Miracle-dz/UniFAR-FTUs huggingface dataset:
Manipulation of the Geometry and Modulation of the Optical Response of Surfactant-Free Gold Nanostars: A Systematic Bottom-Up Synthesis

Among plasmonic nanoparticles, surfactant-free branched gold nanoparticles have exhibited exceptional properties as a nanoplatform for a wide variety of applications ranging from surface-enhanced Raman scattering sensing and imaging applications to photothermal treatment and photoimmunotherapy for cancer treatments. The effectiveness and reliability of branched gold nanoparticles in biomedical applications strongly rely on the consistency and reproducibility of physical, chemical, optical, and therapeutic properties of nanoparticles, which are mainly governed by their morphological features. Herein, we present an optimized bottom-up synthesis that improves the reproducibility and homogeneity of the gold-branched nanoparticles with desired morphological features and optical properties. We identified that the order of reagent addition is crucial for improved homogeneity of the branched nature of nanoparticles that enable a high batch-to-batch reproducibility and reliability. In addition, a different combination of the synthesis parameters, in particular, additive halides and concentration ratios of reactive Au to Ag and Au to Au seeds, which yield branched nanoparticle of similar localized surface plasmon resonances but with distinguishable changes in the dimensions of the branches, was realized. Overall, our study introduces the design parameters for the purpose-tailored manufacturing of surfactant-free gold nanostars in a reliable manner.
Functionally linked resting‐state networks reflect the underlying structural connectivity architecture of the human brain

During rest, multiple cortical brain regions are functionally linked forming resting‐state networks. This high level of functional connectivity within resting‐state networks suggests the existence of direct neuroanatomical connections between these functionally linked brain regions to facilitate the ongoing interregional neuronal communication. White matter tracts are the structural highways of our brain, enabling information to travel quickly from one brain region to another region. In this study, we examined both the functional and structural connections of the human brain in a group of 26 healthy subjects, combining 3 Tesla resting‐state functional magnetic resonance imaging time‐series with diffusion tensor imaging scans. Nine consistently found functionally linked resting‐state networks were retrieved from the resting‐state data. The diffusion tensor imaging scans were used to reconstruct the white matter pathways between the functionally linked brain areas of these resting‐state networks. Our results show that well‐known anatomical white matter tracts interconnect at least eight of the nine commonly found resting‐state networks, including the default mode network, the core network, primary motor and visual network, and two lateralized parietal‐frontal networks. Our results suggest that the functionally linked resting‐state networks reflect the underlying structural connectivity architecture of the human brain. Hum Brain Mapp 2009. © 2009 Wiley‐Liss, Inc.
Is there a role for dietary salicylates in health?*

Acetylsalicylic acid (aspirinTM; 2-acetoxybenzoic acid) has been used for >100 years for pain relief and to treat inflammatory conditions and fevers. More recently, regular intake has been associated with decreased incidence of certain cancers, particularly colon cancer. After absorption aspirin is very rapidly hydrolysed to salicylic acid (2-hydroxybenzoic acid). The anti-cancer effects of aspirin may be a result of salicylic acid reducing the transcription of prostaglandin H2-synthase and thereby the synthesis of pro-inflammatory and potentially-neoplastic prostaglandins. Salicylic acid is widely present in plants and functions as a hormonal mediator of the systemic acquired resistance response to pathogen attack and environmental stress. Thus, it is present in a large range of fruit, vegetables, herbs and spices of dietary relevance. Consequently, the recognised effect of consuming fruit and vegetables on lowering risk of colon cancer may be partly attributable to salicylates in plant-based foods. The present review discusses which types of fruit and vegetables are the richest source of salicylates and whether they are sufficiently released from the food matrix to modify the key cellular events associated with the pathogenesis of colon cancer.
The Relationship of Exposure to Anesthesia on Outcomes in Children With Isolated Oral Clefts

This study evaluated the relationship between exposure to anesthesia and previously identified differences in cognitive functioning, growth, and volumetric brain measures among a sample of children, adolescents, and young adults with isolated oral clefts. Data from a cross-sectional study were combined with a retrospective chart review. Data were obtained for 87 participants with isolated cleft lip and/or palate (55% male), ranging from 7.5 to 27 years old (mean = 15.78, standard deviation = 4.58). Measures of interest included cognitive functioning, growth measures, and brain volumes. Number of surgeries and time under anesthesia were obtained through systematic medical record review. Potential sex and cleft type differences in exposure as well as relationships between anesthesia exposure and outcome measures were evaluated. Participants with isolated cleft lip and palate had more surgeries and were under anesthesia longer. For participants with isolated cleft lip only, more surgeries were correlated to lower verbal IQ and higher frontal lobe volume.
Long-Term Outcomes of Hypertrophic Cardiomyopathy Diagnosed During Childhood: Results From a National Population-Based Study

Background: Late survival and symptomatic status of children with hypertrophic cardiomyopathy have not been well defined. We examined long-term outcomes for pediatric hypertrophic cardiomyopathy. Methods: The National Australian Childhood Cardiomyopathy Study is a longitudinal population-based cohort study of children (0–10 years of age) diagnosed with cardiomyopathy between 1987 and 1996. The primary study end point was time to death or cardiac transplantation. Results: There were 80 patients with hypertrophic cardiomyopathy, with a median age at diagnosis of 0.48 (interquartile range, 0.1, 2.5) years. Freedom from death/transplantation was 86% (95% confidence interval [CI], 77.0–92.0) 1 year after presentation, 80% (95% CI, 69.0–87.0) at 10 years, and 78% (95% CI, 67.0–86.0) at 20 years. From multivariable analyses, risk factors for death/transplantation included symmetrical left ventricular hypertrophy at the time of diagnosis (hazard ratio, 4.20; 95% CI, 1.60–11.05; P=0.004), Noonan syndrome (hazard ratio, 2.88; 95% CI, 1.02–8.08; P=0.045), higher posterior wall thickness z score (hazard ratio, 1.45; 95% CI, 1.22–1.73; P<0.001), and lower fractional shortening z score (hazard ratio, 0.84; 95% CI, 0.74–0.95; P=0.005) during follow-up. Nineteen (23%) subjects underwent left ventricular myectomy. At a median of 15.7 years of follow-up, 27 (42%) of 63 survivors were treated with &bgr;-blocker, and 13 (21%) had an implantable cardioverter-defibrillator. Conclusions: The highest risk of death or transplantation for children with hypertrophic cardiomyopathy is within 1 year after diagnosis, with low attrition rates thereafter. Many subjects receive medical, surgical, or device therapy.
Directing Diarrhoeal Disease Research towards Disease-burden Reduction

Despite gains in controlling mortality relating to diarrhoeal disease, the burden of disease remains unacceptably high. To refocus health research to target disease-burden reduction as the goal of research in child health, the Child Health and Nutrition Research Initiative developed a systematic strategy to rank health research options. This priority-setting exercise included listing of 46 competitive research options in diarrhoeal disease and their critical and quantitative appraisal by 10 experts based on five criteria for research that reflect the ability of the research to be translated into interventions and achieved disease-burden reduction. These criteria included the answerability of the research questions; the efficacy and effectiveness of the intervention resulting from the research; the maximal potential for disease-burden reduction of the interventions derived from the research; the affordability, deliverability, and sustainability of the intervention supported by the research; and the overall effect of the research-derived intervention on equity. Experts scored each research option independently to delineate the best investments for diarrhoeal disease control in the developing world to reduce the burden of disease by 2015. Priority scores obtained for health policy and systems research obtained eight of the top 10 rankings in overall scores, indicating that current investments in health research are significantly different from those estimated to be the most effective in reducing the global burden of diarrhoeal disease by 2015.
A Systematic Review of Naltrexone for Attenuating Alcohol Consumption in Women with Alcohol Use Disorders

Several clinical trials have evaluated naltrexone as a treatment for alcohol use disorders (AUDs), but few have focused on women. The aim of this review was to systematically review and summarize the evidence regarding the impact of naltrexone compared to placebo for attenuating alcohol consumption in women with an AUD. A systematic review was conducted using PubMed, Cochrane, Web of Science, CINAHL, and Alcohol Studies Database to identify relevant peer-reviewed randomized controlled trials (RCTs) published between January 1990 and August 2016. Seven published trials have evaluated the impact of naltrexone on drinking outcomes in women distinct from men; 903 alcohol-dependent or heavy drinking women were randomized to receive once daily oral or depot (injectable) naltrexone or placebo with/without behavioral intervention. Two studies examining the quantity of drinks per day observed trends toward reduction in drinking quantity among women who received naltrexone versus placebo. The 4 studies examining the frequency of drinking had mixed results, with 1 study showing a trend that favored naltrexone, 2 showing a trend that favored placebo, and 1 that showed no difference. Two of the 3 studies examining time to relapse observed trends that tended to favor naltrexone for time to any drinking and time to heavy drinking among women who received naltrexone versus placebo. While the growing body of evidence suggests a variety of approaches to treat AUD, the impact of naltrexone to combat AUD in women is understudied. Taken together, the results suggest that naltrexone may lead to modest reductions in quantity of drinking and time to relapse, but not on the frequency of drinking in women. Future research should incorporate sophisticated study designs that examine gender differences and treatment effectiveness among those diagnosed with an AUD and present data separately for men and women.
Emergent Properties of Patch Shapes Affect Edge Permeability to Animals

Animal travel between habitat patches affects populations, communities and ecosystems. There are three levels of organization of edge properties, and each of these can affect animals. At the lowest level are the different habitats on each side of an edge, then there is the edge itself, and finally, at the highest level of organization, is the geometry or structure of the edge. This study used computer simulations to (1) find out whether effects of edge shapes on animal behavior can arise as emergent properties solely due to reactions to edges in general, without the animals reacting to the shapes of the edges, and to (2) generate predictions to allow field and experimental studies to test mechanisms of edge shape response. Individual animals were modeled traveling inside a habitat patch that had different kinds of edge shapes (convex, concave and straight). When animals responded edges of patches, this created an emergent property of responding to the shape of the edge. The response was mostly to absolute width of the shapes, and not the narrowness of them. When animals were attracted to edges, then they tended to collect in convexities and disperse from concavities, and the opposite happened when animals avoided edges. Most of the responses occurred within a distance of 40% of the perceptual range from the tip of the shapes. Predictions were produced for directionality at various locations and combinations of treatments, to be used for testing edge behavior mechanisms. These results suggest that edge shapes tend to either concentrate or disperse animals, simply because the animals are either attracted to or avoid edges, with an effect as great as 3 times the normal density. Thus edge shape could affect processes like pollination, seed predation and dispersal and predator abundance.
Classification and Disease Localization in Histopathology Using Only Global Labels: A Weakly-Supervised Approach

Analysis of histopathology slides is a critical step for many diagnoses, and in particular in oncology where it defines the gold standard. In the case of digital histopathological analysis, highly trained pathologists must review vast whole-slide-images of extreme digital resolution (100,000^2 pixels) across multiple zoom levels in order to locate abnormal regions of cells, or in some cases single cells, out of millions. The application of deep learning to this problem is hampered not only by small sample sizes, as typical datasets contain only a few hundred samples, but also by the generation of ground-truth localized annotations for training interpretable classification and segmentation models. We propose a method for disease available during training. Even without pixel-level annotations, we are able to demonstrate performance comparable with models trained with strong annotations on the Camelyon-16 lymph node metastases detection challenge. We accomplish this through the use of pre-trained deep convolutional networks, feature embedding, as well as learning via top instances and negative evidence, a multiple instance learning technique fromatp the field of semantic segmentation and object detection.
α-Synuclein Reactive Antibodies as Diagnostic Biomarkers in Blood Sera of Parkinson's Disease Patients

Background Auto-antibodies with specificity to self-antigens have been implicated in a wide variety of neurological diseases, including Parkinson's (PD) and Alzheimer's diseases, being sensitive indicators of neurodegeneration and focus for disease prevention. Of particular interest are the studies focused on the auto-immune responses to amyloidogenic proteins associated with diseases and their applications in therapeutic treatments such as vaccination with amyloid antigens and antibodies in PD, Alzheimer's disease and potentially other neurodegeneration ailments. Methodology/Principal Findings Generated auto-antibodies towards the major amyloidogenic protein involved in PD Lewy bodies – α-synuclein and its amyloid oligomers and fibrils were measured in the blood sera of early and late PD patients and controls by using ELISA, Western blot and Biacore surface plasmon resonance. We found significantly higher antibody levels towards monomeric α-synuclein in the blood sera of PD patients compared to controls, though the responses decreased with PD progression (P<0.0001). This indicates potential protective role of autoimmunity in maintaining the body homeostasis and clearing protein species whose disbalance may lead to amyloid assembly. There were no noticeable immune responses towards amyloid oligomers, but substantially increased levels of IgGs towards α-synuclein amyloid fibrils both in PD patients and controls, which subsided with the disease progression (P<0.0001). Pooled IgGs from PD patients and controls interacted also with the amyloid fibrils of Aβ (1–40) and hen lysozyme, however the latter were recognized with lower affinity. This suggests that IgGs bind to the generic amyloid conformational epitope, displaying higher specificity towards human amyloid species associated with neurodegeneration. Conclusions/Significance Our findings may suggest the protective role of autoimmunity in PD and therefore immune reactions towards PD major amyloid protein – α-synuclein can be of value in the development of treatment and diagnostic strategies, especially during the early disease stages.
Evaluation of alternative sampling methods for Salmonella critical control point determination at broiler processing.

Several sampling methods have been developed for the detection of Salmonella on broiler carcasses during commercial processing. The present study evaluated three sampling methodologies for sensitivity of Salmonella detection on processed broiler carcasses. Furthermore, the effect of crop removal or chill tank exposure on the frequency of Salmonella recovery was also examined. In two experiments, swab, skin, and carcass rinse samples were compared for sensitivity of Salmonella detection. The results indicated that culture of swabs was less effective (P < 0.05) for Salmonella detection than either skin or carcass rinse samples. No significant (P > 0.05) differences were observed in Salmonella recovery from culture of skin or carcass rinse. In two subsequent experiments, skin and carcass rinse samples were found to be equally sensitive in their ability to detect Salmonella. Additionally, the stages of processing between feather and crop removal were observed to cause significant (P < 0.05) increases in Salmonella recovery within an individual flock. Similar increases (P < 0.05) in Salmonella recovery were also observed following crop removal and immediately following immersion chilling in two separate flocks. These results suggest that culture of skin samples obtained from the thoracic inlet region may be a viable alternative to the traditional whole carcass rinse method for sensitivity of Salmonella detection. Furthermore, these experiments provided some evidence that the majority of Salmonella cross-contamination of carcasses prior to immersion chilling occurred following evisceration, with the chill tank potentially providing a major site for cross-contamination between Salmonella-negative and-positive flocks.
Memory antibody responses of broiler and leghorn chickens as influenced by dietary vitamin E and route of sheep red blood cell administration.

Influences of dietary levels of vitamin E fed to hens and their progeny, and routes of SRBC inoculation on antibody responses of diverse populations of chickens were studied. Populations were a commercial broiler sire line (C), 2 commercial broiler dam lines (A and B), and Leghorn lines selected for high (H) or low (L) antibody response to SRBC. Dams from lines A and B were fed diets supplemented with either 10 or 300 IU/kg of vitamin E, whereas dams from lines H and L received only the diet with 10 IU of vitamin E/kg. Progeny from matings of C males with A and B females as well as H and L females mated to males from their respective lines were hatched on the same day and fed diets supplemented with either 10 or 300 IU/kg of vitamin E. Breeders were the same age and eggs were incubated in the same machine. Chicks were inoculated on d 14 intravenously with 0.1 mL of a 0.5% suspension of SRBC or intramuscularly with 0.1 mL of a 25% suspension of SRBC. Antibody response was measured 6 and 14 d later. Chicks received a booster i.m. inoculation of 0.1 mL of 25% SRBC on d 28. Titers were again measured 6 and 14 d later. Level of vitamin E fed to dams did not affect progeny BW or plasma vitamin E levels. Although titers were higher following i.v. than i.m. inoculation, the degree of difference varied among stocks. Dietary vitamin E level interacted with inoculation route with a greater response to the higher than lower level of vitamin E for i.v. , but there was no difference for i.m. There were stock x level of vitamin E and stock x route of inoculation interactions for secondary responses to SRBC inoculation. Stock rankings after the first inoculation were not predictive of the rankings after the second inoculation. The 30-fold increase in dietary level of vitamin E resulted in >12-fold differences in plasma levels of vitamin E. Overall, there was a stock-dependent influence of dietary vitamin E on growth and humoral antibody response.
Modality-Dependent Impact of Hallucinations on Low-Frequency Fluctuations in Schizophrenia

Prior resting-state functional magnetic resonance imaging (fMRI) analyses have identified patterns of functional connectivity associated with hallucinations in schizophrenia (Sz). In this study, we performed an analysis of the mean amplitude of low-frequency fluctuations (ALFF) to compare resting state spontaneous low-frequency fluctuations in patients with Sz who report experiencing hallucinations impacting different sensory modalities. By exploring dynamics across 2 low-frequency passbands (slow-4 and slow-5), we assessed the impact of hallucination modality and frequency range on spatial ALFF variation. Drawing from a sample of Sz and healthy controls studied as part of the Functional Imaging Biomedical Informatics Research Network (FBIRN), we replicated prior findings showing that patients with Sz have decreased ALFF in the posterior brain in comparison to controls. Remarkably, we found that patients that endorsed visual hallucinations did not show this pattern of reduced ALFF in the back of the brain. These patients also had elevated ALFF in the left hippocampus in comparison to patients that endorsed auditory (but not visual) hallucinations. Moreover, left hippocampal ALFF across all the cases was related to reported hallucination severity in both the auditory and visual domains, and not overall positive symptoms. This supports the hypothesis that dynamic changes in the ALFF in the hippocampus underlie severity of hallucinations that impact different sensory modalities.
Joint sparse canonical correlation analysis for detecting differential imaging genetics modules

MOTIVATION Imaging genetics combines brain imaging and genetic information to identify the relationships between genetic variants and brain activities. When the data samples belong to different classes (e.g. disease status), the relationships may exhibit class-specific patterns that can be used to facilitate the understanding of a disease. Conventional approaches often perform separate analysis on each class and report the differences, but ignore important shared patterns. RESULTS In this paper, we develop a multivariate method to analyze the differential dependency across multiple classes. We propose a joint sparse canonical correlation analysis method, which uses a generalized fused lasso penalty to jointly estimate multiple pairs of canonical vectors with both shared and class-specific patterns. Using a data fusion approach, the method is able to detect differentially correlated modules effectively and efficiently. The results from simulation studies demonstrate its higher accuracy in discovering both common and differential canonical correlations compared to conventional sparse CCA. Using a schizophrenia dataset with 92 cases and 116 controls including a single nucleotide polymorphism (SNP) array and functional magnetic resonance imaging data, the proposed method reveals a set of distinct SNP-voxel interaction modules for the schizophrenia patients, which are verified to be both statistically and biologically significant. AVAILABILITY AND IMPLEMENTATION The Matlab code is available at https://sites.google. com/site/jianfang86/JSCCA CONTACT: wyp@tulane.eduSupplementary information: Supplementary data are available at Bioinformatics online.