Miracle-dz/UniFAR-FTUs huggingface dataset:
Apolipoprotein E Allelic Frequency Altered in Women with Early-onset Breast Cancer

Among women, the most prevalent type of cancer is breast cancer, affecting 1 out of every 8 women in the United States; in Puerto Rico, 70 out of every 100,000 will develop some type of breast cancer. Therefore, a better understanding of the potential risk factors for breast cancer could lead to the development of early detection tools. A gene that has been proposed as a risk factor in several populations around the world is Apolipoprotein E (apoE). ApoE functions as a mechanism of transport for lipoproteins and cholesterol throughout the body, with 3 main isoforms present in humans (apoE2, apoE3, and apoE4). Whether or not apoE4 is a risk factor for breast cancer remains controversial. Previous studies have either included test subjects of all ages (20–80) or have focused on late-onset (after age 50) breast cancer; none has concentrated specifically on early-onset (aged 50 and younger) breast cancer. The objectives of this study was to examine (in a Puerto Rican population) the differences in the relative frequency of occurrence of apoE4 in non-breast cancer versus breast cancer patients and to examine, as well, the potential differences of same in early- versus late-onset patients. We found an increased frequency of apoE4 (odds ratio 2.15) only in early-onset breast cancer survivors, which is similar to the findings of those studies that combined or adjusted for age as well as for an association between apoE4 and decreased tumor size. ApoE is also a potential risk factor for long-term cognitive effects after chemotherapy and affects response to hormone replacement. Our data supports the theory that knowing the apoE genotype of women who are at risk of developing breast cancer may be beneficial, as such knowledge would aid in the prediction of tumor size and the development of treatment regimens.
SLCO1B1 gene polymorphisms do not influence plasma rifampicin concentrations in a South Indian population.

OBJECTIVE To determine the effect of SLCO1B1 gene polymorphisms (rs11045819, rs4149032 and rs4149033) on rifampicin (RMP) concentrations in adult tuberculosis (TB) patients from south India. METHODS We genotyped adult TB patients for three SLCO1B1 gene polymorphisms-rs11045819, rs4149032 and rs4149033-and compared 2-h post-dosing RMP concentrations of the different genotypes for each of the polymorphisms. Plasma RMP was determined using high-performance liquid chromatography. Genotyping was performed using direct sequencing. RESULTS Among the 256 study patients, minor allele frequencies were respectively 0.01 (A), 0.46 (C) and 0.07 (A) for rs11045819, rs4149032 and rs4149033 polymorphisms; genotype distributions followed Hardy-Weinberg equilibrium. RMP concentrations did not significantly differ between the different genotypes of the three polymorphisms. CONCLUSION This is the first study to show that rs11045819, rs4149032 and rs4149033 polymorphisms in the SLCO1B1 gene did not influence RMP concentrations in Indian patients.
Compressive Light Field Reconstructions Using Deep Learning

Light field imaging is limited in its computational processing demands of high sampling for both spatial and angular dimensions. Single-shot light field cameras sacrifice spatial resolution to sample angular viewpoints, typically by multiplexing incoming rays onto a 2D sensor array. While this resolution can be recovered using compressive sensing, these iterative solutions are slow in processing a light field. We present a deep learning approach using a new, two branch network architecture, consisting jointly of an autoencoder and a 4D CNN, to recover a high resolution 4D light field from a single coded 2D image. This network decreases reconstruction time significantly while achieving average PSNR values of 26-32 dB on a variety of light fields. In particular, reconstruction time is decreased from 35 minutes to 6.7 minutes as compared to the dictionary method for equivalent visual quality. These reconstructions are performed at small sampling/compression ratios as low as 8%, allowing for cheaper coded light field cameras. We test our network reconstructions on synthetic light fields, simulated coded measurements of real light fields captured from a Lytro Illum camera, and real coded images from a custom CMOS diffractive light field camera. The combination of compressive light field capture with deep learning allows the potential for real-time light field video acquisition systems in the future.
Looking into the black box: a survey of the matching function

We survey the microfoundations, empirical evidence and estimation issues underlying the aggregate matching function. Several microeconomic matching mechanisms have been suggested in the literature with some successes but none is generally accepted as superior to all others. Instead, an aggregate matching function with hires as a function of vacancies and unemployment has been successfully estimated for several countries. The Cobb-Douglas restrictions with constant returns to scale perform well. Recent work has utilized disaggregated data to go beyond aggregate estimates, with many refinements and suggestions for future research.
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets

SUMMARY Recently, several high profile studies collected cell viability data from panels of cancer cell lines treated with many drugs applied at different concentrations. Such drug sensitivity data for cancer cell lines provide suggestive treatments for different types and subtypes of cancer. Visualization of these datasets can reveal patterns that may not be obvious by examining the data without such efforts. Here we introduce Drug/Cell-line Browser (DCB), an online interactive HTML5 data visualization tool for interacting with three of the recently published datasets of cancer cell lines/drug-viability studies. DCB uses clustering and canvas visualization of the drugs and the cell lines, as well as a bar graph that summarizes drug effectiveness for the tissue of origin or the cancer subtypes for single or multiple drugs. DCB can help in understanding drug response patterns and prioritizing drug/cancer cell line interactions by tissue of origin or cancer subtype. AVAILABILITY AND IMPLEMENTATION DCB is an open source Web-based tool that is freely available at: http://www.maayanlab. net/LINCS/DCB CONTACT: avi.maayan@mssm.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Büchi-Kamp Theorems for 1-clock ATA

This paper investigates Kamp-like and B\"uchi-like theorems for 1-clock Alternating Timed Automata (1-ATA) and its natural subclasses. A notion of 1-ATA with loop-free-resets is defined. This automaton class is shown to be expressively equivalent to the temporal logic $\regmtl$ which is $\mathsf{MTL[F_I]}$ extended with a regular expression guarded modality. Moreover, a subclass of future timed MSO with k-variable-connectivity property is introduced as logic $\qkmso$. In a Kamp-like result, it is shown that $\regmtl$ is expressively equivalent to $\qkmso$. As our second result, we define a notion of conjunctive-disjunctive 1-clock ATA ($\wf$ 1-ATA). We show that $\wf$ 1-ATA with loop-free-resets are expressively equivalent to the sublogic $\F\regmtl$ of $\regmtl$. Moreover $\F\regmtl$ is expressively equivalent to $\qtwomso$, the two-variable connected fragment of $\qkmso$. The full class of 1-ATA is shown to be expressively equivalent to $\regmtl$ extended with fixed point operators.
Association between urticaria and nematode infections.

BACKGROUND The association between parasites and urticaria was first suggested in the last century. A wide range, 0-75.4%, of the prevalence of parasitic infection has been reported with chronic urticaria (CU). Moreover, urticaria may be detected in patients with parasitosis. Nematodes are a type of helminth that infect hundreds of millions of people throughout the world. OBJECTIVE The aim of this work was to collect and review the published studies and cases of urticaria associated with nematode infections. METHODS A search of scientific literature data bases from January 1960 until May 2017 was carried out. RESULTS Numerous nematode infections have been associated with urticaria and/or angioedema: Anisakis simplex, Ascaris species (spp.), Dirofilaria spp. , Enterobius vermicularis, Gnathostoma spp. , Loa loa, Mansonella streptocerca; Necator americanus, Onchocerca volvulus, Strongyloides stercoralis, Toxocara spp. , Trichinella spp. , and Wuchereria bancrofti. The pathogenesis of urticaria in these infections generally remains unexplained. In some cases, skin manifestations were caused by the presence of the worm in the skin (Filaria, Gnathostoma); in other cases, such as A. simplex and S. stercoralis infections, there was a clear immunoglobulin E-mediated mechanism that led to allergic reactions, and infection and allergy coexisted; for other nematodes, the association was anecdotal and only a few cases were reported. CONCLUSION It is difficult to detect a certain causal effect, except when urticaria improves or disappears after infection treatment. Cases of isolated urticaria not associated with other symptoms rarely may be caused by helminths. In the current guideline for urticaria, parasitosis is considered to be a rare possible cause of CU in developed industrial countries, Therefore, although a routine screening of parasitic infection in CU is not recommended, in our opinion, testing a patient with urticaria for parasites is a physician's choice based on the characteristics of the patient, such as associated symptoms, dietary habit, provenance country and previous travel.
Heterozygosity at protein loci in inbred and outbred lines of chickens.

Levels of heterozygosity at six polymorphic protein marker loci were determined by electrophoresis in 24 lines of poultry, encompassing 17 White Leghorn inbred lines (WLI) (with inbreeding coefficients, F, ranging from .946 to .988), five Australorp inbred lines (AusI) (with F values ranging from .924 to .961), and two randombred lines (one White Leghorn and one Australorp). Fixation was observed at one locus in WLI lines, and at two loci in the AusI lines. Segregation at the other loci was observed in the inbred lines of the two breeds. Observed heterozygosity in the inbred lines markedly exceeded the expectations under inbreeding theory. In White Leghorns, reproductive fitnesses for heterozygotes were superior to homozygotes in the inbred lines, but not in the control. Consequently, natural selection operating through associative overdominance appears to be responsible for the higher than expected heterozygosities in the inbred lines.
Compressive Hyperspectral Imaging via Sparse Tensor and Nonlinear Compressed Sensing

Recently, compressive hyperspectral imaging (CHI) has received increasing interests, which can recover a large range of scenes with a small number of sensors via compressed sensing (CS) theory. However, most of the available CHI methods separate and vectorize hyperspectral cubes into spatial and spectral vectors, which will result in heavy computational and storage burden in the recovery. Moreover, the complexity of real scene makes the sparsifying difficult and thus requires more measurements to achieve accurate recovery. In this paper, these two issues are addressed, and a new CHI approach via sparse tensors and nonlinear CS (NCS) is advanced for accurate maintenance of image structure with limited number of sensors. Based on a multidimensional multiplexing (MDMP) CS scheme, the observed measurements are denoted as tensors and a nonlinear sparse tensor coding is adopted, to develop a new tensor-NCS (T-NCS) algorithm for noniterative recovery of hyperspectral images. Moreover, two recovery schemes are advanced for T-NCS, including example-aided and self-learning CHI approaches. Finally, some experiments are performed on three real hyperspectral data sets to investigate the performance of T-NCS, and the results demonstrate its efficiency and superiority to the counterparts.
Experience of US Patients Who Self-identify as Having an Overdiagnosed Thyroid Cancer: A Qualitative Analysis

Importance Overdiagnosis of cancer—the identification of cancers that are unlikely to progress—is a source of discomfort and challenge for patients, physicians, and health care systems. A major cause of this discomfort is the inability to know prospectively with certainty which cancers are overdiagnosed. In thyroid cancer, as patients have begun to understand this concept, some individuals are independently deciding not to intervene, despite this practice not yet being widely accepted. Objective To describe the current experience of people who independently self-identify as having an overdiagnosed cancer and elect not to intervene. Design, Setting, and Participants In this qualitative study, semistructured interviews were conducted between July 1 and December 31, 2015, with 22 community-dwelling adults aged 21 to 75 years who had an incidentally identified thyroid finding that was known or suspected to be malignant and who questioned the intervention recommended by their physicians. Verbatim transcripts were analyzed using constant comparative analysis. Main Outcomes and Measures The experience of individuals who self-identify as having an overdiagnosed cancer and elect not to intervene. Results Of the 22 people interviewed (16 females and 6 males; mean age, 48.5 years), 18 had elected not to intervene on their thyroid finding and had been living with the decision for a mean of 39 months (median, 40 months; range, 1-88 months). Twelve of the 18 participants reported that they experienced significant anxiety about cancer progression, but had considered reasons for choosing nonintervention: understanding issues of precision in diagnostic testing and the varied behavior of cancer, surgical risks, medication use, and low risk of death from the cancer. Twelve participants described their decisions as met with nonreassuring, unsupportive responses. Medical professionals, friends, and internet discussion groups told them they were “being stupid,” “were wrong,” or were “crazy” to not intervene. Although 14 individuals said they wished to connect with others about their experiences, only 3 reported success in doing so. Fifteen participants reported that they managed their overall experience through secret keeping. By the time of this study, 5 of the 18 individuals had discontinued surveillance, the recommended alternative to intervention. Despite this, only 7 participants “wished they did not know” about their thyroid finding. Conclusions and Relevance Isolation and anxiety characterize the current experience of patients with thyroid cancer who are living with the decision to not intervene. These patients are at risk of disengaging from health care. Successful de-escalation of intervention for patients who self-identify as having overdiagnosed cancers requires explicit social and health system support and education. We hypothesize that improved support would also promote quality of care by increasing the likelihood that patients could be kept engaged for recommended surveillance.
The effects of restaurant menu calorie labeling on hypothetical meal choices of females with disordered eating

Concerns have been raised that obesity public policy measures may have harmful effects on individuals with eating disorders. However, little research has investigated this topic. We examined the impact of a popular obesity public policy, menu calorie labeling, on hypothetical food choices of women with disordered eating. Seven hundred sixteen adult females completed an online survey in which they were randomly assigned to receive a restaurant menu with or without calorie information listed. Participants selected foods representative of a meal they would choose to consume and answered questions on restaurant ordering and menu labeling. Participants completed the Eating Disorder Examination Questionnaire (Fairburn & Beglin, ) to assess global eating pathology. Diagnoses of anorexia nervosa (AN), bulimia nervosa (BN), and binge-eating disorder (BED) were also derived from this measure. Generalized linear modeling examined the impact of menu label condition, disordered eating, and the menu label by disordered eating interaction on hypothetical food selection and related variables. When disordered eating was examined continuously, menu labeling did not differentially affect food selections of those with elevated disordered eating (p = .45). However, when examined by eating disorder diagnosis, participants with AN or BN ordered significantly fewer (p < .001) and participants with BED ordered significantly more (p = .001) calories in the menu label versus no label condition. Menu labeling may decrease the calories ordered among individuals with AN or BN and increase calories ordered among individuals with BED.
Interfacing of microbial cells with nanoparticles: Simple and cost-effective preparation of a highly sensitive microbial ethanol biosensor

Various types of carbon nanoparticles were directly mixed with microbial cells of Gluconobacter oxydans within a 3-D bionanocomposite in order to prepare a highly sensitive ethanol biosensor with a short response time. From all carbonaceous nanomaterials tested, single- or multi-walled carbon nanotubes provided the highest sensitivity of detection (117–121 µA cm−2 mM−1), but from a practical point of view, Ketjen black 300 and 600 provide very low detection limit (2–6 µM) and high sensitivity for the ethanol analysis (84–88 µA cm−2 mM−1)with a shortresponse time (14–33 s). Moreover, the price of Ketjen black is a few orders of magnitude lower compared to that of carbon nanotubes. Finally, the study showed that the morphology of nanoparticles rather than their surface modification is the key element in achieving high sensitivity of ethanol detection.
Hippocampal Neurogenesis Regulates Forgetting During Adulthood and Infancy

Forget It! When examining the relationship between the production of new neurons in the hippocampus and memory, studies have generally first manipulated hippocampal neurogenesis and afterward investigated memory formation and found that new neurons help to encode new memories. However, when investigating how similar manipulations of neurogenesis impact established hippocampus-dependent memories, Akers et al. (p. 598; see the Perspective by Mongiat and Schinder) uncovered a role for neurogenesis in memory clearance. Thus, the continuous addition of new neurons both degrades existing information stored in hippocampal circuits and simultaneously provides substrates for new learning. Addition of new neurons leads to remodeling of hippocampal circuitry and memory degradation. [Also see Perspective by Mongiat and Schinder] Throughout life, new neurons are continuously added to the dentate gyrus. As this continuous addition remodels hippocampal circuits, computational models predict that neurogenesis leads to degradation or forgetting of established memories. Consistent with this, increasing neurogenesis after the formation of a memory was sufficient to induce forgetting in adult mice. By contrast, during infancy, when hippocampal neurogenesis levels are high and freshly generated memories tend to be rapidly forgotten (infantile amnesia), decreasing neurogenesis after memory formation mitigated forgetting. In precocial species, including guinea pigs and degus, most granule cells are generated prenatally. Consistent with reduced levels of postnatal hippocampal neurogenesis, infant guinea pigs and degus did not exhibit forgetting. However, increasing neurogenesis after memory formation induced infantile amnesia in these species.
Prevalence of Bovine Trypanosomosis in Gimbi district, West Wollega, Western Oromiya of Ethiopia

A cross-sectional study was carried out from March to May 2014 to determine the prevalence of bovine trypanosomosis in Gimbi district. The method employed during the study was buffy coat technique for parasitological study. Blood samples were collected from ear vein of 445 heads of cattle to assess trypanosome species. The overall prevalence of the disease was 4.9 % and was vary in different peasant associations (PAs) of the study area with 2.7 %, 11.8 % and 0 % in Tole, Jogir and Inango Denbeli, respectively. Out of 22 infected animals 63.64 % cattle were found to be infected by T. congolense, (31.8 %) T. vivax, and (4.55 %) mixed parasites (T. congolense and T. vivax). The results showed that, T. congolense was the most prevalent in the study areas and followed by mixed parasites. There was statistically significant difference (p<0.05) in distribution of trypanosoma infection. The prevalence of disease recorded among age groups was 0 %, 4.7 % and 5.5 % in calves (<3years), youngs (3-9 years) and adults (>9 years), respectively. The results also showed the prevalence between sexes was 4.95 % (male) and 4.93 % (female). The infection rates between different ages and sexes of animals showed no significant difference. The mean PCV value of parasitaemic animals was 22.78 %, of aparasitaemic animals was 26.51 % and the overall mean PCV value was 24.65 %. Analysis of the mean PCV values of parasitaemic and aparasitaemic animals showed statistically significant difference (p<0.05). The results of the study suggested that trypanosomosis in the area was decreasing. However, due to its impact on the livestock, an appropriate tsetse control methods should be expanded to reach tsetse infested area in a sustainable manner to alleviate the problem of trypanosomosis in the area.
Transient Temperature Response Modeling in IAMs: The Effects of Over Simplification on the SCC

Abstract Integrated Assessment Models (IAMs) couple representations of the natural climate system with models of the global economy to evaluate climate and energy policies. Such models are currently used to derive the benefits of carbon mitigation policies through estimates of the social cost of carbon (SCC). To remain tractable these models often utilize highly simplified representations of complex natural, social, and economic systems. The authors consider three prominent IAMs, DICE, FUND, and PAGE, and compare their highly simplified temperature response models to two upwelling diffusion energy balance models that better reflect the progressive heat uptake of the deep ocean. They find that all three IAMs fail to fully capture important characteristics in the dynamics of temperature response, especially for high equilibrium climate sensitivities. This has serious implications given these models are often run with distributions for the equilibrium climate sensitivity which have a positive probability for such states of the world. The authors find that, all else equal, the temperature response model in FUND can lead to estimates of the expected SCC that are 10–75% lower than those derived using more realistic climate models, while the models in DICE and PAGE lead to expected SCC estimates that are 10–110% and 40–260% higher, respectively.