Miracle-dz/UniFAR-FTUs huggingface dataset:
Microfossil evidence for trophic changes during the Eocene–Oligocene transition in the South Atlantic (ODP Site 1263, Walvis Ridge)

Abstract. The biotic response of calcareous nannoplankton to environmental and climatic changes during the Eocene–Oligocene transition was investigated at a high resolution at Ocean Drilling Program (ODP) Site 1263 (Walvis Ridge, southeast Atlantic Ocean) and compared with a lower-resolution benthic foraminiferal record. During this time interval, global climate, which had been warm under high levels of atmospheric CO2 (pCO2) during the Eocene, transitioned into the cooler climate of the Oligocene, at overall lower pCO2. At Site 1263, the absolute nannofossil abundance (coccoliths per gram of sediment; N g−1) and the mean coccolith size decreased distinctly after the E–O boundary (EOB; 33.89 Ma), mainly due to a sharp decline in abundance of large-sized Reticulofenestra and Dictyococcites, occurring within a time span of ~ 47 kyr. Carbonate dissolution did not vary much across the EOB; thus, the decrease in abundance and size of nannofossils may reflect an overall decrease in their export production, which could have led to variations in the food availability for benthic foraminifers. The benthic foraminiferal assemblage data are consistent with a global decline in abundance of rectilinear species with complex apertures in the latest Eocene (~ 34.5 Ma), potentially reflecting changes in the food source, i.e., phytoplankton. This was followed by a transient increased abundance of species indicative of seasonal delivery of food to the sea floor (Epistominella spp.; ~ 33.9–33.4 Ma), with a short peak in overall food delivery at the EOB (buliminid taxa; ~ 33.8 Ma). Increased abundance of Nuttallides umbonifera (at ~ 33.3 Ma) indicates the presence of more corrosive bottom waters and possibly the combined arrival of less food at the sea floor after the second step of cooling (Step 2). The most important changes in the calcareous nannofossil and benthic communities occurred ~ 120 kyr after the EOB. There was no major change in nannofossil abundance or assemblage composition at Site 1263 after Step 2 although benthic foraminifera indicate more corrosive bottom waters during this time. During the onset of latest-Eocene–earliest-Oligocene climate change, marine phytoplankton thus showed high sensitivity to fast-changing conditions as well as to a possibly enhanced, pulsed nutrient supply and to the crossing of a climatic threshold (e.g., pCO2 decline, high-latitude cooling and changes in ocean circulation).
Mining Pixels: Weakly Supervised Semantic Segmentation Using Image Labels

We consider the task of learning a classifier for semantic segmentation using weak supervision, in this case, image labels specifying the objects within the image. Our method uses deep convolutional neural networks (CNNs) and adopts an Expectation-Maximization (EM) based approach maintaining the uncertainty on pixel labels. We focus on the following three crucial aspects of the EM based approach: (i) initialization; (ii) latent posterior estimation (E step) and (iii) the parameter update (M step). We show that saliency and attention maps provide good cues to learn an initialization model and allows us to skip the bad local maximum to which EM methods are otherwise traditionally prone. In order to update the parameters, we propose minimizing the combination of the standard softmax loss and the KL divergence between the true latent posterior and the likelihood given by the CNN. We argue that this combination is more robust to wrong predictions made by the expectation step of the EM method. We support this argument with empirical and visual results. We additionally incorporate an approximate intersection-over-union (IoU) term into the loss function for better parameter estimation. Extensive experiments and discussions show that: (i) our method is very simple and intuitive; (ii) requires only image-level labels; and (iii) consistently outperforms other weakly/semi supervised state-of-the-art methods with a very high margin on the PASCAL VOC 2012 dataset.
Adipocyte Secretome Increases Radioresistance of Malignant Melanocytes by Improving Cell Survival and Decreasing Oxidative Status

Radiotherapy is a treatment option for the majority of malignancies. However, because melanoma is known to be radioresistant, the use of ionizing radiation as an adjuvant therapy in cutaneous melanoma patients is ineffective. Obesity has now been recognized as a risk factor for melanoma. High adiposity is generally associated with a more pro-oxidative status. Oxidative stress is a major player in radiation therapy and also a common link between obesity and cancer. Several adipocyte-released proteins are known to have a role in controlling cellular growth and pro-survival signaling. For that reason, we investigated the influence of 3T3-L1 mature adipocyte secretome in B16-F10 malignant melanocyte radiosensitivity. We evaluated B16-F10 cell survival and redox homeostasis when exposed to four daily doses of ionizing radiation (2 Gy per day) up to a total of 8 Gy in a medical linear accelerator. B16-F10 melanocytes exhibited slight alterations in survival, catalase activity, nitrative stress and total oxidant concentration after the first 2 Gy irradiation. The motility of the melanocytes was also delayed by ionizing radiation. Subsequent irradiations of the malignant melanocytes led to more prominent reductions in overall survival. Remarkably, 3T3-L1 adipocyte-secreted molecules were able to increase the viability and migration of melanocytes, as well as lessen the pro-oxidant burden induced by both the single and cumulative X-ray doses. In vitro adipocyte-released factors protected B16-F10 malignant melanocytes from both oxidative stress and loss of viability triggered by radiation, enhancing the radioresistant phenotype of these cells with a concomitant activation of the AKT signaling pathway. These results both help to elucidate how obesity influences melanoma radioresistance and support the usage of conventional medical linear accelerators as a valid model for the in vitro radiobiological study of tumor cell lines.
Disseminated Histoplasmosis in a Bengal Tiger (Panthera tigris)

Abstract: Disseminated infection with Histoplasma capsulatum was diagnosed in a 7-yr-old female Bengal tiger (Panthera tigris). Clinical signs were nonspecific with the exception of brief periods of tachypnea for 5 days prior to death. H. capsulatum organisms were found in the lungs, tracheobronchial lymph nodes, and liver. Diagnosis was confirmed by tracheal wash, urine H. capsulatum enzyme immunoassay, and necropsy results. This report represents the first published account of disseminated histoplasmosis in a tiger.
Xenobiotics and Loss of Cell Adhesion Drive Distinct Transcriptional Outcomes by Aryl Hydrocarbon Receptor Signaling

The aryl hydrocarbon receptor (AhR) is a signal-regulated transcription factor, which is canonically activated by the direct binding of xenobiotics. In addition, switching cells from adherent to suspension culture also activates the AhR, representing a nonxenobiotic, physiological activation of AhR signaling. Here, we show that the AhR is recruited to target gene enhancers in both ligand [isopropyl-2-(1,3-dithietane-2-ylidene)-2-[N-(4-methylthiazol-2-yl)carbamoyl]acetate (YH439)]-treated and suspension cells, suggesting a common mechanism of target gene induction between these two routes of AhR activation. However, gene expression profiles critically differ between xenobiotic- and suspension-activated AhR signaling. Por and Cldnd1 were regulated predominantly by ligand treatments, whereas, in contrast, ApoER2 and Ganc were regulated predominantly by the suspension condition. Classic xenobiotic-metabolizing AhR targets such as Cyp1a1, Cyp1b1, and Nqo1 were regulated by both ligand and suspension conditions. Temporal expression patterns of AhR target genes were also found to vary, with examples of transient activation, transient repression, or sustained alterations in expression. Furthermore, sequence analysis coupled with chromatin immunoprecipitation assays and reporter gene analysis identified a functional xenobiotic response element (XRE) in the intron 1 of the mouse Tiparp gene, which was also bound by hypoxia-inducible factor-1α during hypoxia and features a concatemer of four XRE cores (GCGTG). Our data suggest that this XRE concatemer site concurrently regulates the expression of both the Tiparp gene and its cis antisense noncoding RNA after ligand- or suspension-induced AhR activation. This work provides novel insights into how AhR signaling drives different transcriptional programs via the ligand versus suspension modes of activation.
An apoA-I mimetic peptide increases LCAT activity in mice through increasing HDL concentration

Lecithin cholesterol acyltransferase (LCAT) plays a key role in the reverse cholesterol transport (RCT) process by converting cholesterol to cholesteryl ester to form mature HDL particles, which in turn deliver cholesterol back to the liver for excretion and catabolism. HDL levels in human plasma are negatively correlated with cardiovascular risk and HDL functions are believed to be more important in atheroprotection. This study investigates whether and how D-4F, an apolipoprotein A-I (apoA-I) mimetic peptide, influences LCAT activity in the completion of the RCT process. We demonstrated that the apparent rate constant value of the LCAT enzyme reaction gives a measure of LCAT activity and determined the effects of free metals and a reducing agent on LCAT activity, showing an inhibition hierarchy of Zn2+>Mg2+>Ca2+ and no inhibition with β-mercaptoethanol up to 10 mM. We reconstituted nano-disc particles using apoA-I or D-4F with phospholipids. These particles elicited good activity in vitro in the stimulation of cholesterol efflux from macrophages through the ATP-binding cassette transporter A1 (ABCA1). With these particles we studied the LCAT activity and demonstrated that D-4F did not activate LCAT in vitro. Furthermore, we have done in vivo experiments with apoE-null mice and demonstrated that D-4F (20 mg/kg body weight, once daily subcutaneously) increased LCAT activity and HDL level as well as apoA-I concentration at 72 hours post initial dosing. Finally, we have established a correlation between HDL concentration and LCAT activity in the D-4F treated mice.
Effects of creatine supplementation during recovery from rapid body mass reduction on metabolism and muscle performance capacity in well-trained wrestlers.

BACKGROUND The aim of the study was to test the hypothesis that creatine supplementation with concomitant carbohydrate ingestion during recovery period after rapid body mass reduction accelerates the restoration of body mass and physical performance in well-trained wrestlers. METHODS A double-blind, placebo-controlled cross-over study was conducted on five young healthy male wrestlers, who reduced their body mass by 4.5-5.3% in two series of investigations separated by one month. During 17 hrs recovery period they consumed controlled diet supplemented in random order with glucose (GL trial) or with glucose plus creatine (GL+CR trial). The capacity of the subjects to perform submaximal and maximal (W(max)) intensity work was measured using 5 min intermittent intensity test exercise at the Cybex II device before (Test 1) and after body mass loss (Test 2), also after the recovery (Test 3) on both trials. RESULTS There was no effect of treatment on the extent of body mass regain during 17 hrs recovery. A significant increase (19.2%) in W(max) from Test 2 to Test 3 was observed in GL+CR trial whereas no change was evident with GL treatment. A strong correlation (r=0.92) was established between the whole body creatine retention and the extent of change in W(max) from Test 2 to Test 3. CONCLUSIONS The results suggest that creatine supplementation with concomitant glucose ingestion during 17 hrs recovery from rapid body mass loss does not accelerate the restoration of body mass but still stimulates the regain of physical performance in maximal intensity efforts in well-trained wrestlers.
Baseline Renal Function among Antiretroviral Therapy-Naive, HIV-Infected Patients in Southeast Nigeria

Background: Renal insufficiency has been shown to be a significant, independent risk factor for mortality among HIV-infected patients. Unfortunately, little is known about the prevalence and nature of renal impairment in African populations initiating antiretroviral treatment. This study aims to find the prevalence of abnormal renal function among antiretroviral therapy (ART)-naive, HIV-infected patients in the South Eastern geopolitical zone of Nigeria. Method: This is a cross-sectional hospital-based study, involving 300 ART-naive HIV-positive patients, seen over a 1-year period, aged from 18 years and older, presenting to the clinic for the first time. Results: A total of 300 patients were included in the study, 104 (34.7%) males and 196 (65.3%) females. The prevalence of significant renal disease was 24.3% (73 of 300), while 38.3% (115 of 300) had mild renal impairment. Using logistic regression, age, CD4 count, urea, creatinine, and hemoglobin were significantly associated with renal impairment. Conclusion: The authors observed a high prevalence of significant renal impairment among HIV-infected patients at the time of ART initiation.
Effects of Entomopathogens on Mortality of Western Corn Rootworm (Coleoptera: Chrysomelidae) and Fitness Costs of Resistance to Cry3Bb1 Maize

ABSTRACT Fitness costs can delay pest resistance to crops that produce insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt), and past research has found that entomopathogens impose fitness costs of Bt resistance. In addition, entomopathogens can be used for integrated pest management by providing biological control of pests. The western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is a major pest of maize and is currently managed by planting of Bt maize. We tested whether entomopathogenic nematodes and fungi increased mortality of western corn rootworm and whether these entomopathogens increased fitness costs of resistance to Cry3Bb1 maize. We exposed western corn rootworm larvae to two species of nematodes, Heterorhabditis bacteriophora Poinar (Rhabditida: Heterorhabditidae) and Steinernema feltiae Filipjev (Rhabditida: Steinernematidae), and to two species of fungi, Beauveria bassiana (Balsamo) Vuillemin (Hypocreales: Cordycipitaceae) (strain GHA) and Metarhizium brunneum (Metschnikoff) Sorokin (Hypocreales: Clavicipitaceae) (strain F52) in two assay types, namely, seedling mat and small cup. Larval mortality increased with the concentration of H. bacteriophora and S. feltiae in the small cup assay, and with the exception of S. feltiae and B. bassiana in the seedling mat assay, mortality from entomopathogens was significantly greater than zero for the remaining entomopathogens in both assays. However, no fitness costs were observed in either assay type for any entomopathogen. Increased mortality of western corn rootworm larvae caused by these entomopathogens supports their potential use in biological control; however, the lack of fitness costs suggests that entomopathogens will not delay the evolution of Bt resistance in western corn rootworm.
Environmental Transmission of Typhoid Fever in an Urban Slum

Background Enteric fever due to Salmonella Typhi (typhoid fever) occurs in urban areas with poor sanitation. While direct fecal-oral transmission is thought to be the predominant mode of transmission, recent evidence suggests that indirect environmental transmission may also contribute to disease spread. Methods Data from a population-based infectious disease surveillance system (28,000 individuals followed biweekly) were used to map the spatial pattern of typhoid fever in Kibera, an urban informal settlement in Nairobi Kenya, between 2010–2011. Spatial modeling was used to test whether variations in topography and accumulation of surface water explain the geographic patterns of risk. Results Among children less than ten years of age, risk of typhoid fever was geographically heterogeneous across the study area (p = 0.016) and was positively associated with lower elevation, OR = 1.87, 95% CI (1.36–2.57), p <0.001. In contrast, the risk of typhoid fever did not vary geographically or with elevation among individuals less than 6b ten years of age. Conclusions Our results provide evidence of indirect, environmental transmission of typhoid fever among children, a group with high exposure to fecal pathogens in the environment. Spatially targeting sanitation interventions may decrease enteric fever transmission.
Attitudes and behaviors towards clinical guidelines: the clinicians' perspective.

Objectives--To find out what attitudes hospital doctors have towards the culture of clinical guidelines; to ascertain perceived knowledge and use of clinical guidelines; and to investigate why hospital doctors think that clinical guidelines may not be used and how they think that the use of guidelines can be encouraged. Design--Postal questionnaire survey be tween October 1993 and January 1994. Setting--Hospitals within Oxford region. Subjects--409 doctors of all grades working in one of six specialties (anaesthetics, paediatrics, general surgery, general medicine, obstetrics and gynaecology and accident and emergency medicine). 47 were randomly picked as part of the pilot study, 362 were extracted from hospital staffing lists. Results--268 clinicians (66%) responded to the questionnaire. Most respondents (77%, 208) expressed welcoming attitudes towards guidelines but 51%(136) perceived the attitudes of their colleagues as being less favourable. Over three quarters of respondents claimed to use guidelines at least once a month. Most respondents learnt about guidelines from discussions with their peers (50%, 134 respondents) or senior doctors 37%, 99) or from journals (39%, 105). Reasons why guidelines may not be used included being unaware of particular guidelines (80%, 213 respondents) and the fact that guidelines had been poorly developed (64%, 171) or were impractical (49%, 132). The best ways to encourage the use of guidelines were thought to be encouragement from senior doctors (72%, 193 respondents) and peers (59%, 157) and by monitoring behaviour and providing feedback (68%, 181). Conclusion--The decision to use a guide line was based on the perceived value of each guideline and was influenced by other clinicians' behaviour. The results provide an insight into aspects of dissemination and implementation which are perceived as influential by the recipients of guidelines.
The Streaming Capacity of Sparsely Connected P2P Systems With Distributed Control

Peer-to-peer (P2P) streaming technologies can take advantage of the upload capacity of clients, and hence can scale to large content distribution networks with lower cost. A fundamental question for P2P streaming systems is the maximum streaming rate that all users can sustain. Prior works have studied the optimal streaming rate for a complete network, where every peer is assumed to be able to communicate with all other peers. This is, however, an impractical assumption in real systems. In this paper, we are interested in the achievable streaming rate when each peer can only connect to a small number of neighbors. We show that even with a random peer-selection algorithm and uniform rate allocation, as long as each peer maintains Ω(logN) downstream neighbors, where N is the total number of peers in the system, the system can asymptotically achieve a streaming rate that is close to the optimal streaming rate of a complete network. These results reveal a number of important insights into the dynamics of the system, based on which we then design simple improved algorithms that can reduce the constant factor in front of the Ω(logN) term, yet can achieve the same level of performance guarantee. Simulation results are provided to verify our analysis.
A polygenic risk score analysis of psychosis endophenotypes across brain functional, structural, and cognitive domains

This large multi‐center study investigates the relationships between genetic risk for schizophrenia and bipolar disorder, and multi‐modal endophenotypes for psychosis. The sample included 4,242 individuals; 1,087 patients with psychosis, 822 unaffected first‐degree relatives of patients, and 2,333 controls. Endophenotypes included the P300 event‐related potential (N = 515), lateral ventricular volume (N = 798), and the cognitive measures block design (N = 3,089), digit span (N = 1,437), and the Ray Auditory Verbal Learning Task (N = 2,406). Data were collected across 11 sites in Europe and Australia; all genotyping and genetic analyses were done at the same laboratory in the United Kingdom. We calculated polygenic risk scores for schizophrenia and bipolar disorder separately, and used linear regression to test whether polygenic scores influenced the endophenotypes. Results showed that higher polygenic scores for schizophrenia were associated with poorer performance on the block design task and explained 0.2% (p = 0.009) of the variance. Associations in the same direction were found for bipolar disorder scores, but this was not statistically significant at the 1% level (p = 0.02). The schizophrenia score explained 0.4% of variance in lateral ventricular volumes, the largest across all phenotypes examined, although this was not significant (p = 0.063). None of the remaining associations reached significance after correction for multiple testing (with alpha at 1%). These results indicate that common genetic variants associated with schizophrenia predict performance in spatial visualization, providing additional evidence that this measure is an endophenotype for the disorder with shared genetic risk variants. The use of endophenotypes such as this will help to characterize the effects of common genetic variation in psychosis.
Hip fracture and increased short-term but not long-term mortality in healthy older women.

BACKGROUND Fractures have been associated with subsequent increases in mortality, but it is unknown how long that increase persists. METHODS A total of 5580 women from a large community-based, multicenter US prospective cohort of 9704 (Study of Osteoporotic Fractures) were observed prospectively for almost 20 years. We age-matched 1116 hip fracture cases with 4 control participants (n = 4464). To examine the effect of health status, we examined a healthy older subset (n = 960) 80 years or older who attended the 10-year follow-up examination and reported good or excellent health. Incident hip fractures were adjudicated from radiology reports by study physicians. Death was confirmed by death certificates. RESULTS Hip fracture cases had 2-fold increased mortality in the year after fracture compared with controls (16.9% vs 8.4%; multivariable adjusted odds ratio [OR], 2.4; 95% CI, 1.9-3.1]. When examined by age and health status, short-term mortality was increased in those aged 65 to 69 years (16.3% vs 3.7%; OR, 5.0; 95% CI, 2.6-9.5), 70 to 79 years (16.5% vs 8.9%; OR, 2.4; 95% CI, 1.8-3.3), and only in those 80 years or older with good or excellent health (15.1% vs 7.2%; multivariable adjusted OR, 2.8; 95% CI, 1.5-5.2). After the first year, survival of hip fracture cases and controls was similar except in those aged 65 to 69 years, who continued to have increased mortality. CONCLUSIONS Short-term mortality is increased after hip fracture in women aged 65 to 79 years and in exceptionally healthy women 80 years or older. Women 70 years or older return to previous risk levels after a year. Interventions are needed to decrease mortality in the year after hip fracture, when mortality risk is highest.