Miracle-dz/UniFAR-FTUs huggingface dataset:
Significant Correlation Between the Infant Gut Microbiome and Rotavirus Vaccine Response in Rural Ghana

Background. Rotavirus (RV) is the leading cause of diarrhea-related death in children worldwide and 95% of RV-associated deaths occur in Africa and Asia where RV vaccines (RVVs) have lower efficacy. We hypothesize that differences in intestinal microbiome composition correlate with the decreased RVV efficacy observed in poor settings. Methods. We conducted a nested, case-control study comparing prevaccination, fecal microbiome compositions between 6-week old, matched RVV responders and nonresponders in rural Ghana. These infants' microbiomes were then compared with 154 age-matched, healthy Dutch infants' microbiomes, assumed to be RVV responders. Fecal microbiome analysis was performed in all groups using the Human Intestinal Tract Chip. Results. We analyzed findings in 78 Ghanaian infants, including 39 RVV responder and nonresponder pairs. The overall microbiome composition was significantly different between RVV responders and nonresponders (FDR, 0.12), and Ghanaian responders were more similar to Dutch infants than nonresponders (P = .002). RVV response correlated with an increased abundance of Streptococcus bovis and a decreased abundance of the Bacteroidetes phylum in comparisons between both Ghanaian RVV responders and nonresponders (FDR, 0.008 vs 0.003) and Dutch infants and Ghanaian nonresponders (FDR, 0.002 vs 0.009). Conclusions. The intestinal microbiome composition correlates significantly with RVV immunogenicity and may contribute to the diminished RVV immunogenicity observed in developing countries.
High‐resolution integrated calcareous plankton biostratigraphy and magnetostratigraphy at the Oligocene–Miocene transition in Southwestern Atlantic Ocean

After the formalization of the base of the Miocene in the Lemme‐Carrosio section (Italy) at the base of Subchron C6Cn.2n, the calcareous plankton biostratigraphy was refined in several open ocean Deep Sea Drilling Project/Ocean Drilling Program sites. However, high‐resolution quantitative biostratigraphic studies, integrating planktonic foraminifera and calcareous nannofossils, are still lacking for the time interval spanning the Oligocene–Miocene transition. Here, we present a reinvestigation of Deep Sea Drilling Project Hole 516F (Rio Grande Rise) and 4 oil wells drilled by Petróbras Brasileiro SA in the Campos Basin (SW Atlantic Ocean). We identified 12 planktonic foraminiferal and 18 calcareous nannofossil bioevents that have been integrated with an updated magnetostratigraphy of Hole 516F allowing the correlation with the GPTS and the identification of the Oligocene/Miocene boundary (base of Subchron C6Cn.2n) between the Top of Sphenolithus delphix and the Base of common Paragloborotalia kugleri. Furthermore, our results give new insights on the reliability of major calcareous plankton events across the Oligocene–Miocene transition: (a) the Sphenolithus ciperoensis Top, the S. delphix Base and Top, and the Sphenolithus cometa Base are reliable events at a global scale; (b) the Bases of Globoquadrina dehiscens and Sphenolithus disbelemnos > 4 μm are correlatable events only within the study sector of the SW Atlantic Ocean; and (c) the Globoturborotalita ciperoensis Top, Globoturborotalita angulisuturalis Top, and Sphenolithus procerus Base are diachronous. Finally, previously unreported biostratigraphic data, such as the distribution range of S. disbelemnos < 4 μm and Sphenolithus cf. S. pseudoheteromorphus, the Tenuitellinata praestainforthi acme interval, and the Top of common Globigerinoides primordius were identified in the Campos Basin.
Bridging SMT and TM with Translation Recommendation

We propose a translation recommendation framework to integrate Statistical Machine Translation (SMT) output with Translation Memory (TM) systems. The framework recommends SMT outputs to a TM user when it predicts that SMT outputs are more suitable for post-editing than the hits provided by the TM. We describe an implementation of this framework using an SVM binary classifier. We exploit methods to fine-tune the classifier and investigate a variety of features of different types. We rely on automatic MT evaluation metrics to approximate human judgements in our experiments. Experimental results show that our system can achieve 0.85 precision at 0.89 recall, excluding exact matches. Furthermore, it is possible for the end-user to achieve a desired balance between precision and recall by adjusting confidence levels.
A NEW VIEW ON THE FUNDAMENTAL THEOREM OF ASSET PRICING FOR LARGE FINANCIAL MARKETS

In the context of large financial markets we formulate the notion of no asymptotic free lunch with vanishing risk (NAFLVR), under which we can prove a version of the fundamental theorem of asset pricing (FTAP) in markets with an (uncountably) infinite number of assets, as it is for instance the case in bond markets. We work in the general setting of admissible portfolio wealth processes as laid down by Y. Kabanov [6] under a relaxed concatenation property and adapt the FTAP proof variant obtained in [1] for the classical small market situation to large financial markets. In the case of countably many assets, our setting allows to embed the large financial market model considered by M. De Donno et al. [2]. The notion of (NAFLVR) turns out to be an economically meaningful “no arbitrage” condition allowing to conclude the existence of a separating measure whose existence was assumed in [2] to obtain results on super-replication and utility maximization in large financial markets. In view of previous “no arbitrage” conditions considered in the literature, we can show equivalence between (NAFLVR) and the (NAFL) condition introduced in [12], whose definition however – in contrast to (NAFLVR) – involves weak-∗-closures in L∞.
New highways, house prices, and Urban development: A case study of toll roads in orange county, Ca

Abstract We examine the link between highways and urban development by employing both hedonic analysis and multiple sales techniques to study the impact of the construction of toll roads in Orange County, California, on house prices. Urban economic theory predicts that if highways improve accessibility, that accessibility premium will be reflected in higher land prices. Our empirical analyses of house sales prices provide strong evidence that the toll roads, the Foothill Transportation Corridor Backbone in particular, created an accessibility premium; home buyers are willing to pay for the increased access that the new roads provide. Such willingness to pay influences both development patterns and, potentially, induced travel (the association between increases in highway capacity and increases in vehicle miles of travel). The results are consistent with the idea that induced travel is caused, in part, by changes in urban development patterns that are linked to increases in highway capacity.
Unsupervised learning of natural languages

We address the problem, fundamental to linguistics, bioinformatics, and certain other disciplines, of using corpora of raw symbolic sequential data to infer underlying rules that govern their production. Given a corpus of strings (such as text, transcribed speech, chromosome or protein sequence data, sheet music, etc.), our unsupervised algorithm recursively distills from it hierarchically structured patterns. The adios (automatic distillation of structure) algorithm relies on a statistical method for pattern extraction and on structured generalization, two processes that have been implicated in language acquisition. It has been evaluated on artificial context-free grammars with thousands of rules, on natural languages as diverse as English and Chinese, and on protein data correlating sequence with function. This unsupervised algorithm is capable of learning complex syntax, generating grammatical novel sentences, and proving useful in other fields that call for structure discovery from raw data, such as bioinformatics.
Spatial prediction models for landslide hazards: review, comparison and evaluation

Abstract. The predictive power of logistic regression, support vector machines and bootstrap-aggregated classification trees (bagging, double-bagging) is compared using misclassification error rates on independent test data sets. Based on a resampling approach that takes into account spatial autocorrelation, error rates for predicting "present" and "future" landslides are estimated within and outside the training area. In a case study from the Ecuadorian Andes, logistic regression with stepwise backward variable selection yields lowest error rates and demonstrates the best generalization capabilities. The evaluation outside the training area reveals that tree-based methods tend to overfit the data.
Two distinct mechanisms for redistribution of lymphocyte surface macromolecules. II. Contrasting effects of local anesthetics and a calcium ionophore

In the previous study, lymphocyte surface molecules were separated into two subsets depending on whether capping was associated was associated with redistribution of cytoplasmic myosin. In the present study, the effects of the local anesthetic chlorpromazine and of the Ca2+ ionophore A23187 were compared. Both drugs affected the surface redistribution of immunoglobulin (Ig), Fc receptors, and the TL antigen- -molecules that appear to cap by association with microfilaments--but had no effect on the Thy.1 (theta) and H2 antigens--molecules that cap slowly, apparently unlinked to microfilament function. The capping of Ig, Fc receptor, and TL was inhibited while that of H2 and theta was not. Both drugs reversed the Ig Fc receptor, and TL caps but not the H2 and theta caps. In the former group, the reversal of caps was accompanied by a parallel reversal of the myosin segregated to the cap area. The appearance of myosin after drug treatment varied: chlorpromazine resulted in a diffuse pattern similar to that of normal lymphocytes, whereas A23187 produced an array of aggregates and coarse filaments. The results are compatible with the view that two mechanisms for capping exist in the lymphocyte. The Ca2+ ionophore may affect capping of microfilament-dependent caps by producing a systemic activation of contractile proteins while chlorpromazine may act by disrupting a Ca2+-dependent link between surface complexes and the contractile proteins.
On secure distributed hypothesis testing

The distributed binary hypothesis testing problem with communication and security constraints is investigated. A legitimate statistician (referred to as Bob) is interested in detecting the joint probability distribution of two remotely located sources. To this end, Bob has access to analog and coded data where the later is observed at another node (referred to as Alice) and communicated over a public noise-less channel of finite rate. An eavesdropper (referred to as Eve) has access to the encoded bits. In this framework, we study the tradeoff between the maximum achievable error exponent at Bob, i.e., the minimum Type II error probability for a fixed Type I probability of error, the rate and the equivocation rate. We first derive an achievable rate-exponent-equivocation region. Then, we investigate the special case of testing against independence for which we provide the optimal rate-exponent-equivocation region. An application example to binary sources is also considered.
The Role of Melanin Concentrating Hormone (MCH) in the Central Chemoreflex: A Knockdown Study by siRNA in the Lateral Hypothalamus in Rats

Melanin concentrating hormone (MCH), a neuropeptide produced mainly in neurons localized to the lateral hypothalamic area (LHA), has been implicated in the regulation of food intake, energy balance, sleep state, and the cardiovascular system. Hypothalamic MCH neurons also have multisynaptic connections with diaphragmatic motoneurons and project to many central chemoreceptor sites. However, there are few studies of MCH involvement in central respiratory control. To test the hypothesis that MCH plays a role in the central chemoreflex, we induced a down regulation of MCH in the central nervous system by knocking down the MCH precursor (pMCH) mRNA in the LHA using a pool of small interfering RNA (siRNA), and measured the resultant changes in breathing, metabolic rate, body weight, and blood glucose levels in conscious rats. The injections of pMCH-siRNA into the LHA successfully produced a ∼62% reduction of pMCH mRNA expression in the LHA and a ∼43% decrease of MCH levels in the cerebrospinal fluid relative to scrambled-siRNA treatment (P = 0.006 and P = 0.02 respectively). Compared to the pretreatment baseline and the scrambled-siRNA treated control rats, knockdown of MCH resulted in: 1) an enhanced hypercapnic chemoreflex (∼42 & 47% respectively; P < 0.05) only in wakefulness; 2) a decrease in body weight and basal glucose levels; and 3) an unchanged metabolic rate. Our results indicate that MCH participates not only in the regulation of glucose and sleep-wake homeostasis but also the vigilance-state dependent regulation of the central hypercapnic chemoreflex and respiratory control.
Role of the WASP and WAVE family proteins in breast cancer invasion and metastasis

The Wiskott–Aldrich syndrome protein (WASP) and WASP family verprolin-homologous protein (WAVE) family are a group of molecules that form a key link between GTPases and the actin cytoskeleton. The role of WASP/WAVE family proteins in the control of actin polymerization through activation of the actin-related protein 2/3 complex is critical in the formation of the actin-based membrane protrusions seen in cell migration and invasion. For this reason, the activity of the WASP/WAVE family in cancer cell invasion and migration has been of great interest in recent years. Many reports have highlighted the potential of targeting the WASP/WAVE family as a therapy for the prevention of cancer progression, in particular breast cancer. This review focuses on the role of the WASP/WAVE family in breast cancer cell invasion and migration and how this relates to the molecular mechanisms of WASP/WAVE activity, their exact contributions to the stages of cancer progression, and how this can lead to the development of anticancer drugs that target the WASP/WAVE family and related pathways.
Three-dimensional reconstruction volume: a novel method for volume measurement in kidney cancer.

BACKGROUND AND PURPOSE The role of volumetric estimation is becoming increasingly important in the staging, management, and prognostication of benign and cancerous conditions of the kidney. We evaluated the use of three-dimensional reconstruction volume (3DV) in determining renal parenchymal volumes (RPV) and renal tumor volumes (RTV). We compared 3DV with the currently available methods of volume assessment and determined its interuser reliability. PATIENTS AND METHODS RPV and RTV were assessed in 28 patients who underwent robot-assisted laparoscopic partial nephrectomy for kidney cancer. Patients with a preoperative creatinine level of <1.2 mg/dL with available scans were selected. RPV and RTV were then assessed using 3DV, as well as cylindrical approximation for RPV and spherical approximation for RTV as described previously in the literature. Measures of the same quantity from each method were then compared. In addition, interuser reliability was determined for 3DV. RESULTS Calculated volumes differed widely in comparison with 3DV. For example, cylindrical volumes for the contralateral kidney pre- and postsurgery overestimated 3D reconstruction volumes by 15% to 102% and 12% to 101%, respectively. In addition, volumes obtained from 3DV displayed high interuser reliability regardless of experience. CONCLUSIONS 3DV provides a highly reliable way of assessing kidney volumes. Given that 3DV takes into account visible anatomy, the differences observed using previously published methods can be attributed to the failure of geometry to accurately approximate kidney or tumor shape. 3DV provides a more accurate, reproducible, and clinically useful tool for urologists looking to improve patient care using analysis related to volume.
Diagnosis of Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is a diagnosis of exclusion, with other androgen excess and ovulatory dysfunction disorders to be ruled out. There are 3 principal features of the syndrome, including hyperandrogenism, ovulatory dysfunction, and polycystic ovarian morphology. These features have been included in slightly different permutations in the 3 criteria currently available to diagnose PCOS, including that of the National Institutes of Health (NIH) 1990, Rotterdam 2003, and the Androgen Excess Society 2006. Overall, at least 1 in 15 women of reproductive age will be affected by PCOS, making this disorder the most common endocrine abnormality in this age group, with a health burden of over 4 billion dollars in the United States alone.
Acute Phase IL-10 Plasma Concentration Associates with the High Risk Sources of Cardiogenic Stroke

Background Etiological assessment of stroke is essential for accurate treatment decisions and for secondary prevention of recurrence. There is evidence that interleukin-10 (IL-10) associates with ischemic stroke. The aim of this prospective study was to assess the levels of IL-10 in ischemic stroke with unknown or suspected cardiogenic etiology, and evaluate the correlation between IL-10 plasma concentration and the number of diagnosed high risk sources for cardioembolism. Methods A total of 141 patients (97 males; mean age 61±11 years) with acute ischemic stroke with unknown etiology or suspected cardiogenic etiology other than known atrial fibrillation (AF) underwent imaging investigations to assess high risk sources for cardioembolic stroke established by the European Association of Echocardiography (EAE). IL-10 was measured on admission to the hospital and on a three month follow-up visit. Results Acute phase IL-10 concentration was higher in patients with EAE high risk sources, and correlated with their number (p<0.01). In patients with no risk sources (n = 104), the mean IL-10 concentration was 2.7±3.1 ng/L (range 0.3–16.3 ng/L), with one risk source (n = 26) 3.7±5.5 ng/L (0.3–23.6 ng/L), with two risk sources (n = 10) 7.0±10.0 ng/L (1.29–34.8 ng/L) and with three risk sources (n = 1) 37.2 ng/L. IL-10 level was not significantly associated with cerebral infarct volume, presence of previous or recent myocardial infarction, carotid/vertebral artery atherosclerosis, paroxysmal AF registered on 24-hour ECG Holter monitoring or given intravenous thrombolytic treatment. Conclusion IL-10 plasma concentration correlates independently with the number of EAE cardioembolic risk sources in patients with acute stroke. IL-10 may have potential to improve differential diagnostics of stroke with unknown etiology.
Human Surfactant Protein A2 Gene Mutations Impair Dimmer/Trimer Assembly Leading to Deficiency in Protein Sialylation and Secretion

Surfactant protein A2 (SP-A2) plays an essential role in surfactant metabolism and lung host defense. SP-A2 mutations in the carbohydrate recognition domain have been related to familial pulmonary fibrosis and can lead to a recombinant protein secretion deficiency in vitro. In this study, we explored the molecular mechanism of protein secretion deficiency and the subsequent biological effects in CHO-K1 cells expressing both wild-type and several different mutant forms of SP-A2. We demonstrate that the SP-A2 G231V and F198S mutants impair the formation of dimmer/trimer SP-A2 which contributes to the protein secretion defect. A deficiency in sialylation, but not N-linked glycosylation, is critical to the observed dimmer/trimer impairment-induced secretion defect. Furthermore, both mutant forms accumulate in the ER and form NP-40-insoluble aggregates. In addition, the soluble mutant SP-A2 could be partially degraded through the proteasome pathway but not the lysosome or autophagy pathway. Intriguingly, 4-phenylbutyrate acid (4-PBA), a chemical chaperone, alleviates aggregate formation and partially rescued the protein secretion of SP-A2 mutants. In conclusion, SP-A2 G231V and F198S mutants impair the dimmer/trimer assembly, which contributes to the protein sialylation and secretion deficiency. The intracellular protein mutants could be partially degraded through the proteasome pathway and also formed aggregates. The treatment of the cells with 4-PBA resulted in reduced aggregation and rescued the secretion of mutant SP-A2.
Distinct Network Interactions in Particle-Associated and Free-Living Bacterial Communities during a Microcystis aeruginosa Bloom in a Plateau Lake

Particle-associated bacteria (PAB) and free-living bacteria (FLB) from aquatic environments during phytoplankton blooms differ in their physical distance from algae. Both the interactions within PAB and FLB community fractions and their relationship with the surrounding environmental properties are largely unknown. Here, by using high-throughput sequencing and network-based analyses, we compared the community and network characteristics of PAB and FLB from a plateau lake during a Microcystis aeruginosa bloom. Results showed that PAB and FLB differed significantly in diversity, structure and microbial connecting network. PAB communities were characterized by highly similar bacterial community structure in different sites, tighter network connections, important topological roles for the bloom-causing M. aeruginosa and Alphaproteobacteria, especially for the potentially nitrogen-fixing (Pleomorphomonas) and algicidal bacteria (Brevundimonas sp.). FLB communities were sensitive to the detected environmental factors and were characterized by significantly higher bacterial diversity, less connectivity, larger network size and marginal role of M. aeruginosa. In both networks, covariation among bacterial taxa was extensive (>88% positive connections), and bacteria potentially affiliated with biogeochemical cycling of nitrogen (i.e., denitrification, nitrogen-fixation and nitrite-oxidization) were important in occupying module hubs, such as Meganema, Pleomorphomonas, and Nitrospira. These findings highlight the importance of considering microbial network interactions for the understanding of blooms.
Arbitrarily Varying Multiple-Access Channels Part I - Ericson's Symmetrizability Is Adequate, Gubner's Conjecture Is True

Ericson's conjecture has been established by Csiszar and Narayan (1988). In the theory of identification the cycle closes: both, the non-single letter separability by random words and symmetrizability are used and needed. Gubner extends the decoding rule of Csiszar and Narayan to the multiple-access situation by following "conditional decoding". This is a suboptimal decoding rule, but was suited for the discovery of the capacity theorem for the multiple-access channel (MAC). Its drawback for systems of channels was soon realized by Ahlswede (1974), where for the derivation of the capacity theorem for the compound MAC maximum likelihood decoding could be analysed. For the arbitrarily varying MAC (AVMAC) suboptimality of the conditional decoding rule becomes even more significant. The authors examine if Gubner's conjecture is true.