Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational landscape of MCPyV-positive and MCPyV-negative Merkel cell carcinomas with implications for immunotherapy

Merkel cell carcinoma (MCC) is a rare but highly aggressive cutaneous neuroendocrine carcinoma, associated with the Merkel cell polyomavirus (MCPyV) in 80% of cases. To define the genetic basis of MCCs, we performed exome sequencing of 49 MCCs. We show that MCPyV-negative MCCs have a high mutation burden (median of 1121 somatic single nucleotide variants (SSNVs) per-exome with frequent mutations in RB1 and TP53 and additional damaging mutations in genes in the chromatin modification (ASXL1, MLL2, and MLL3), JNK (MAP3K1 and TRAF7), and DNA-damage pathways (ATM, MSH2, and BRCA1). In contrast, MCPyV-positive MCCs harbor few SSNVs (median of 12.5 SSNVs/tumor) with none in the genes listed above. In both subgroups, there are rare cancer-promoting mutations predicted to activate the PI3K pathway (HRAS, KRAS, PIK3CA, PTEN, and TSC1) and to inactivate the Notch pathway (Notch1 and Notch2). TP53 mutations appear to be clinically relevant in virus-negative MCCs as 37% of these tumors harbor potentially targetable gain-of-function mutations in TP53 at p.R248 and p.P278. Moreover, TP53 mutational status predicts death in early stage MCC (5-year survival in TP53 mutant vs wild-type stage I and II MCCs is 20% vs. 92%, respectively; P = 0.0036). Lastly, we identified the tumor neoantigens in MCPyV-negative and MCPyV-positive MCCs. We found that virus-negative MCCs harbor more tumor neoantigens than melanomas or non-small cell lung cancers (median of 173, 65, and 111 neoantigens/sample, respectively), two cancers for which immune checkpoint blockade can produce durable clinical responses. Collectively, these data support the use of immunotherapies for virus-negative MCCs.
Binary Jumbled Pattern Matching via All-Pairs Shortest Paths

In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to node-labeled trees and graphs by replacing "substring" with "connected subgraph". In this paper, we give an ${n^2}/{2^{\Omega(\log n/\log \log n)^{1/2}}}$ time solution for both strings and trees. This odd-looking time complexity improves the state of the art $O(n^2/\log^2 n)$ solutions by more than any poly-logarithmic factor. It originates from the recent seminal algorithm of Williams for min-plus matrix multiplication. We obtain the result by giving a black box reduction from trees to strings. This is then combined with a reduction from strings to min-plus matrix multiplications.
The preterm prediction study: granulocyte colony-stimulating factor and spontaneous preterm birth. National Institute of Child Health and Human Development Maternal-Fetal Medicine Units Network.

OBJECTIVE Granulocyte colony-stimulating factor is elevated in the amniotic fluid and plasma of women with chorioamnionitis and active preterm labor. We investigated the relationship between plasma granulocyte colony-stimulating factor and subsequent spontaneous preterm birth in pregnant women without symptoms. STUDY DESIGN We performed a nested case-control study involving 194 women who had a singleton spontaneous preterm birth and 194 matched term control subjects from the patient pool (n = 2929) enrolled in the Preterm Prediction Study. Plasma collected at 24 and 28 weeks' gestation was analyzed for granulocyte colony-stimulating factor, and the results were compared with subsequent spontaneous preterm birth. RESULTS Compared with term control subjects, women who were delivered of their infants spontaneously at <28 weeks' gestation had increased mean granulocyte colony-stimulating factor values at 24 weeks' gestation (84.7 +/- 38.4 vs 67.7 +/- 28.6 pg/mL; P =.049), and women who were delivered of their infants at <32 weeks' gestation had increased mean plasma granulocyte colony-stimulating factor values at 28 weeks' gestation (80.4 +/- 24.1 vs 55.9 +/- 16.5 pg/mL; P =. 001). At 24 weeks' gestation a granulocyte colony-stimulating factor value >75th percentile in control subjects (approximately 80 pg/mL) was found in 48.9% (23/47) of all women delivered of their infants at <32 weeks' gestation versus 14.9% (7/47) of the term control subjects (adjusted odds ratio, 6.2; 95% confidence interval, 1.8-20. 8). At 28 weeks' gestation a granulocyte colony-stimulating factor value >75th percentile was found in 36.8% (7/19) of women delivered of their infants at <32 weeks' gestation versus 5.3% (1/19) of term control subjects (adjusted odds ratio, 25.7; 95% confidence interval, 1.5-470.4). When measured at 24 or 28 weeks' gestation, granulocyte colony-stimulating factor did not predict spontaneous preterm birth at 32 to 34 weeks' gestation or at 35 to 36 weeks' gestation. CONCLUSION In pregnant women without symptoms at 24 and 28 weeks' gestation, elevated plasma granulocyte colony-stimulating factor levels are associated with subsequent early (<32 weeks' gestation) spontaneous preterm birth, especially within the next 4 weeks, but not with late spontaneous preterm birth. These data provide further evidence that early spontaneous preterm birth is associated with an inflammatory process that is identifiable by the presence of a cytokine in maternal plasma several weeks before the early spontaneous preterm birth; however, later spontaneous preterm birth is not associated with this process.
Generating Text from Functional Brain Images

Recent work has shown that it is possible to take brain images acquired during viewing of a scene and reconstruct an approximation of the scene from those images. Here we show that it is also possible to generate text about the mental content reflected in brain images. We began with images collected as participants read names of concrete items (e.g., “Apartment’’) while also seeing line drawings of the item named. We built a model of the mental semantic representation of concrete concepts from text data and learned to map aspects of such representation to patterns of activation in the corresponding brain image. In order to validate this mapping, without accessing information about the items viewed for left-out individual brain images, we were able to generate from each one a collection of semantically pertinent words (e.g., “door,” “window” for “Apartment’’). Furthermore, we show that the ability to generate such words allows us to perform a classification task and thus validate our method quantitatively.
Improving the detection of environmental enteric dysfunction: a lactulose, rhamnose assay of intestinal permeability in children aged under 5 years exposed to poor sanitation and hygiene

Background Environmental enteric dysfunction (EED) is an asymptomatic intestinal disorder affecting populations living in conditions of poor sanitation and hygiene. The study tested intestinal barrier function in infants with EED. Methods We prospectively studied an advanced high-performance liquid chromatography mass spectrometry assay of urine collected after oral intake of the monosaccharide, L-rhamnose and the disaccharide, lactulose, in 112 children from three continents. Findings Compared to the US cohort (n=27), the cohorts of children from Peru (n=19) and Zambia (n=85) were older with evidence of growth impairment. The median (range) of age (months) was 8.0 (2.0 to 13.0), 27.0 (15.0 to 29.0) and 21.0 (12.0 to 36.0), respectively. The median (range) of height for age Z score was −0.1 (−1.8 to 2.4), −1.8 (−3.3 to −0.2) and −2.3 (−8.5 to 1.2), respectively. Among children with valid sugar data (n=22 USA, n=19 Peru, n=73 Zambia), there were no significant differences in the median rhamnose urine concentrations between the three groups. The median (range) lactulose concentration (µg/mL) was 6.78 (0.29 to 31.90), 47.60 (4.23 to 379.00) and 75.40 (0.67 to 873.00) in the US, Peruvian and Zambian cohorts, respectively (p<0.001). The lactulose/rhamnose ratio (LRR) was higher in cohorts from Peru (0.75, 0.15, 5.02) and Zambia (2.26, 0.08, 14.48) compared to the US (0.14, 0.06, 1.00) cohort (p<0.001). In a multivariate effect modification model, higher weight-for-age z scores were associated with lower post-dose lactulose when rhamnose excretion was constant (p=0.003). Conclusions This non-invasive two saccharide permeability protocol measures changes in intestinal permeability in children with EED and permits the identification of individuals for interventional trials.
Creating Opportunities for Rural Producers: Impact Evaluation of a Pilot Program in Colombia

Abstract This paper presents the impact evaluation of a pilot program that treated 57 small organizations of agricultural producers with high risk of getting involved in illegal drug production in Colombia. The program supported producers mainly by facilitating the commercialization of their new licit alternative sources of income. We combine propensity score matching, regression discontinuity, and Bayesian decision theory, with unique and rich panel data to assess the economic impact of the program. Our results suggest that the program was successful on increasing total sales and improving the product’s quality for the treated producers. The intervention was more successful when combined with other programs that gave producers incentives to abandon illegal drug production definitely.
Distribution of Thelastomatoid Nematodes (Nematoda: Oxyurida) in Endemic and Introduced Cockroaches on the Galápagos Island Archipelago, Ecuador

Abstract: The thelastomatoid pinworm fauna (Nematoda: Oxyurida: Thelastomatoidea) was surveyed in 3 endemic species and 6 introduced species of cockroach hosts (Insecta: Blattaria) in the Galápagos Islands, Ecuador. A total of 658 host specimens were examined from preserved collections that had been collected between 1966 and 2003 from 7 islands in the archipelago. Eight species of pinworms were identified from these cockroach hosts, including the dominant species Cephalobellus ovumglutinosus and a Severianoia sp. as well as Leidynema appendiculata, Hammerschmidtiella diesingi, an unidentified Cephalobellus species resembling Cephalobellus magalhaesi, an unidentified Protrellus species closely resembling Protrellus shamimi, and an undescribed Blattophila sp. Five new host records are identified for C. ovumglutinosus including the endemic Galápagos cockroaches Chorisoneura carpenteri, Ischnoptera snodgrassii, and Ischnoptera santacruzensis. These endemics were also infected with an undescribed Blatticola sp. Other species recorded resemble known pinworms from other hosts around the world. Prevalence between islands and between host species was variable, but total prevalence for individual pinworm species was consistently low (<10%). A single host specimen examined was infected with more than 1 pinworm species; otherwise only a single species was observed in each infected host. At least 1 introduced pinworm species carried to the islands via invasive cockroach hosts was present in endemic host species, but several globally widespread introduced pinworm species were absent from endemic cockroaches. Santa Cruz was inhabited by the greatest number of pinworm species, likely due to a higher rate of invasive host introduction. This survey, the first from this region, showed that the distribution and transmission of pinworms in the Galápagos Islands is complex and may provide future models of invertebrate dispersal and speciation in an ecosystem already rich with examples of evolution.
Sex Roles and Marital Adjustment in Indian Couples

Background: Marital theorists suggest a link between sex role differences and close relationships for men and women. Marriage is often a context for the activation and expression of sex roles. As marital adjustment is influenced by complementarity of roles between husband and wife, the same could hold true for sex roles as well. Aim: To study the relationship between sex roles and marital adjustment in Indian couples. Methods: The sample consisted of 20 distressed and 20 non-distressed couples from a marital and family therapy centre in the city of Bangalore, India. The measures used included a sociodemographic data sheet, the Dyadic Adjustment Scale, the Bem Sex Role Inventory and a semi-structured interview schedule for gendered experiences. Means, percentages and ANOVAS were used to analyse statistically the data. Content analysis was applied on material from the semistructured interview schedule. Results: The study revealed that: (a) the group as a whole showed greater femininity than masculinity; (b) more non-distressed individuals show high androgyny; (c) androgynous dyads show better marital adjustment; and (d) qualitative analysis suggests a trend for couples to move towards more gender-neutral constructions of marriage. Conclusions: The results indicate a link between androgyny and marital adjustment. The results also suggest the type of match between dyads.
Removal of priority and emerging substances by biological and tertiary treatments

My researches are divided in two principal parts. The first part concerns the fate of micropollutants in conventional wastewater treatment plants (WWTPs) composed by primary and biological treatments. Different studies have been held by OPUR research program on primary treatments, conventional activated sludge (CAS) and biofiltration (BF), the thesis will synthesize them and add data from measurement campaigns on industrial scale membrane bioreactor (MBR) unit. This will allow comparing existing units together and to increase knowledge on a very promising and innovative intensive process (MBR). Second part of researches concerns tertiary treatments, which are imported from drinking water industry, to improve quality of treatment regarding priority and emerging pollutants, and will monitor pharmaceuticals, pesticides and priority substances in a powdered activated carbon process at semi industrial scale, placed after a BF unit. Some laboratory scale tests will be held to better understand fundamental mechanisms and parameters which are involved in such a process. The interest of this project is to test a very promising technology on a large scale WWTP, and to provide data on a large range of micropollutants removal by adsorption tertiary treatment, which doesn't create by products contrary to oxidation processes. In the context of regulations hardening and better understanding of micropollutants effects on environment and health, these new data are very relevant and interesting for scientists and water managers who wants to anticipate and not undergo regulations.
Combined non-invasive anatomical and functional assessment with MSCT and MRI for the detection of significant coronary artery disease in patients with an intermediate pre-test likelihood

Objectives To compare magnetic resonance myocardial perfusion imaging (MRI) with anatomical assessment by multislice computed tomography (MSCT) coronary angiography and conventional coronary angiography. Design and patients In this prospective study, 53 patients (60% male, average age 57±9 years, 83% intermediate pre-test likelihood) underwent 1.5 T MRI, 64-slice MSCT and conventional coronary angiography. Main outcome measures The presence of significant stenosis (≥50% luminal narrowing) was determined on MSCT and conventional coronary angiography. Ischaemia on MRI was defined as a stress perfusion abnormality in the absence of delayed contrast enhancement. Results A significant stenosis was seen on MSCT in 15 (28%) patients, while ischaemia on MRI was seen in 19 (36%). In the 38 patients without significant stenosis on MSCT, normal perfusion was seen in 29 (76%). In patients with a significant stenosis on MSCT, ischaemia was seen in 10 (67%). In all patients without significant stenosis on MSCT and normal perfusion on MRI (n=29), significant stenosis was absent on conventional coronary angiography. All patients with both MSCT and MRI abnormal (n=10) had significant stenoses on conventional coronary angiography. Conclusion The anatomical and functional data obtained with MSCT and MRI are complementary for the assessment of coronary artery disease. These findings support the sequential or combined assessment of anatomy and function.
Decreased expression of TGF-β type II receptor in bronchial glands of smokers with COPD

Background: The role of transforming growth factor-β1 (TGF-β1) in chronic obstructive pulmonary disease is still controversial, but it has been proposed that it may protect from mucus hypersecretion since it is able to downregulate mucin production. A study was undertaken to investigate the expression of TGF-β1 and its type II receptor (TGF-β RII) in the bronchial glands of smokers with COPD. Methods: The expression of TGF-β1 and TGF-β RII were examined immunohistochemically in the bronchial glands of 24 smokers undergoing lung resection for solitary peripheral nodules: 12 with airflow limitation (smokers with COPD) and 12 with normal lung function. Results: The expression of TGF-β1 in bronchial glands was similar in the two groups of subjects while that of TGF-β RII was lower in smokers with COPD than in smokers with normal lung function (p = 0.004). TGF-β RII expression was inversely correlated with the values of Reid’s index, a measure of gland size (p = 0.02, r = −0.50). Conclusions: In the bronchial glands of smokers with COPD there is decreased expression of TGF-β RII which is associated with bronchial gland enlargement. These findings support the view that the absence of TGF-β signalling may induce structural changes in the bronchial glands which, in turn, may promote mucus hypersecretion.
Bounds on the tau and muon neutrino vector and axial vector charge radius

A Majorana neutrino is characterized by just one flavor diagonal electromagnetic form factor: the anapole moment, that in the static limit corresponds to the axial vector charge radius . Experimental information on this quantity is scarce, especially in the case of the tau neutrino. We present a comprehensive analysis of the available data on the single photon production process $e^+ e^- -> \nu \bar\nu \gamma$ off Z-resonance, and we discuss the constraints that these measurements can set on for the tau neutrino. We also derive limits for the Dirac case, when the presence of a vector charge radius is allowed. Finally, we comment on additional experimental data on $\nu_\mu$ scattering from the NuTeV, E734, CCFR and CHARM-II collaborations, and estimate the limits implied for and for the muon neutrino.
A Study of Thyroid 131I Activity of Five Human Subjects Exposed to a Radioactive Plume at Tamura City in Fukushima

AbstractThyroid 131I activities were determined for five human subjects from a disaster medical assistance team of Fukui Prefectural Hospital. The team was dispatched to the Tamura City Sports Park, 40 km from the Fukushima Daiichi nuclear power plant. They were exposed to a radioactive plume on 15 March 2011. In vivo measurements at Fukui Prefectural Hospital were conducted around 17 h after the team left the park. A thyroid counter equipped with a 51‐mm-diameter × 51‐mm-thick NaI(Tl) detector with a 20‐mm‐thick lead collimator was used. Mock iodine (133Ba and 137Cs) with a thyroid uptake neck phantom was used for calibration. On 16 March 2011, at 11:30, thyroid activity of a member of the team age 53 y, who was never administered stable iodine, was 268 ± 38 Bq. The remaining four men, aged 49, 35, 34, and 27 y, ingested two stable iodine pills (a total of 100 mg of potassium iodide) approximately 36 h before being exposed to the plume. Their thyroid activity values were 249 ± 86 Bq, 676 ± 107 Bq, 569 ± 96 Bq, and 1,082 ± 119 Bq, respectively. An inverse relationship between age and thyroid activity was observed among those who ingested potassium iodide before exposure, indicating that stable iodine administration may have a protective effect. Thyroid 131I activity was reduced by approximately 70% in the oldest person. This can be explained by the iodine metabolism in the thyroid of younger individuals being significantly faster than that of older individuals.
Analysis of the Impact of Early Surgery on In-Hospital Mortality of Native Valve Endocarditis: Use of Propensity Score and Instrumental Variable Methods to Adjust for Treatment-Selection Bias

Background— The impact of early surgery on mortality in patients with native valve endocarditis (NVE) is unresolved. This study sought to evaluate valve surgery compared with medical therapy for NVE and to identify characteristics of patients who are most likely to benefit from early surgery. Methods and Results— Using a prospective, multinational cohort of patients with definite NVE, the effect of early surgery on in-hospital mortality was assessed by propensity-based matching adjustment for survivor bias and by instrumental variable analysis. Patients were stratified by propensity quintile, paravalvular complications, valve perforation, systemic embolization, stroke, Staphylococcus aureus infection, and congestive heart failure. Of the 1552 patients with NVE, 720 (46%) underwent early surgery and 832 (54%) were treated with medical therapy. Compared with medical therapy, early surgery was associated with a significant reduction in mortality in the overall cohort (12.1% [87/720] versus 20.7% [172/832]) and after propensity-based matching and adjustment for survivor bias (absolute risk reduction [ARR] −5.9%, P<0.001). With a combined instrument, the instrumental-variable–adjusted ARR in mortality associated with early surgery was −11.2% (P<0.001). In subgroup analysis, surgery was found to confer a survival benefit compared with medical therapy among patients with a higher propensity for surgery (ARR −10.9% for quintiles 4 and 5, P=0.002) and those with paravalvular complications (ARR −17.3%, P<0.001), systemic embolization (ARR −12.9%, P=0.002), S aureus NVE (ARR −20.1%, P<0.001), and stroke (ARR −13%, P=0.02) but not those with valve perforation or congestive heart failure. Conclusions— Early surgery for NVE is associated with an in-hospital mortality benefit compared with medical therapy alone.
A novel geometrically inspired polynomial kernel for robot inverse dynamics

In this paper we introduce a novel data driven inverse dynamics estimator based on Gaussian Process Regression. Driven by the fact that the inverse dynamics can be described as a polynomial function on a suitable input space, we propose the use of a novel kernel, called Geometrically Inspired Polynomial Kernel (GIP). The resulting estimator behaves similarly to model based approaches as concerns data efficiency. Indeed, we proved that the GIP kernel defines a finite dimensional Reproducing Kernel Hilbert Space that contains the inverse dynamics function computed through the Rigid Body Dynamics. The proposed kernel is based on the recently introduced Multiplicative Polynomial Kernel, a redefinition of the classical polynomial kernel equipped with a set of parameters which allows for an higher regularization. We tested the proposed approach in a simulated environment, and also in real experiments with a UR10 robot. The obtained results confirm that, compared to other data driven estimators, the proposed approach is more data efficient and exhibits better generalization properties. Instead, with respect to model based estimators, our approach requires less prior information and is not affected by model bias.