Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping of functions to brain regions: A neuro-phonetic model of speech production, perception, and acquisition

A model has been computer-implemented which is capable of producing and/or perceiving speech items (sounds, syllables, words, or short utterances). The organization of the model is given in Fig. 1 (see also Kröger et al. 2009a). Its cognitive linguistic module is not modelled in detail in this neurophonetic approach but it can be assumed that this module is subdivided into a procedural and a declarative part (Ullman 2001). Here it is assumed that phonemic word forms are selected from a mental lexicon (Levelt 1992, Levelt et al. 1999, Indefrey & Levelt 2004) forming the main part of the declarative memory. These forms pass linguistic processing modules including the syllabification module (procedural memory and appropriate processing modules) and subsequently they build up a chain of phonemically specified speech items on the level of the phonemic map (Fig. 1). The subsequent part of the model is the phonetic or sensorimotor module. Within all parts of the model, a neural map is defined as an ensemble of neurons located in a specific brain region which can be associated with a distinct cognitive or sensorimotor representation or state of a speech item. Different neural activation patterns occurring within a neural map represent different neural states and different speech items. Coming back to the phonemic map, thus the phonemic description of each speech item generated by the cognitive linguistic module is coded by a distinct neural activation pattern or neural state within the phonemic map. Subsequently within the phonetic or sensorimotor module, speech production can be separated in sensorimotor feedforward and feedback control (cf. Guenther 2006 and Guenther et al. 2006). Feedforward control is the direct generation of articulatory movements from a specific phonemic state. Sensorimotor feedback control is activated during production in order to control, whether the phonetic realization of a speech item is correct and, if it is not, to correct its production.
Evaluation of the physicochemical and heavy metal content of ground water sources in Bantaji and Rafin-Kada settlements of Wukari Local Government Area, Taraba State, Nigeria

Boreholes and hand dug wells from Bantaji and Rafin-Kada settlements of Wukari L.G. A. were analyzed for fourteen physicochemical parameters and seven heavy metals collected within July, 2015 to March, 2016 using standard methods. The mean difference in concentration of dissolved oxygen between the wet and dry seasons in the Bantaji boreholes was statistically significant at p<0.05. In addition, the electrical conductivity, nitrate nitrogen, phosphate and dissolved oxygen concentration were also statistically significant in the Rafin-Kada Boreholes. For the well water samples, total dissolved solids (TDS), nitrate nitrogen and chlorides were also statistically significant between the wet and dry seasons of the Bantaji wells while in the Rafin-Kada wells, with only dissolved oxygen having mean concentration that was statistically significant at p<0.05. All the physicochemical parameters in the boreholes and hand dug wells fall within the Nigerian Standards for Drinking Water Quality (NSDWQ) acceptable limits. The heavy metals, Pb and Mn had mean concentrations in the wet and dry seasons that were statistically significant in the Bantaji borehole, Bantaji well and Rafin-Kada borehole while Rafin-Kada borehole had statistically significant mean concentrations of Cd, As and Mn at p<0.05. All the heavy metals analyzed fall within the NSDWQ acceptable limits except Pb which had higher mean concentrations in the wet and dry seasons than the acceptable limits from Rafin-Kada wells (0.0190 and 0.0203 mg/L), Bantaji boreholes (0.1487 and 0.1086 mg/L) and Bantaji wells (0.0145 and 0.0154 mg/L). The mean concentrations of Pb reported may indicate presence of lead containing materials around the water sources. Frequent monitoring of these water sources is recommended over time. Key words: Boreholes, wells, Bantaji, Rafin-Kada, physic-chemical parameters, heavy metals, groundwater.
A novel regulatory circuit in base excision repair involving AP endonuclease 1, Creb1 and DNA polymerase β

DNA repair is required to maintain genome stability in stem cells and early embryos. At critical junctures, oxidative damage to DNA requires the base excision repair (BER) pathway. Since early zebrafish embryos lack the major polymerase in BER, DNA polymerase ß, repair proceeds via replicative polymerases, even though there is ample polb mRNA. Here, we report that Polb protein fails to appear at the appropriate time in development when AP endonuclease 1 (Apex), the upstream protein in BER, is knocked down. Because polb contains a Creb1 binding site, we examined whether knockdown of Apex affects creb1. Apex knockdown results in loss of Creb1 and Creb complex members but not Creb1 phosphorylation. This effect is independent of p53. Although both apex and creb1 mRNA rescue Creb1 and Polb after Apex knockdown, Apex is not a co-activator of creb1 transcription. This observation has broad significance, as similar results occur when Apex is inhibited in B cells from apex+/− mice. These results describe a novel regulatory circuit involving Apex, Creb1 and Polb and provide a mechanism for lethality of Apex loss in higher eukaryotes.
Relationship Between White Matter Hyperintensities, Cortical Thickness, and Cognition

Background and Purpose— White matter hyperintensities (WMH) are associated with clinically heterogeneous symptoms that cannot be explained by these lesions alone. It is hypothesized that these lesions are associated with distant cortical atrophy and cortical thickness network measures, which can result in an additional cognitive impairment. Here, we investigated the relationships between WMH, cortical thickness, and cognition in subjects with cerebral small vessel disease. Methods— A total of 426 subjects with cerebral small vessel disease were included, aged between 50 and 85 years, without dementia, and underwent MRI scanning. Cortical thickness analysis was performed, and WMH were manually segmented. Graph theory was applied to examine the relationship between network measures and WMH, and structural covariance matrices were constructed using inter-regional cortical thickness correlations. Results— Higher WMH load was related to lower cortical thickness in frontotemporal regions, whereas in paracentral regions, this was related to higher cortical thickness. Network analyses revealed that measures of network disruption were associated with WMH and cognitive performance. Furthermore, WMH in specific white matter tracts were related to regional-specific cortical thickness and network measures. Cognitive performances were related to cortical thickness in frontotemporal regions and network measures, and not to WMH, while controlling for cortical thickness. Conclusions— These cross-sectional results suggest that cortical changes (regional-specific damage and network breakdown), mediated (in)directly by WMH (tract-specific damage) and other factors (eg, vascular risk factors), might lead to cognitive decline. These findings have implications in understanding the relationship between WMH, cortical morphology, and the possible attendant cognitive decline and eventually dementia.
The Global Epidemiology of Syphilis in the Past Century – A Systematic Review Based on Antenatal Syphilis Prevalence

Background How can we explain the uneven decline of syphilis around the world following the introduction of penicillin? In this paper we use antenatal syphilis prevalence (ASP) to investigate how syphilis prevalence varied worldwide in the past century, and what risk factors correlate with this variance. Methods 1) A systematic review using PubMed and Google Scholar was conducted to identify countries with published data relating to ASP estimates from before 1952 until the present. Eleven countries were identified (Canada, Denmark, Finland, India, Japan, Norway, Singapore, South Africa, United States of America (USA), United Kingdom (UK) and Zimbabwe). The ASP epidemic curve for each population was depicted graphically. In South Africa and the USA, results are reported separately for the black and white populations. 2) National antenatal syphilis prevalence estimates for 1990 to 1999 and 2008 were taken from an Institute for Health Metrics and Evaluation database on the prevalence of syphilis in low risk populations compiled for the Global Burden of Diseases study and from a recent review paper respectively. National ASPs were depicted graphically and regional median ASPs were calculated for both time periods. 3) Linear regression was used to test for an association between ASP in 1990–1999 and 2008 and four risk factors (efficacy of syphilis screening/treatment, health expenditure, GDP per capita and circumcision prevalence). WHO world regions were included as potential explanatory variables. Results In most populations, ASP dropped to under 1% before 1960. In Zimbabwe and black South Africans, ASP was high in the pre-penicillin period, dropped in the post-penicillin period, but then plateaued at around 6% until the end of the 20th century when ASP dropped to just above 1%. In black Americans, ASP declined in the post penicillin period, but plateaued at 3–5% thereafter. ASP was statistically significantly higher in sub-Saharan Africa in 1990–1999 and 2008 than in the other world regions (P < 0.001). On multivariate analysis in both time periods, ASP was only associated with residence in sub-Saharan Africa. Conclusions Further research is necessary to elucidate the reasons for the higher prevalence of syphilis in sub-Saharan Africa.
Caesar: high-speed and memory-efficient forwarding engine for future internet architecture

In response to the critical challenges of the current Internet architecture and its protocols, a set of so-called clean slate designs has been proposed. Common among them is an addressing scheme that separates location and identity with self-certifying, flat and non-aggregatable address components. Each component is long, reaching a few kilobits, and would consume an amount of fast memory in data plane devices (e.g., routers) that is far beyond existing capacities. To address this challenge, we present Caesar, a high-speed and length-agnostic forwarding engine for future border routers, performing most of the lookups within three fast memory accesses. To compress forwarding states, Caesar constructs scalable and reliable Bloom filters in Ternary Content Addressable Memory (TCAM). To guarantee correctness, Caesar detects false positives at high speed and develops a blacklisting approach to handling them. In addition, we optimize our design by introducing a hashing scheme that reduces the number of hash computations from k to log(k) per lookup based on hash coding theory. We handle routing updates while keeping filters highly utilized in address removals. We perform extensive analysis and simulations using real traffic and routing traces to demonstrate the benefits of our design. Our evaluation shows that Caesar is more energy-efficient and less expensive (in terms of total cost) compared to optimized IPv6 TCAM-based solutions by up to 67% and 43% respectively. In addition, the total cost of our design is approximately the same for various address lengths.
On critical groups

The concept of critical group was introduced by D. C. Cross (as reported by G. Higman in [5]): a finite group is called critical if it is not contained in the variety generated by its proper factors. (The factors of a group G are the groups H/K where K H ≦ G, and H/K is a proper factor of G unless H = G and K =1). Some investigations concerning finite groups and varieties depend on the investigator's ability to decide whether a given group is critical or not. (For instance, one of the crucial points in the important paper [9] of Sheila Oates and M. B. Powell is a necessary condition of criticality: their Lemma 2.4.2.) An obvious necessary condition is that the group should have only one minimal normal subgroup: the group is then called monolithic, and the minimal normal subgroup its monolith. This is, however, far from being a sufficient condition, and it is the purpose of the present paper to give some sufficient conditions for the criticality of monolithic groups. (We consider the trivial group neither monolithic nor critical.) The basis of our results is an analysis of the following situation.
Existing data sources for clinical epidemiology: The Western Denmark Heart Registry

Background: The Western Denmark Heart Registry (WDHR) has not previously been described as a research tool in clinical epidemiology. Objectives: We examined the setting, organization, content, data quality, and research potential of the WDHR. Method: We collected information from members of the WDHR organization, including the committee of representatives, the board, the data management group, and physicians reporting to the database. We retrieved 2008 data from the WDHR to illustrate database variables. Results: The WDHR is a clinical database within a population-based health care system. It was launched on 1 January 1999 to monitor and improve the quality of cardiac intervention in Western Denmark (population: 3.3 million) and to allow for clinical and health-service research. More than 200,000 interventions, with 50–150 variables each, have been registered. The data quality is ensured by automatic validation rules at data entry combined with systematic validation procedures and random spot-checks after entry. Conclusions: The WDHR is a valuable research tool because it provides ongoing longitudinal registration of detailed patient and procedural data. The Danish national health care system enables this research because it allows complete follow-up for medical events after cardiac intervention by linkage with multiple medical databases.
Multiple levels of control of the stage- and region-specific expression of rat intestinal lactase

To elucidate the mechanisms leading to the functional regionalization of the digestive epithelium, lactase expression was analyzed at the protein, mRNA and gene levels, along the intestinal tract at various stages of the rat postnatal development. In the colon of neonates, the transient expression of mRNA and enzyme correlated well with gene transcription. In contrast to the colon, complex patterns were observed in the small intestine. In suckling animals, the mRNA was present at a high level despite the progressive decline of enzyme activity. Crypts were devoid of mRNA and the transcript mainly accumulated in the lower half of the villi. From weaning onwards, a functional regionalization of the epithelium was defined, characterized by the modification of the longitudinal distribution of lactase mRNA. Indeed the transcript remained abundant in the distal duodenum, jejunum and proximal ileum, but decreased in the proximal duodenum and became virtually absent in the distal ileum. Concomitantly, the mRNA and enzyme distribution along the villi changed in the different segments of the small intestine. Patterns similar to those described in sucklings were retained in the adult jejunum. In contrast, mRNA and enzyme could no longer be detected in the distal ileum, while mosaicism appeared in the proximal duodenum. In vitro transcription assays carried out with isolated nuclei suggested that the decay of lactase mRNA in the proximal duodenum at weaning was associated with a decreasing rate of transcription of the gene. However active gene transcription was retained in the nuclei of the adult jejunum and ileum. The loss of mRNA in the adult distal ileum despite the maintenance of active transcription did not result from an intragenic block of pre-RNA elongation, as shown by transcription assays carried out at various positions of the lactase gene. In addition, we looked for the ontogenic decline of lactase protein despite the maintenance of a high amount of mRNA in the jejunum, and it became evident that the fraction of mRNA present in polysomes was constant with age. Taken together, these data indicate that lactase constitutes an unusual marker of development and of functional regionalization of the intestinal tract which exhibits a complex time- and space-specific pattern of gene, mRNA, and protein expression. The distinct patterns occurring in the duodenum, jejunum, ileum, and the colon of pre- and postweaned rats depend on a combination of transcriptional, posttranscriptional, and posttranslational levels of regulation. and are associated with a different mRNA distribution along villi in each intestinal segment.
Implicit interest indicators

Recommender systems provide personalized suggestions about items that users will find interesting. Typically, recommender systems require a user interface that can ``intelligently'' determine the interest of a user and use this information to make suggestions. The common solution, ``explicit ratings'', where users tell the system what they think about a piece of information, is well-understood and fairly precise. However, having to stop to enter explicit ratings can alter normal patterns of browsing and reading. A more ``intelligent'' method is to useimplicit ratings, where a rating is obtained by a method other than obtaining it directly from the user. These implicit interest indicators have obvious advantages, including removing the cost of the user rating, and that every user interaction with the system can contribute to an implicit rating. Current recommender systems mostly do not use implicit ratings, nor is the ability of implicit ratings to predict actual user interest well-understood. This research studies the correlation between various implicit ratings and the explicit rating for a single Web page. A Web browser was developed to record the user's actions (implicit ratings) and the explicit rating of a page. Actions included mouse clicks, mouse movement, scrolling and elapsed time. This browser was used by over 80 people that browsed more than 2500 Web pages. Using the data collected by the browser, the individual implicit ratings and some combinations of implicit ratings were analyzed and compared with the explicit rating. We found that the time spent on a page, the amount of scrolling on a page and the combination of time and scrolling had a strong correlation with explicit interest, while individual scrolling methods and mouse-clicks were ineffective in predicting explicit interest.
Lithium transport pathways in human red blood cells

In human red cells, Li is extruded against its own concentration gradient if the external medium contains Na as a dominant cation. This uphill net Li extrusion occurs in the presence of external Na but not K, Rb, Cs, choline, Mg, or Ca, is ouabain-insensitive, inhibited by phloretin, and does not require the presence of cellular ATP. Li influx into human red cells has a ouabain-sensitive and a ouabain-insensitive but phloretin-sensitive component. Ouabain-sensitive Li influx is competitively inhibited by external K and Na and probably involves the site on which the Na-K pump normally transports K into red cells. Ouabain does not inhibit Li efflux from red cells containing Li concentrations below 10 mM in the presence of high internal Na or K, whereas a ouabain-sensitive Li efflux can be measured in cells loaded to contain 140 mM Li in the presence of little or no internal Na or K. Ouabain-insensitive Li efflux is stimulated by external Na and not by K, Rb, Cs, choline, Mg, or Ca ions. Na-dependent Li efflux does not require the presence of cellular ATP and is inhibited by phloretin, furosemide, quinine, and quinidine. Experiments carried out in cells loaded in the presence of nystatin to contain either only K or only Na show that the ouabain-insensitive, phloretin-inhibited Li movements into or out of human red cells are stimulated by Na on the trans side and inhibited by Na on the cis side of the red cell membrane. The characteristics of the Na-dependent unidirectional Li fluxes and uphill Li extrusion are similar, suggesting that they are mediated by the same Na-Li countertransport system.
A Japanese Encephalitis Vaccine From India Induces Durable and Cross-protective Immunity Against Temporally and Spatially Wide-ranging Global Field Strains.

BACKGROUND Japanese encephalitis (JE) is a vaccine-preventable acute disease. We report the results of a phase 2/3 trial of JENVAC, a Vero cell-derived vaccine developed using an Indian strain of JE virus (JEV). METHODS JENVAC was administered in 2 doses 28 days apart, and immunogenicity was compared to that from a single dose of SA-14-14-2, the only approved JE vaccine and regimen at the time in India. RESULTS After both the doses, seroconversion and seroprotection were >90% for JENVAC. For SA-14-14-2, seroconversion and seroprotection were 57.69% and 77.56%, respectively, on day 28 and 39.74% and 60.26%, respectively, on day 56. The geometric mean titers at day 28 and day 56 were 145.04 and 460.53, respectively, for JENVAC and 38.56 and 25.29, respectively, for SA-14-14-2. With a single dose of JENVAC, seroprotection titers lasted at least 12 months in >80% of the subjects. Following receipt of 2 doses, 61.17% of subjects retained seroprotection titers at 24 months, and immunogenicity criteria were higher than that for SA-14-14-2 at 12, 18, and 24 months each. Sera from JENVAC subjects neutralized JEV genotypes I, II, III, and IV equally well. Adverse events were not significantly different between the 2 vaccines. CONCLUSIONS JENVAC elicits long-lasting, broadly protective immunity. CLINICAL TRIALS REGISTRATION CTRI/2011/07/001855.
3 Canonical Correlation Analysis for Deriving Word Embeddings

Canonical correlation analysis (CCA) is a method for reducing the dimension of data represented using two views. It has been previously used to derive word embeddings, where one view indicates a word, and the other view indicates its context. We describe a way to incorporate prior knowledge into CCA, give a theoretical justification for it, and test it by deriving word embeddings and evaluating them on a myriad of datasets.
Lexical stress modeling for improved speech recognition of spontaneous telephone speech in the jupiter domain

This paper examines an approach of using lexical stress models to improve the speech recognition performance on spontaneous telephone speech. We analyzed the correlation of various pitch, energy, and duration measurements with lexical stress on a large corpus of spontaneous utterances, and identified the most informative features of stress using classification experiments. We incorporated the stress models into the recognizer first-pass Viterbi search and obtained modest but statistically significant improvements over a state-of-the-art real-time performance on the JUPITER weather information domain [1].