Miracle-dz/UniFAR-FTUs huggingface dataset:
Can You Judge a Disease Host by the Company It Keeps? Predicting Disease Hosts and Their Relative Importance: A Case Study for Leishmaniasis

Zoonoses are an important class of infectious diseases. An important element determining the impact of a zoonosis on domestic animal and human health is host range. Although for particular zoonoses some host species have been identified, until recently there have been no methods to predict those species most likely to be hosts or their relative importance. Complex inference networks infer potential biotic interactions between species using their degree of geographic co-occurrence, and have been posited as a potential tool for predicting disease hosts. Here we present the results of an interdisciplinary, empirical study to validate a model based on such networks for predicting hosts of Leishmania (L.) mexicana in Mexico. Using systematic sampling to validate the model predictions we identified 22 new species of host (34% of all species collected) with the probability to be a host strongly dependent on the probability of co-occurrence of vector and host. The results confirm that Leishmania (L.) mexicana is a generalist parasite but with a much wider host range than was previously thought. These results substantially change the geographic risk profile for Leishmaniasis and provide insights for the design of more efficient surveillance measures and a better understanding of potential dispersal scenarios.
Estimating Welfare Effects Consistent with Forward-Looking Behavior. Part Ii: Empirical Results

In this paper, we provide estimates of welfare benefit effects on a set of behaviors that includes welfare participation, fertility, marriage, work and schooling using approximations to the decision rules that would be derived from an explicit dynamic optimization problem. We use the stylized model and associated simulations from Part I as a guide in specifying the approximate decision rules that we estimate here. The estimates are based on data from the 1979 youth cohort of the National Longitudinal Surveys of Labor Market Experience (NLSY79).
The Trotter procedure: a forgotten approach?

Anatomically, the surgical management of tongue base lesions is a challenging prospect for any head and neck surgeon. William Trotter described a median labio-mandibular glossotomy for access to such lesions (Meis JM, Enzinger FM. Myolipoma of soft tissue. Am J Surg Pathol 1991;15:121–5). Not widely reported, this approach still remains an important tool in the armamentarium of head and neck surgeons. We outline the use of this approach to remove a myolipoma from the tongue base.
Are Two Heads Better Than One?: Monetary Policy by Committee

Are Two Heads Better Than One? : Monetary Policy by Committee by Alan S. Blinder and John Morgan * Princeton University University of California, Berkeley 1. Introduction and Motivation The old saw “it works in practice, now let’s see if it works in theory” has a direct application to the design of monetary policy institutions. In recent years, central banking practice has exhibited a notable shift from individual to group decisionmaking, that is, toward more monetary policy committees (MPCs). For example, J.P. Morgan’s “Guide to Central Bank Watching” (March 2000, p. 4) noted that “One of the most notable developments of the past few years has been the shift of monetary policy decision-making to meetings of central bank policy boards. ” Two of the best-known examples of this institutional change are the Bank of England and the Bank of Japan, which (roughly) switched from individual to group decisionmaking in 1997 and 1999 respectively. The Governing Council of the European System of Central Banks, patterned loosely on the Federal Open Market Committee, also opened for business in 1999, although the Bundesbank Council had made decisions as a group long before that. Nevertheless, economic theory has had precious little to say on the pros and cons of making monetary policy individually or in groups. 1 Nor is there substantial empirical evidence on the relative merits of the two types of monetary policy decisionmaking processes. Correspondence to John Morgan: morgan@haas.berkeley. edu. We gratefully acknowledge financial support from Princeton’s Center for Economic Policy Studies and thank Felix Vardy for excellent and extensive research assistance. See, among other sources, Goodfriend (2000), Kristen (2001), and Gersbach and Hahn (2001) for recent discussions of the pros and cons of group versus committee decisionmaking on monetary policy. Blinder (forthcoming, 2003) contains a reasonably comprehensive survey of the (limited) literature on the question.
DNMT3A Mutations in Patients with Acute Myeloid Leukemia in South Brazil

Acute myeloid leukemia (AML) is a complex and heterogeneous hematopoietic tissue neoplasm. Several molecular markers have been described that help to classify AML patients into risk groups. DNA methyltransferase 3A (DNMT3A) gene mutations have been recently identified in about 22% of AML patients and associated with poor prognosis as an independent risk factor. Our aims were to determine the frequency of somatic mutations in the gene DNMT3A and major chromosomal translocations in a sample of patients with AML. We investigated in 82 samples of bone marrow from patients with AML for somatic mutations in DNMT3A gene by sequencing and sought major fusion transcripts by RT-PCR. We found mutations in the DNMT3A gene in 6 patients (8%); 3 were type R882H. We found fusion transcripts in 19 patients, namely, AML1/ETO (n = 5; 6.1%), PML/RARα (n = 12; 14.6%), MLL/AF9 (0; 0%), and CBFβ/MYH11 (n = 2; 2.4%). The identification of recurrent mutations in the DNMT3A gene and their possible prognostic implications can be a valuable tool for making treatment decisions. This is the first study on the presence of somatic mutations of the DNMT3A gene in patients with AML in Brazil. The frequency of these mutations suggests a possible ethnogeographic variation.
The Science Behind Pre‐Columbian Evidence of Syphilis in Europe: Research by Documentary

This article discusses the presentation of scientific findings by documentary, without the process of peer review. We use, as an example, PBS's “The Syphilis Enigma,” in which researchers presented novel evidence concerning the origin of syphilis that had never been reviewed by other scientists. These “findings” then entered the world of peer‐reviewed literature through citations of the documentary itself or material associated with it. Here, we demonstrate that the case for pre‐Columbian syphilis in Europe that was made in the documentary does not withstand scientific scrutiny. We also situate this example from paleopathology within a larger trend of “science by documentary” or “science by press conference,” in which researchers seek to bypass the peer review process by presenting unvetted findings directly to the public. © 2012 Wiley Periodicals, Inc.
Understanding the cultures of fishing communities : a key to fisheries management and food security

The purpose of this paper is to help fisheries officials gain a clearer understanding of small-scale fishing community cultures. By doing so, they will be better prepared to develop more successful management policies and practices, and to help people in such communities to improve their livelihoods. The paper suggests methods that might help fisheries managers to obtain reliable information about fishing cultures in an ethical manner, including the rapid acquisition of important information while working within tight budgetary and time constraints. It also gives recommendations on how the foregoing objectives can be achieved, underscoring the importance of sustaining small-scale fishers' rights of access to resources and integration of cultural considerations into fisheries-management policies and practices. Six contemporary case studies from distinct cultural regions of the world are annexed, richly exemplifying many of the issues discussed in the paper.
Misaligned spin-orbit in the XO-3 planetary system?†

Abstract The SOPHIE Consortium started a large program of exoplanets search and characterization in the Northern hemisphere with the new spectrograph SOPHIE at the 1.93-m telescope of Haute-Provence Observatory, France. The objectives of this program are to characterize the zoo of exoplanets and to bring strong constraints on their processes of formation and evolution using the radial velocity technique. We present here new SOPHIE measurements of the transiting planet host star XO-3. This allowed us to observe the Rossiter-McLaughlin effect and to refine the parameters of the planet. The unusual shape of the radial velocity anomaly during the transit provides a hint for a nearly transverse Rossiter-McLaughlin effect. The sky-projected angle between the planetary orbital axis and the stellar rotation axis should be λ = 70° ± 15° to be compatible with our observations. This suggests that some close-in planets might result from gravitational interaction between planets and/or stars rather than migration. This result requires confirmation by additional observations.
Molecular Evidence for Metabolically Active Bacteria in the Atmosphere

Bacterial metabolisms are responsible for critical chemical transformations in nearly all environments, including oceans, freshwater, and soil. Despite the ubiquity of bacteria in the atmosphere, little is known about the metabolic functioning of atmospheric bacterial communities. To gain a better understanding of the metabolism of bacterial communities in the atmosphere, we used a combined empirical and model-based approach to investigate the structure and composition of potentially active bacterial communities in air sampled at a high elevation research station. We found that the composition of the putatively active bacterial community (assayed via rRNA) differed significantly from the total bacterial community (assayed via rDNA). Rare taxa in the total (rDNA) community were disproportionately active relative to abundant taxa, and members of the order Rhodospirillales had the highest potential for activity. We developed theory to explore the effects of random sampling from the rRNA and rDNA communities on observed differences between the communities. We found that random sampling, particularly in cases where active taxa are rare in the rDNA community, will give rise to observed differences in community composition including the occurrence of “phantom taxa”, taxa which are detected in the rRNA community but not the rDNA community. We show that the use of comparative rRNA/rDNA techniques can reveal the structure and composition of the metabolically active portion of bacterial communities. Our observations suggest that metabolically active bacteria exist in the atmosphere and that these communities may be involved in the cycling of organic compounds in the atmosphere.
Associations of various gene polymorphisms with toxicity in colorectal cancer patients receiving oral uracil and tegafur plus leucovorin: a prospective study.

BACKGROUND To assess the predictive value of polymorphism in nine genes, primarily thymidylate synthase (TS) and orotate phosphoribosyltransferase (OPRT), which relates to 5-fluorouracil (5-FU) metabolism, for toxicity in patients treated with oral uracil/tegafur (UFT) plus leucovorin (LV). PATIENTS AND METHODS We treated 99 patients with stage II or III colorectal carcinoma with oral UFT + LV. Germline DNA from patients was genotyped for 5-FU and folate metabolism-relating genes. CYP2A6, tegafur-activating enzyme, and uridine diphosphate-glucuronosyltransferase 1A1 genetic variation were also assessed. Toxicity was graded by the National Cancer Institute Common Toxicity Criteria, version 2.0. RESULTS The multivariate logistic regression revealed that OPRT 638G>C polymorphism was associated with grade 3 diarrhea [odds ratio (OR) 19.84 for patients with the C/C homozygous type compared with patients with wild type, P = 0.014] and polymorphisms of UGT1A1 were associated with hyperbilirubinemia (OR 38.76 for homozygotes and double heterozygotes of *6 or *28 compared with wild type, P = 0.0008). No relationships were observed between TS polymorphisms and any toxicity. CONCLUSIONS OPRT polymorphism predicts toxicity, especially grade 3 or greater diarrhea to oral UFT + LV adjuvant chemotherapy, whereas TS does not, in our study cohort. UGT1A1 polymorphism seems to be a risk factor for hyperbilirubinemia due to UFT+LV.
Identification of potential therapeutic targets for colorectal cancer by bioinformatics analysis

The aim of the present study was to identify potential therapeutic targets for colorectal cancer (CRC). The gene expression profile GSE32323, containing 34 samples, including 17 specimens of CRC tissues and 17 of paired normal tissues from CRC patients, was downloaded from the Gene Expression Omnibus database. Following data preprocessing using the Affy and preprocessCore packages, the differentially-expressed genes (DEGs) between the two types of samples were identified with the Linear Models for Microarray Analysis package. Next, functional and pathway enrichment analysis of the DEGs was performed using the Database for Annotation Visualization and Integrated Discovery. The protein-protein interaction (PPI) network was established using the Search Tool for the Retrieval of Interacting Genes database. Utilizing WebGestalt, the potential microRNAs (miRNAs/miRs) of the DEGs were screened and the integrated miRNA-target network was built. A cohort of 1,347 DEGs was identified, the majority of which were mainly enriched in cell cycle-related biological processes and pathways. Cyclin-dependent kinase 1 (CDK1), cyclin B1 (CCNB1), MAD2 mitotic arrest deficient-like 1 (MAD2L1) and BUB1 mitotic checkpoint serine/threonine kinase B (BUB1B) were prominent in the PPI network, while the over-represented genes in the integrated miRNA-target network were SRY (sex determining region Y)-box 4 (SOX4; targeted by hsa-mir-129), v-myc avian myelocytomatosis viral oncogene homolog (MYC; targeted by hsa-let-7c and hsa-mir-145) and cyclin D1 (CCND1; targeted by hsa-let-7b). CDK1, CCNB1 and CCND1 were also associated with the p53 signaling pathway. Overall, several genes associated with the cell cycle and p53 pathway were identified as biomarkers for CRC. CDK1, CCNB1, MAD2L1, BUB1B, SOX4, collagen type I α2 chain and MYC may play significant roles in CRC progression by affecting the cell cycle-related pathways, while CDK1, CCNB1 and CCND1 may serve as crucial regulators in the p53 signaling pathway. Furthermore, SOX4, MYC and CCND1 may be targets of miR-129, hsa-mir-145 and hsa-let-7c, respectively. However, further validation of these data is required.
A study of X-ray flares – I. Active late-type dwarfs

We present temporal and spectral characteristics of X-ray flares observed from six late-type G–K active dwarfs (V368 Cep, XI Boo, IM Vir, V471 Tau, CC Eri and EP Eri) using data from observations with the XMM–Newton observatory. All the stars were found to be flaring frequently and altogether a total of 17 flares were detected above the ‘quiescent’ state X-ray emission which varied from 0.5 to 8.3 × 1029 erg s−1. The largest flare was observed in a low-activity dwarf XI Boo with a decay time of 10 ks and ratio of peak flare luminosity to ‘quiescent’ state luminosity of 2. We have studied the spectral changes during the flares by using colour–colour diagram and by detailed spectral analysis during the temporal evolution of the flares. The exponential decay of the X-ray light curves, and time evolution of the plasma temperature and emission measure are similar to those observed in compact solar flares. We have derived the semiloop lengths of flares based on the hydrodynamic flare model. The size of the flaring loops is found to be less than the stellar radius. The hydrodynamic flare decay analysis indicates the presence of sustained heating during the decay of most flares.
Cellular approximations and the Eilenberg-Moore spectral-sequence

We set up machinery for recognizing k-cellular modules and k-cellular approximations, where k is an R-module and R is either a ring or a ring-spectrum. Using this machinery we can identify the target of the Eilenberg-Moore cohomology spectral sequence for a fibration in various cases. In this manner we get new proofs for known results concerning the Eilenberg-Moore spectral sequence and generalize another result.
Extreme mass ratio inspiral rates: dependence on the massive black hole mass

We study the rate at which stars spiral into a massive black hole (MBH) due to the emission of gravitational waves (GWs), as a function of the mass M• of the MBH. In the context of our model, it is shown analytically that the rate approximately depends on the MBH mass as M−1/4•. Numerical simulations confirm this result, and show that for all MBH masses, the event rate is highest for stellar black holes, followed by white dwarfs, and lowest for neutron stars. The Laser Interferometer Space Antenna (LISA) is expected to see hundreds of these extreme mass ratio inspirals per year. Since the event rate derived here formally diverges as M• → 0, the model presented here cannot hold for MBHs of masses that are too low, and we discuss what the limitations of the model are.
On Asymptotic Capacity of Wireless Multi-hop Networks

Multi-hop could bring advantages such as low up-front cost, easy network maintenance, robustness, reliable service coverage etc for the next generation wireless networking. However, to be more available, wireless multi-hop network confront with much more challenge. First of all, the capacity of multi-hop is an open issue, for the optimal schedule of the distributed node is still illegible. Derived from the reference, in this paper we decouple the multi-hop channel by feasible probability model, and then give analytical asymptotic capacity function for the multi-hop networking with practical parameters. By the new model we get a clear analytical capacity constraint relationship among the density of node, the number of nodes and networking, and the user sending probability.
Slope filtrations for relative Frobenius

The slope filtration theorem gives a partial analogue of the eigenspace decomposition of a linear transformation, for a Frobenius-semilinear endomorphism of a finite free module over the Robba ring (the ring of germs of rigid analytic functions on an unspecified open annulus of outer radius 1) over a discretely valued field. In this paper, we give a third-generation proof of this theorem, which both introduces some new simplifications (particularly the use of faithfully flat descent, to recover the theorem from a classification theorem of Dieudonne-Manin type) and extends the result to allow an arbitrary action on coefficients (previously the action on coefficients had to itself be a lift of an absolute Frobenius). This extension is relevant to a study of (phi, Gamma)-modules associated to families of p-adic Galois representations, presently being initiated by Berger and Colmez.
Neonatal Thyroid-Stimulating Hormone Concentrations in Belgium: A Useful Indicator for Detecting Mild Iodine Deficiency?

It has been proposed that neonatal thyroid-stimulating hormone (TSH) concentrations are a good indicator of iodine deficiency in the population. A frequency of neonatal TSH concentrations above 5 mU/L below 3% has been proposed as the threshold indicating iodine sufficiency. The objective of the present study was to evaluate feasibility and usefulness of nation-wide neonatal TSH concentration screening results to assess iodine status in Belgium. All newborns born in Belgium during the period 2009–2011 (n = 377713) were included in the study, except those suffering from congenital hypothyroidism and premature neonates. The frequency of neonatal TSH concentrations above 5 mU/L from 2009 to 2011 in Belgium fluctuated between 2.6 and 3.3% in the centres using the same TSH assay. There was a significant inverse association between neonatal TSH level and birth weight. The longer the duration between birth and screening, the lower the TSH level. Neonatal TSH levels were significantly lower in winter than in spring or autumn and significantly lower in spring and summer than in autumn while significantly higher in spring compared to summer. In conclusion, despite that pregnant women in Belgium are mildly iodine deficient, the frequency of neonatal TSH concentrations above 5 mU/L was very low, suggesting that the neonatal TSH threshold proposed for detecting iodine deficiency needs to be re-evaluated. Although neonatal TSH is useful to detect severe iodine deficiency, it should not be recommended presently for the evaluation of iodine status in mildly iodine deficient regions.
A Single Nucleotide Polymorphism Associates With the Response of Muscle ATP Synthesis to Long-Term Exercise Training in Relatives of Type 2 Diabetic Humans

OBJECTIVE Myocellular ATP synthesis (fATP) associates with insulin sensitivity in first-degree relatives of subjects with type 2 diabetes. Short-term endurance training can modify their fATP and insulin sensitivity. This study examines the effects of moderate long-term exercise using endurance or resistance training in this cohort. RESEARCH DESIGN AND METHODS A randomized, parallel-group trial tested 16 glucose-tolerant nonobese relatives (8 subjects in the endurance training group and 8 subjects in the resistance training group) before and after 26 weeks of endurance or resistance training. Exercise performance was assessed from power output and oxygen uptake (Vo2) during incremental tests and from maximal torque of knee flexors (MaxTflex) and extensors (MaxText) using isokinetic dynamometry. fATP and ectopic lipids were measured with 1H/31P magnetic resonance spectroscopy. RESULTS Endurance training increased power output and Vo2 by 44 and 30%, respectively (both P < 0.001), whereas resistance training increased MaxText and MaxTflex by 23 and 40%, respectively (both P < 0.001). Across all groups, insulin sensitivity (382 ± 90 vs. 389 ± 40 mL ⋅ min−1 ⋅ m−2) and ectopic lipid contents were comparable after exercise training. However, 8 of 16 relatives had 26% greater fATP, increasing from 9.5 ± 2.3 to 11.9 ± 2.4 μmol ⋅ mL−1 ⋅ m−1 (P < 0.05). Six of eight responders were carriers of the G/G single nucleotide polymorphism rs540467 of the NDUFB6 gene (P = 0.019), which encodes a subunit of mitochondrial complex I. CONCLUSIONS Moderate exercise training for 6 months does not necessarily improve insulin sensitivity but may increase ATP synthase flux. Genetic predisposition can modify the individual response of the ATP synthase flux independently of insulin sensitivity.