation of tumor cells was found in five patients. PCR for EBV genomes gave positive results in five patients; the virus was subtyped as A in three patients and as B in two. The ISH provided positive signals in nine samples, including all five specimens positive for PCR. Four of the nine cases with detectable EBV by PCR and/or ISH expressed LMP-1. The present study shows that adrenal lymphoma is EBV associated and has a B-cell phenotype.
The distribution of coarse-grained sediments in modern Lake Turkana, Kenya: implications for clastic sedimentation models of rift lakes

Field: Earth and Planetary Sciences (Physical Sciences)

Summary The nearshore environment of Lake Turkana, Kenya was studied to determine how coarse clastic sediments are being distributed in the modern lake. Four lake margin study localities were examined in detail: (1) an area of basaltic colluvial headlands; (2) an area of sand, sandy silt and silty mud substrates; (3) an area of highly variable substrate conditions; and (4) an area of alternating basaltic headlands and gravel/shingle terraces. Based upon quantitative observations in these areas and qualitative observations elsewhere in the lake, we believe that two interacting factors have the greatest influence on the distribution of nearshore clastics. The first is a sediment distribution system which is primarily dependent on localized supply, via rockfall and intermittent streams. The second is the presence of physiographic barriers, principally faulted and eroded volcanic flows, which border on local coarse sediment delivery systems and isolate them from adjacent systems. Volcanic barriers may operate at various scales in regulating the delivery systems of clastic sediments in rift lakes, from localized facies disruption, as observed in Lake Turkana, to the isolation of entire sedimentary basins. At the largest levels the presence or absence of volcanic activity may have an important bearing on the controversy of hydrocarbon accumulation in rift lakes.
Early and Late Neurodevelopmental Disturbances in Schizophrenia and Their Functional Consequences

Field: Neuroscience (Life Sciences)

Objective: The evidence from structural imaging studies supports the notion that schizophrenia arises from an early abnormality in brain development. In this paper we review the timing of structural changes in schizophrenia and argue that schizophrenia is a neurodevelopmental disorder with limited progressive brain changes occurring during the evolution and early phase of psychosis. Method: The available cross-sectional and longitudinal studies are reviewed, along with data from our own research. Results: The current literature, including our own data, suggests that structural brain changes are apparent premorbidly, consistent with a neurodevelopmental lesion. These are prominent in frontal and cingulate regions, and appear related to premorbid neuropsychological deficits in executive function. However, there appear to be additional brain changes over the transition to illness and beyond. Conclusions: We propose first, that an early neurodevelopmental insult interacts with either normal or abnormal postpubertal brain maturation to produce further (late neurodevelopmental) brain structural and functional changes; and second, that the effect of such neurodevelopmental lesions will have different consequences for functions that normally develop early in life, such as memory, compared with functions developing later, such as executive functions. A model is presented suggesting that the structural and functional abnormalities in schizophrenia can be understood as a consequence of the neurodevelopmental stage at which brain changes occur.
An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling

Field: Computer Science (Physical Sciences)

Markov State Model (MSM) has become a popular approach to study the conformational dynamics of complex biological systems in recent years. Built upon a large number of short molecular dynamics simulation trajectories, MSM is able to predict the long time scale dynamics of complex systems. However, to achieve Markovianity, an MSM often contains hundreds or thousands of states (microstates), hindering human interpretation of the underlying system mechanism. One way to reduce the number of states is to lump kinetically similar states together and thus coarse-grain the microstates into macrostates. In this work, we introduce a probabilistic lumping algorithm, the Gibbs lumping algorithm, to assign a probability to any given kinetic lumping using the Bayesian inference. In our algorithm, the transitions among kinetically distinct macrostates are modeled by Poisson processes, which will well reflect the separation of time scales in the underlying free energy landscape of biomolecules. Furthermore, to facilitate the search for the optimal kinetic lumping (i.e., the lumped model with the highest probability), a Gibbs sampling algorithm is introduced. To demonstrate the power of our new method, we apply it to three systems: a 2D potential, alanine dipeptide, and a WW protein domain. In comparison with six other popular lumping algorithms, we show that our method can persistently produce the lumped macrostate model with the highest probability as well as the largest metastability. We anticipate that our Gibbs lumping algorithm holds great promise to be widely applied to investigate conformational changes in biological macromolecules.
FRP strengthening of metallic structures: From research to practice

Field: Engineering (Physical Sciences)

This paper presents an overview of FRP strengthening of metallic structures from research to practice. The major topics covered include (i) recent applications; (ii) bond behaviour; (iii) flexural strengthening; (iv) compression strengthening; (v) strengthening under dynamic and cyclic loading; (vi) future research. A comprehensive list of publication in this field is made available online to readers.
Induction of apoptosis at different oxygen tensions: evidence that oxygen radicals do not mediate apoptotic signaling.

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Apoptosis has been hypothesized to be mediated through the induction of free radicals via oxidative pathways. Furthermore, it has been proposed that Bcl-2 acts to inhibit apoptosis induced by a wide variety of stimuli by preventing the production of oxygen-derived free radicals. Since the generation of oxygen free radicals is dependent upon oxygen concentration, this hypothesis would lead to the prediction that the concentration of oxygen should affect the induction of apoptosis. In order to test this prediction, we have examined the induction of apoptosis in T-lymphoma cell lines S49.1 and WEHI 7.1 by dexamethasone and by withdrawal of serum from myc-immortalized fibroblasts in 95% oxygen, atmospheric oxygen (20%), and hypoxic conditions of up to 125-fold less oxygen. Culture in 95% oxygen induced apoptosis in all cells tested, confirming that oxidative damage can lead to apoptosis. However, for one cell line, WEHI 7.1, hypoxia also induced apoptosis. Furthermore, for the other cell lines tested, induction of apoptosis by either dexamethasone or by serum withdrawal was not affected by hypoxia. These results are not consistent with the hypothesis that apoptosis is mediated via oxygen-generated free radical formation.
Applicability of extended vortex identification methods for two-phase separation in multiphase pump

Field: Engineering (Physical Sciences)

Abstract In the process of multiphase flow transport, there is a slip velocity between phases, which affects the interphase force and leads to the separation of two phases. In order to analyze the flow structure of phases separation motion, the extended vortex identification methods in a multiphase pump is evaluated. The results show that the generation of two-phase separation structure inside the fluid machinery will seriously affect the phase distribution characteristics of the fluid machinery, and then affect the internal flow field and external performance. The extended vortex identification methods can characterize the intensity, location and evolution of two-phase separation in the pump. The research can offer a pertinent theoretical foundation for subsequent flow analysis and design optimization.
Numerical Study on the Characteristics of Bow-Flare and Stern Asymmetric Slamming for Container Ships

Field: Engineering (Physical Sciences)

Abstract The large bow flare and flat stern of container ships can result in a significant slamming phenomenon. Asymmetric slamming often occurs in oblique waves. The slamming can lead to ship vibration, reduced speed, and direct structural damage in severe cases. However, the prediction of slamming loads remains a challenge due to the highly nonlinear characteristics of the free surface and the physical surface conditions. This paper aims to provide a deeper analysis of the mechanisms of the oblique water entry process of the bow and stern of container ships. A numerical model of the two dimensional (2D) section is established using the open-source software OpenFOAM, incorporating the Volume of Fluid (VOF) method to solve the water-air phase flow. The free surface flow, slamming forces and the distribution of slamming pressures along the section were obtained. The numerical model is validated against available experimental data from the literature and the accuracy of the algorithm is discussed. The differences in slamming characteristics resulting from various shape features of the bow and stern is explored. Additionally. the comprehensive effects of geometric asymmetry during water entry are investigated by systematically altering the section’s roll angle. This study is expected to provide a reliable algorithmic framework for coupling slamming loads with the ship motion in the future.
Emergent reinforcement learning behaviors through novel testing conditions

Field: Computer Science (Physical Sciences)

In adversarial multi-agent paradigms, it is often difficult to describe what is learned by reinforcement-learning agents and to measure the robustness of the learned policies. To achieve a better view, we explore the effect of manipulating agent capabilities and policies in a predator-prey pursuit task. In these experiments, we trained a single prey using multi-agent reinforcement learning with three slower predators, then tested the prey against three faster predators using fixed "interceptor" strategies (head to the closest possible intersection with the prey assuming the prey maintains its current velocity) instead of their learned policies. While the prey's performance was impressive under these novel conditions, it varied widely. Initial locations and velocities (randomized during training and testing) were limited in explaining differences in prey's performance across test conditions. Nevertheless, visual inspection indicates that more successful prey quickly begin a circling pattern, whereas less successful prey often become cornered and double back into predator collisions. To quantify this behavior, we computed windowed entropy measures of the prey's angle relative to the arena origin to show when an agent transitioned in and out of this unsuccessful behavior. Ultimately, these transitions suggest that circling is triggered by coming close to the center of the arena. By varying agents' capabilities and predator policies upon evaluation, we achieve a more comprehensive view of the prey's learned policy, and we suggest that these windowed entropy measures, along with correlations between entropy and performance, result in a quantification of the learned policy.
On the influence of dynamic stress variations on strain accumulation in fault zones

Field: Earth and Planetary Sciences (Physical Sciences)

In this paper, a numerical study of the influence of the stress state of interface of the block medium structural elements on the deformation response of interface to the dynamic impacts. It is shown that the basic characteristics of the stress state determining the deformation response of the interface are the values of shear stress and mean stress. It is found that the dependence of the irreversible displacement at the interface zone initiated by dynamic impact on the reduced shear stress is described by the logistic function. Herewith, the influence of the mean stress and dynamic impact energy on the value of displacement initiated by dynamic impact can be taken into account by dependence of the logistic function numerator on these parameters.
Herpes simplex virus glycoprotein D mediates interference with herpes simplex virus infection

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

We showed that the expression of a single protein, glycoprotein D (gD-1), specified by herpes simplex virus type 1 (HSV-1) renders cells resistant to infection by HSV but not to infection by other viruses. Mouse (LMtk-) and human (HEp-2) cell lines containing the gene for gD-1 under control of the human metallothionein promoter II expressed various levels of gD-1 constitutively and could be induced to express higher levels with heavy metal ions. Radiolabeled viruses bound equally well to gD-1-expressing and control cell lines. Adsorbed viruses were unable to penetrate cells expressing sufficient levels of gD-1, based on lack of any cytopathic effects of the challenge virus and on failure to detect either the induction of viral protein synthesis or the shutoff of host protein synthesis normally mediated by a virion-associated factor. The resistance to HSV infection conferred by gD-1 expression was not absolute and depended on several variables, including the amount of gD-1 expressed, the dosage of the challenge virus, the serotype of the challenge virus, and the properties of the cells themselves. The interference activity of gD-1 is discussed in relation to the role of gD-1 in virion infectivity and its possible role in permitting escape of progeny HSV from infected cells.
Synthesis, transfer, and phosphorylation of phosphoinositides in cardiac membranes

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Compartmentation of phosphoinositide synthesis and transfer of endogenous phosphatidylinositol (PI) were characterized in membrane fractions prepared from rabbit myocardium. De novo synthesis of PI was highly enriched in free sarcoplasmic reticulum (551 pmol.mg-1. min-1) compared with that in sarcolemma (26.8 pmol.mg-1. min-1) and junctional sarcoplasmic reticulum (178 pmol.mg-1. min-1). In contrast, PI phosphorylation was highly enriched in sarcolemma (2.69 nmol.mg-1.min-1) compared with that in free sarcoplasmic reticulum (0.22 nmol.mg-1.min-1) and junctional sarcoplasmic reticulum (0.38 nmol.mg-1.min-1). Phosphorylation of endogenous phosphatidylinositol 4-phosphate to phosphatidylinositol 4,5-bisphosphate was also enriched in sarcolemma (38.5 pmol.mg-1.min-1) compared with that in free sarcoplasmic reticulum (less than 5.0 pmol.mg-1.min-1) and junctional sarcoplasmic reticulum (6.5 pmol.mg-1.min-1). Transfer of endogenous PI was characterized as a mechanism to overcome compartmentation of PI synthesis in cardiac membranes. A 29-kDa PI transfer protein was purified 1,500-fold from cytosol of rabbit myocardium. Both cytosol and purified PI transfer protein catalyzed the transfer of endogenous PI from microsomal sites of synthesis to sarcolemma. In conclusion, synthesis of PI is highly enriched in free sarcoplasmic reticulum, whereas phosphorylation of phosphoinositides is highly enriched in sarcolemma. A 29-kDa PI transfer protein in myocardial cytosol can mediate in vitro transfer of de novo-synthesized PI to the sarcolemma.