Miracle-dz/UniFAR-FTUs huggingface dataset:
The genetic drift of human papillomavirus type 16 is a means of reconstructing prehistoric viral spread and the movement of ancient human populations

We have investigated the diversity of a hypervariable segment of the human papillomavirus type 16 (HPV-16) genome among 301 virus isolates that were collected from 25 different ethnic groups and geographic locations. Altogether, we distinguished 48 different variants that had diversified from one another along five phylogenetic branches. Variants from two of these branches were nearly completely confined to Africa. Variants from a third branch were the only variants identified in Europeans but occurred at lower frequency in all other ethnic groups. A fourth branch was specific for Japanese and Chinese isolates. A small fraction of all isolates from Asia and from indigenous as well as immigrant populations in the Americas formed a fifth branch. Important patterns of HPV-16 phylogeny suggested coevolution of the virus with people of the three major human races, namely, Africans, Caucasians, and East Asians. But several minor patterns are indicative of smaller bottlenecks of viral evolution and spread, which may correlate with the migration of ethnic groups in prehistoric times. The colonization of the Americas by Europeans and Africans is reflected in the composition of their HPV-16 variants. We discuss arguments that today's HPV-16 genomes represent a degree of diversity that evolved over a large time span, probably exceeding 200,000 years, from a precursor genome that may have originated in Africa. The identification of molecular variants is a powerful epidemiological and phylogenetic tool for revealing the ancient spread of papillomaviruses, whose trace through the world has not yet been completely lost.
Deep density networks and uncertainty in recommender systems

Building robust online content recommendation systems requires learning complex interactions between user preferences and content features. The field has evolved rapidly in recent years from traditional multi-arm bandit and collaborative filtering techniques, with new methods employing Deep Learning models to capture non-linearities. Despite progress, the dynamic nature of online recommendations still poses great challenges, such as finding the delicate balance between exploration and exploitation. In this paper we show how uncertainty estimations can be incorporated by employing them in an optimistic exploitation/exploration strategy for more efficient exploration of new recommendations. We provide a novel hybrid deep neural network model, Deep Density Networks (DDN), which integrates content-based deep learning models with a collaborative scheme that is able to robustly model and estimate uncertainty. Finally, we present online and offline results after incorporating DNN into a real world content recommendation system that serves billions of recommendations per day, and show the benefit of using DDN in practice.
Response Developments and the Fieldwork Strategy

Le développement du taux de réponse et la stratégie du travail sur le terrain. La non-réponse dans les enquêtes auprès des ménages est un sujet de recherche important dans plusieurs pays. Néanmoins, la réponse ne décroît pas pour toutes les enquêtes, ni dans tous les pays. Les taux de réponse sont influencés en grande partie par la structure du questionnaire et des questions de passation sur le terrain. La comparaison des taux de réponse et les caractértstiques des enquêtes pour plusieurs pays renforcent cette thèse. Avec une enquête bien planifiée, des taux de réponse très forts peuvent être obtenus si le déroulement sur le terrain est bien réglé.
Amiloride delays the ischemia-induced rise in cytosolic free calcium.

An increase in cytosolic free calcium (Cai) has been shown to occur early during ischemia in perfused rat, ferret, and rabbit hearts. It has been proposed that this increase in Cai may occur as a result of exchange of Nai for Cao, which occurs as a result of an increase in Nai arising from exchange of Nao for H+i. The latter exchange is stimulated by the intracellular acidification that occurs during ischemia. To test this hypothesis, we examined Cai, Nai, ATP, and pHi during ischemia in rats in the presence and absence of 1 mM amiloride, a Na-H exchange inhibitor. Cai was measured using 19F nuclear magnetic resonance (NMR) of 1,2-bis(2-amino-5-fluorophenoxy)ethane-N,N,N',N'-tetra-acetic acid (5F-BAPTA)-loaded rat hearts. Nai was measured using 23Na NMR, and the shift reagent 1,4,7,10-tetraazacyclododecane-N,N',N",N"'-tetramethylenephosph onate (Tm[DOTP]-5) was used to separate Nai and Nao. ATP and pH were determined from 31P NMR measurements. During 20 minutes of ischemia, amiloride did not significantly alter the ATP decline but did significantly attenuate the rise in Nai and Cai. After 20 minutes of ischemia, time-averaged Cai was 1.0 +/- 0.2 microM (mean +/- SEM) in amiloride-treated hearts compared with 2.3 +/- 0.9 microM in nontreated hearts. After 20 minutes of ischemia, Nai in the untreated heart was threefold greater than control, whereas in the amiloride-treated heart, Nai was not significantly different from control. These data are consistent with the involvement of Na-Ca exchange in the rise in Cai during ischemia. (ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of the DNA Gyrase from the Thermoacidophilic Archaeon Thermoplasma acidophilum

ABSTRACT Thermoplasma acidophilum is sensitive to the antibiotic drug novobiocin, which inhibits DNA gyrase. We characterized DNA gyrases from T. acidophilum strains in vitro. The DNA gyrase from a novobiocin-resistant strain and an engineered mutant were less sensitive to novobiocin. The novobiocin-resistant gyrase genes might serve as T. acidophilum genetic markers.
Spin gaps and spin-flip energies in density-functional theory

Energy gaps are crucial aspects of the electronic structure of finite and extended systems. Whereas much is known about how to define and calculate charge gaps in density-functional theory (DFT), and about the relation between these gaps and derivative discontinuities of the exchange-correlation functional, much less is know about spin gaps. In this paper we give density-functional definitions of spin-conserving gaps, spin-flip gaps and the spin stiffness in terms of many-body energies and in terms of single-particle (Kohn-Sham) energies. Our definitions are as analogous as possible to those commonly made in the charge case, but important differences between spin and charge gaps emerge already on the single-particle level because unlike the fundamental charge gap spin gaps involve excited-state energies. Kohn-Sham and many-body spin gaps are predicted to differ, and the difference is related to derivative discontinuities that are similar to, but distinct from, those usually considered in the case of charge gaps. Both ensemble DFT and time-dependent DFT (TDDFT) can be used to calculate these spin discontinuities from a suitable functional. We illustrate our findings by evaluating our definitions for the Lithium atom, for which we calculate spin gaps and spin discontinuities by making use of near-exact Kohn-Sham eigenvalues and, independently, from the single-pole approximation to TDDFT. The many-body corrections to the Kohn-Sham spin gaps are found to be negative, i.e., single particle calculations tend to overestimate spin gaps while they underestimate charge gaps.
Spread of Injectate During C6 Stellate Ganglion Block and Fascial Arrangement in the Prevertebral Region: An Experimental Study Using Donated Cadavers

Background and Objectives The precise fascial space through which the injectate spreads during stellate ganglion block (SGB) remains unclear. Recent studies using magnetic resonance imaging or computed tomography have suggested that the injectate is deposited around and/or within the longus colli muscle during SGB. However, a fascial space, close to the longus colli, is the most likely route of spread. We identified the prevertebral interlaminal space (PVILS), situated between the anterior and posterior laminae of the prevertebral layer of the fascia, as an important route for the spread of the injectate and as a potential pathway to the ganglion. The danger of downward spread of deep infections through this space has previously been recognized. Methods and Results Using the 6th cervical vertebra paratracheal approach technique, we performed experimental SGB with 10 mL latex on donated cadavers. Spreading of latex into the PVILS was observed in 45 of 52 (86.5%) cadavers that had been fixed with formaldehyde after death, and 5 of 8 (62.5%) fresh cadavers. In these experiments, the latex usually reached the ganglion via the PVILS (39 of 45 and 5 of 5, respectively). Moreover, after direct injection into the PVILS, latex reached the ganglion in 13 of a further 19 (68.4%) postmortem-fixed donated cadavers. Conclusion These results suggest that the PVILS plays a critical role in the spread of injectate as well as being a potential pathway to the stellate ganglion during SGB.
Acquisition of Iron Is Required for Growth of Salmonella spp. in Tomato Fruit

ABSTRACT Salmonella remains a leading cause of bacterial food-borne disease, sickening millions each year. Although outbreaks of salmonellosis have traditionally been associated with contaminated meat products, recent years have seen numerous disease cases caused by the consumption of produce. Tomatoes have been specifically implicated, due to the ability of Salmonella spp. to enter the tomato fruit and proliferate within, making the decontamination of the raw product impossible. To investigate the genetic means by which Salmonella is able to survive and proliferate within tomatoes, we conducted a screen for bacterial genes of Salmonella enterica serovar Montevideo specifically induced after inoculation into ripe tomato fruit. Among these genes, we found 17 members of the previously described anaerobic Fur (ferric uptake regulator) regulon. Fur is a transcriptional and posttranscriptional regulator known to sense iron, suggesting the importance of this mineral to Salmonella within tomatoes. To test whether iron acquisition is essential for Salmonella growth in tomatoes, we tested a ΔfepDGC mutant, which lacks the ability to import iron-associated siderophores. This mutant grew significantly more poorly within tomatoes than did the wild type, but the growth defect of the mutant was fully reversed by the addition of exogenous iron, demonstrating the need for bacterial iron scavenging. Further, dependence upon iron was not apparent for Salmonella growing in filtered tomato juice, implicating the cellular fraction of the fruit as an important mediator of iron acquisition by the bacteria.
TOWARD THE 24-HOUR KNOWLEDGE FACTORY IN SOFTWARE DEVELOPMENT

Working Paper Series Introduction " The Sun never sets on the British Empire, " was a notion emphasized during the eighteenth and nineteenth centuries to highlight that the British Empire was far-flung, and that the sun was always visible from some part of this vast empire. While the British Empire has gradually disintegrated, we can now coin an equivalent notion: " The Sun never sets on the 24-hour Knowledge Factory! " The notion of the 24-hour Knowledge Factory can be traced back to the industrial revolution. Since the installed equipment was scarce and costly, the employees were scheduled to work in shifts of 8-16 hours in order to use the manufacturing facilities on a round-the-clock basis. With the advent of electronic computers and diminishing costs for telecommunications, one developed the notion of 24-hour Call Centers. Depending on the time of the call, it is automatically directed to a call center that is active at that time. Using a cluster of 3 to 4 call centers located in time zones 6-8 hours apart from the time zone of the neighboring call center, one can ensure that all employees of these geographically distributed call centers are working during daytime in their respective countries. The notion of multiple support centers was subsequently adapted for supporting global communications networks over time. Now it has become feasible for one to use a geographically distributed workforce of highly trained professionals to complete an endeavor in a much shorter timeframe as compared to a scenario in which all personnel are based at one location, irrespective of where location is. By involving specialized microchip design engineers located at multiple places around the world, a semiconductor chip design firm may create virtual " 24-hour knowledge factories ". This allows for an efficient design process that has a faster turnaround time. It provides the firm with access to high-talent designers who would otherwise have to move to a different country, or work at odd hours of the night; some persons call the latter type of shift as the " graveyard shift ". The creation of professional service teams that transcend geographic and temporal boundaries offers the potential to change the face of many industries. This innovation will dramatically impact the manner in which companies build, test, sell and support their products and services. Years ago, people in India and the United States thought the time difference was a negative-they thought …
Detection of Cervical Intraepithelial Neoplasias and Cancers in Cervical Tissue by In Vivo Light Scattering

Objective. This study aimed to examine the utility of in vivo elastic light scattering measurements, to identify cervical intraepithelial neoplasias 2,3 and cancers in women undergoing colposcopy, and to determine the effects of patient characteristics such as menstrual status on the elastic light scattering spectroscopic measurements. Materials and Methods. A fiber optic probe was used to measure light transport in the cervical epithelium of patients undergoing colposcopy. Spectroscopic results from 151 patients were compared with histopathology of the measured and biopsied sites. A method of classifying the measured sites into 2 clinically relevant categories was developed and tested using 5-fold cross-validation. Results. Statistically significant effects by age at diagnosis, menopausal status, timing of the menstrual cycle, and oral contraceptive use were identified, and adjustments based on these measurements were incorporated in the classification algorithm. A sensitivity of 77% ± 5% and a specificity of 62% ± 2% were obtained for separating cervical intraepithelial neoplasia 2,3 and cancer from other pathologies and normal tissue. Conclusions. The effects of both menstrual status and age should be taken into account in the algorithm for classifying tissue sites based on elastic light scattering spectroscopy. When this is done, elastic light scattering spectroscopy shows good potential for real-time diagnosis of cervical tissue at colposcopy. Guiding biopsy location is one potential near-term clinical application area, whereas facilitating "see and treat" protocols is a longer term goal. Improvements in accuracy are essential.
Adaptive motion estimation based on texture analysis

Texture classification applied to the frame difference signals can be used to design adaptive algorithms for a variety of video applications. In this paper an adaptive block matching motion estimation algorithm based on the interframe texture analysis is presented. The algorithm adaptively changes the size and shape of the search window of each block depending on the values of textural features. The chosen features are extracted from the temporal difference histogram and provide information about the speed of the moving objects and the most likely direction of their motion. Applications of the proposed algorithm to the normal and hierarchical motion estimators are shown. Compared to the known techniques, the presented methods reduce the computational effort by saving unnecessary searches while offering higher performance. >
What frames of reference underlie self-ratings of oral health?

OBJECTIVES This study aimed to investigate the referents and meanings that underlie self-ratings of oral health and to determine whether they vary by participants' characteristics. METHODS Semistructured interviews were conducted with a convenience sample of 80 adults who were asked to rate their oral health and explain the reasons for their ratings. The interviews were tape-recorded, transcribed in full, and subject to a content analysis that involved identification and coding of their frames of reference. These codes were collapsed to create a smaller number of categories to allow for comparisons of the proportions invoking each frame of reference. RESULTS There was considerable variation in the accounts offered to support the self-ratings of oral health. The most common referents used were biomedical, involving current oral problems, treatment needs and treatment histories, and behavioral, which included oral self-care practices, other health behaviors, and dental visiting patterns. Pain and tooth loss were also common. Most notable was the absence of functional and psychosocial referents that are prominent in contemporary definitions and measures of "oral-health-related quality of life. " There was some variation in the referents used according to sociodemographic characteristics, with age being the main source of variation. There was also variation according to the category of the self-rating used; those with favorable ratings tended to use different frames of reference than those with unfavorable ratings. CONCLUSIONS The biomedical model and professional ideologies and values provide the main frames of reference that give meaning to self-ratings of oral health. Variations in the meanings of the self-ratings have some implications for the use of this item in quantitative studies, which warrants further investigation.
The step size impact on the computational cost of spiking neuron simulation

Spiking neurons are mathematical models that simulate the generation of the electrical pulse at the neuron membrane. Most spiking neurons are expressed as a non-linear system of ordinary differential equations. Because these systems are hard to solve analytically, they must be solved using a numerical method through a discrete sequence of time steps. The step length is a factor affecting both the accuracy and computational cost of spiking neuron simulation. It is known the step size implications on the accuracy for some spiking neurons. However, it is unknown in which way the step size impacts the computational cost. We found that the computational cost as a function of the step length follows a power-law distribution. We reviewed the Leaky Integrate-and-Fire, Izhikevich, and Hodgkin-Huxley spiking neurons. Additionally, it was found that, with any step size, simulating the cerebral cortex in a sequential processing computer is prohibitive.
Flames of transformation: the role of fire in cremation practices

Abstract This paper explores the transformative power of fire, its fundamental ability to change material worlds and affect our experience of its materiality. The paper examines material transformations related to death as a means of illustrating the powerful property of fire as a materially destructive yet socially generative and creative element. While fire has been widely discussed archaeologically as a technological element, and recently coupled with the social and symbolic powers of pyrotechnology, we focus on the sensuous staging of fire in disposal practices. The paper employs two case studies focusing on cremation burial from Bronze Age (c.1300–1100 bc) and modern Denmark in order to demonstrate widely different sensuous engagements with fire and its experiential significance in a cremation context.
Transgenic Expression of Stromal Cell-Derived Factor-1/CXC Chemokine Ligand 12 Enhances Myeloid Progenitor Cell Survival/Antiapoptosis In Vitro in Response to Growth Factor Withdrawal and Enhances Myelopoiesis In Vivo

Hemopoiesis is regulated in part by survival/apoptosis of hemopoietic stem/progenitor cells. Exogenously added stromal cell-derived factor-1 ((SDF-1)/CXC chemokine ligand (CXCL)12) enhances survival/antiapoptosis of myeloid progenitor cells in vitro. To further evaluate SDF-1/CXCL12 effects on progenitor cell survival, transgenic mice endogenously expressing SDF-1/CXCL12 under a Rous sarcoma virus promoter were produced. Myeloid progenitors (CFU-granulocyte-macrophage, burst-forming unit-erythroid, CFU-granulocyte-erythrocyte-megakaryocyte-monocyte) from transgenic mice were studied for in vitro survival in the context of delayed addition of growth factors. SDF-1-expressing transgenic myeloid progenitors were enhanced in survival and antiapoptosis compared with their wild-type littermate counterparts. Survival-enhancing effects were due to release of low levels of SDF-1/CXCL12 and mediated through CXCR4 and Gαi proteins as determined by ELISA, an antagonist to CXCR4, Abs to CXCR4 and SDF-1, and pertussis toxin. Transgenic effects of low SDF-1/CXCR4 may be due to synergy of SDF-1/CXCL12 with other cytokines; low SDF-1/CXCL12 synergizes with low concentrations of other cytokines to enhance survival of normal mouse myeloid progenitors. Consistent with in vitro results, progenitors from SDF-1/CXCL12 transgenic mice displayed enhanced marrow and splenic myelopoiesis: greatly increased progenitor cell cycling and significant increases in progenitor cell numbers. These results substantiate survival effects of SDF-1/CXCL12, now extended to progenitors engineered to endogenously produce low levels of this cytokine, and demonstrate activity in vivo for SDF-1/CXCL12 in addition to cell trafficking.
A framework for relating cognitive to neural systems.

Abstract : This paper outlines a framework for relating cognitive activities of daily life (typing, reading) to underlying neural systems. The framework uses five levels of analysis. These are as follows: task, elementary operations, components facilitation and inhibition, neural systems and cellular level. Evidence is outlined which supports the idea that component facilitations and inhibitions in performance can be systematically linked to the activity of neural populations. The evidence is in the area of spatial attention and uses results of normals and patients as well as data from surface EEG and recording of single cells during selective attention tasks.
Structural Basis of NR2B-Selective Antagonist Recognition by N-Methyl-d-aspartate Receptors

N-Methyl-d-aspartate receptors (NMDARs) are ionotropic glutamate receptors endowed with unique pharmacological and functional properties. In particular, their high permeability to calcium ions confers on NMDARs a central role in triggering long term changes in synaptic strength. Under excitotoxic pathological conditions, such as those occurring during brain trauma, stroke, or Parkinson's or Huntington's diseases, calcium influx through NMDAR channels can also lead to neuronal injury. This argues for the use of NMDAR antagonists as potential therapeutic agents. To date, the most promising NMDAR antagonists are ifenprodil and derivatives, compounds that act as noncompetitive inhibitors selective for NMDARs containing the NR2B subunit. Recent studies have identified the large N-terminal domain (NTD) of NR2B as the region controlling ifenprodil sensitivity of NMDARs. We present here a detailed characterization of the ifenprodil binding site using both experimental and computational approaches. 3D homology modeling reveals that ifenprodil fits well in a closed cleft conformation of the NRB NTD; however, ifenprodil can adopt either of two possible binding orientations of opposite direction. By studying the effects of cleft mutations, we show that only the orientation in which the phenyl moiety points deep toward the NTD hinge is functionally relevant. Moreover, based on our model, we identify novel NTD NR2B residues that are crucial for conferring ifenprodil sensitivity and provide functional evidence that these residues directly interact with the ifenprodil molecule. This work provides a general insight into the origin of the subunit-selectivity of NMDAR noncompetitive antagonists and offer clues for the discovery of novel NR2B-selective antagonists.