Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Origin of the Treponematoses: A Phylogenetic Approach

Background Since the first recorded epidemic of syphilis in 1495, controversy has surrounded the origins of the bacterium Treponema pallidum subsp. pallidum and its relationship to the pathogens responsible for the other treponemal diseases: yaws, endemic syphilis, and pinta. Some researchers have argued that the syphilis-causing bacterium, or its progenitor, was brought from the New World to Europe by Christopher Columbus and his men, while others maintain that the treponematoses, including syphilis, have a much longer history on the European continent. Methodology/Principal Findings We applied phylogenetics to this problem, using data from 21 genetic regions examined in 26 geographically disparate strains of pathogenic Treponema. Of all the strains examined, the venereal syphilis-causing strains originated most recently and were more closely related to yaws-causing strains from South America than to other non-venereal strains. Old World yaws-causing strains occupied a basal position on the tree, indicating that they arose first in human history, and a simian strain of T. pallidum was found to be indistinguishable from them. Conclusions/Significance Our results lend support to the Columbian theory of syphilis's origin while suggesting that the non-sexually transmitted subspecies arose earlier in the Old World. This study represents the first attempt to address the problem of the origin of syphilis using molecular genetics, as well as the first source of information regarding the genetic make-up of non-venereal strains from the Western hemisphere.
Back to the Future: Dimensions Revisited

Most recent work on reasoning with cases in law has taken the style of rea- soning used in the CATO system as its model, and uses the notion of factors, as found in that system. Fundamental to CATO, a successor the HYPO system, were factors, which are closely related to HYPO-style dimensions. In this paper, we will argue that the simplification involved in using factors, while it has proved pragmatically useful both for clarifying understanding of certain aspects of reasoning with cases and for implementation, causes problems with domain analysis and precludes certain kinds of argument that we would wish to model. We therefore believe that the time is now ripe to go back to the original notion of dimensions, while retaining the insights that have been gained from working with the simpler notion of factors. The paper uses two case studies to argue that this is so.
Effect of chronic thyroxine treatment on IGF-I, IGF-II and IGF-binding protein expression in mammary gland and liver during pregnancy and early lactation in rats.

OBJECTIVE Hyperthyroidism in rats produces organ hypertrophy and increases in circulating IGF-I and IGF-binding protein (IGFBP)-3. Chronic treatment with thyroxine (T(4)) during pregnancy advances parturition, blocks lactation and changes several hormone receptors in mammary gland and liver. Since IGFs are implicated in mammary and liver growth and in differentiation, we studied the effects of hyperthyroidism, induced by daily injections of T(4) (0.25 mg/kg). DESIGN AND METHODS Using quantitative RT-PCR and in situ hybridization, the gene expression of IGF-I, IGF-II and the IGFBPs was determined in mammary gland and liver of rats at estrus and days 7, 14 and 21 of pregnancy (G7, G14, G21), day 1 postpartum (L1) and 3 days after removing the litter (L4). Circulating levels of IGF-I, tri-iodothyronine (T(3)), PRL and GH were measured. RESULTS T(4) treatment (HT) increased circulating T(3) save on G21, did not change serum IGF-I, increased PRL on G21 and decreased GH on L1. PRL decreased on L1 because of the absence of lactation. Hepatic IGF-I mRNA was low during pregnancy and increased on L4. HT advanced this increase to L1. In controls, liver IGFBP-3 mRNA levels decreased from G14 to G21, whereas IGFBP-4 showed an inverse pattern. HT lowered IGFBP-3 mRNA and increased IGFBP-4. Increases in mammary concentrations of IGF-I, IGFBP-3 and IGFBP-4 mRNAs were seen on G21. HT delayed these peaks to L1. Mammary IGF-II and IGFBP-2 mRNA levels were high on G7 and G14, and fell afterwards, with HT having no effects. IGFBP-5 mRNA decreased during pregnancy and increased on L1. HT increased IGFBP-5 levels in early pregnancy and on L1. IGF-I mRNA localized to connective and epithelial mammary tissue, while IGFBP-2 and IGFBP-5 mRNA was only in epithelial cells. CONCLUSION These results imply a role for IGF-I, IGFBP-3 and IGFBP-4 in terminal mammary development, while IGF-II and IGFBP-2 may be implicated in early growth. IGFBP-5 has been implicated in mammary apoptosis, and the HT-induced increase may play a role in the premature mammary involution of the HT rats.
Tephra fallout from the long-lasting Tungurahua eruptive cycle (1999-2014): Variations through eruptive style transition and deposition processes

The Tungurahua volcano (Northern Andean Volcanic Zone) has been erupting since 1999, with at least four eruptive phases up to present. Although a dozen of research focuses in tephra fall deposits during this period, none of them cover the full eruptive cycle. We investigated the eruptive mechanisms and tephra fall deposition processes at Tungurahua between 1999 and 2014, through systematic analyses of tephra samples collected westward of the volcano using mechanical sieving grain size analysis, lithology, scanning electron microscopy, X-Ray fluorescence and X-Ray diffraction. Tephra is compounded by varying amounts of scoria (black and brown), lithics, hydrothermally altered fragments, pumice, glass shards and free crystals. Textural analyses of juvenile grains (scoria, pumice and glass shards) revealed a diversity of features concerning to their vesicularity, shape and surface/perimeter. Initially, tephra was characterized by hydrothermally altered fragments related to a phreatic phase which then evolved to a pure magmatic activity with Strombolian eruptions. A homogeneous andesitic composition was observed between 1999 and 2003; however silicarich compositions occurred later in 2006. Similarly, the mineral assemblage contained plagioclase, pyroxene and olivine, but magnetite and akermanite were then included during 2006, thus indicating the eruption of a new, probably mixed magma. As consequence, Plinian activity occurred in August 2006. Further activity in 2007 ejected notable amounts (40-65%) of recycled material during Vulcanian eruptions. New eruptions occurred between 2008 and 2010, and juvenile ash revealed the interplay between brittle and ductile fragmentation through ash explosions, jetting events and Strombolian activity. The activity between 2010 and 2012 incorporated hydrothermally altered material at time that eruptive silences became longer and frequent, thus suggesting the development of a sporadic hydrothermal system. Finally, between 2013 and 2014 a series of Vulcanian events occurred. Observed grain size distributions allow us to propose three different processes occurring during tephra deposition: 1) deposition of multiple ash plumes, 2) contributions from elutriated pyroclastic density currents or grain size mixing due to major eruptions, and 3) the aggregation of particles due to rain and/or lighting. From mineralogy and grain size we infer that exposition to ash may produce acute human health effects.
MRI-Based Attenuation Correction for PET/MRI Using Ultrashort Echo Time Sequences

One of the challenges in PET/MRI is the derivation of an attenuation map to correct the PET image for attenuation. Different methods have been suggested for deriving the attenuation map from an MR image. Because the low signal intensity of cortical bone on images acquired with conventional MRI sequences makes it difficult to detect this tissue type, these methods rely on some sort of anatomic precondition to predict the attenuation map, raising the question of whether these methods will be usable in the clinic when patients may exhibit anatomic abnormalities. Methods: We propose the use of the transverse relaxation rate, derived from images acquired with an ultrashort echo time sequence to classify the voxels into 1 of 3 tissue classes (bone, soft tissue, or air), without making any assumptions on patient anatomy. Each voxel is assigned a linear attenuation coefficient corresponding to its tissue class. A reference CT scan is used to determine the voxel-by-voxel accuracy of the proposed method. The overall accuracy of the MRI-based attenuation correction is evaluated using a method that takes into account the nonlocal effects of attenuation correction. Results: As a proof of concept, the head of a pig was used as a phantom for imaging. The new method yielded a correct tissue classification in 90% of the voxels. Five human brain PET/CT and MRI datasets were also processed, yielding slightly worse voxel-by-voxel performance, compared to a CT-derived attenuation map. The PET datasets were reconstructed using the segmented MRI attenuation map derived with the new method, and the resulting images were compared with segmented CT-based attenuation correction. An average error of around 5% was found in the brain. Conclusion: The feasibility of using the transverse relaxation rate map derived from ultrashort echo time MR images for the estimation of the attenuation map was shown on phantom and clinical brain data. The results indicate that the new method, compared with CT-based attenuation correction, yields clinically acceptable errors. The proposed method does not make any assumptions about patient anatomy and could therefore also be used in cases in which anatomic abnormalities are present.
Optimal Properties of Analog Perceptrons with Excitatory Weights

The cerebellum is a brain structure which has been traditionally devoted to supervised learning. According to this theory, plasticity at the Parallel Fiber (PF) to Purkinje Cell (PC) synapses is guided by the Climbing fibers (CF), which encode an ‘error signal’. Purkinje cells have thus been modeled as perceptrons, learning input/output binary associations. At maximal capacity, a perceptron with excitatory weights expresses a large fraction of zero-weight synapses, in agreement with experimental findings. However, numerous experiments indicate that the firing rate of Purkinje cells varies in an analog, not binary, manner. In this paper, we study the perceptron with analog inputs and outputs. We show that the optimal input has a sparse binary distribution, in good agreement with the burst firing of the Granule cells. In addition, we show that the weight distribution consists of a large fraction of silent synapses, as in previously studied binary perceptron models, and as seen experimentally.
Continuing medical education: What delivery format do physicians prefer?

Background: Although physicians are in a unique position to prevent life threatening outcomes by counseling patients to stop smoking, many of them miss the opportunity to intervene in their patients' use of tobacco. Nicotine Dependence Across the Lifespan was developed as a continuing medical education (CME) program to teach and encourage physicians to deliver effective tobacco prevention and tobacco cessation counseling. Methods: This CME program was offered to Texas physicians, free of charge, in three formats: live lectures, videotapes, and World Wide Web–based training. The program targeted physicians in four rural areas of Texas (San Angelo, Harlingen, Tyler, and Lubbock), where high smoking rates are prevalent and the number of professional smoking cessation services is low. We examined the sociodemographic characteristics of the participating physicians, factors in their decisions to participate in the program, and the extent to which their reported CME format preferences were associated with age, gender, race, profession, and location. Results: The four factors identified—professional development, cost, personal control, and convenience/complexity—explained 76.9% of the variance describing the reasons physicians participated in the CME offering. The physicians' preferred CME format was live lectures: based on responses, this did not differ across age, gender, race/ethnicity, and location. Discussion: Live lecture continues to be a preferred format of CME for physicians in four rural areas of Texas, yet research continues to show that lecture results in only the lowest level of behavioral change.
Path Splicing: Reliable Connectivity with Rapid Recovery

We present path splicing, a primitive that constructs network paths from multiple independent routing processes that run over a single network topology. The routing processes compute distinct routing trees using randomly perturbed link weights. A few additional bits in packet headers give end systems access to a large number of paths. By changing these bits, nodes can redirect traffic without detailed knowledge of network paths. Assembling paths by “splicing” segments can yield up to an exponential improvement in path diversity for only a linear increase in storage and message complexity. We present randomized approaches for slice construction and failure recovery that achieve nearoptimal performance and are extremely simple to configure. Our evaluation of path splicing on realistic ISP topologies demonstrates a dramatic increase in reliability that approaches the best possible using only a small number of slices and for only a small increase in latency.
Augernome & XtremWeb: Monte Carlos computation on a global computing platform

In this paper, we present XtremWeb, a Global Computing platform used to generate monte carlos showers in Auger, an HEP experiment to study the highest energy cosmic rays at Mallargue-Mendoza, Argentina.XtremWeb main goal, as a Global Computing platform, is to compute distributed applications using idle time of widely interconnected machines. It is especially dedicated to -but not limited to- multi-parameters applications such as monte carlos computations; its security mechanisms ensuring not only hosts integrity but also results certification and its fault tolerant features, encouraged us to test it and, finally, to deploy it as to support our CPU needs to simulate showers.We first introduce Auger computing needs and how Global Computing could help. We then detail XtremWeb architecture and goals. The fourth and last part presents the profits we have gained to choose this platform. We conclude on what could be done next.
The Quest for LEDBAT Fairness

BitTorrent developers have recently introduced a new application layer congestion control algorithm based on UDP framing at transport layer and currently under definition at the IETF ledbat Working Group. Ledbat is a delay-based protocol which aims at offering a ``lower than Best Effort'''' data transfer service, with a lower priority with respect to elastic TCP and interactive traffic (e.g., VoIP, game). However, in its current specification, ledbat is affected by a late-comer advantage: indeed the last flow arriving at the bottleneck is more aggressive due to a wrong estimation of the base delay and finally takes over all resources. In this work, we study several solutions to the late-comer problem by means of packet level simulations and simple analysis: in the investigation process, we individuate the root cause for LEDBAT unfairness and propose effective countermeasures.
Photoperiod, Ambient Temperature, and Food Availability Interact to Affect Reproductive and Immune Function in Adult Male Deer Mice (Peromyscus maniculatus)

Winter is often stressful. Increased energetic demands in winter and concurrent reductions in energy availability can lead to an energetic imbalance and compromise survival. To increase the odds of surviving winter, individuals of some nontropical rodent species have evolved mechanisms to enhance immune function in advance of harsh winter conditions. Short day lengths provide a proximate cue for enhancement of immune function, an adaptive functional response to counter environmental stress-induced reduction in immune function. In the present study, photoperiod, ambient temperature, and food availability were manipulated and reproductive function and cell-mediated immunity were assessed in adult male deer mice (Peromyscus maniculatus). Mice maintained in short days regressed their reproductive systems and displayed enhanced immune function compared to long-day animals. Reduced food availability elevated corticosterone concentrations and suppressed reproductive and immune function, whereas ambient temperature alone had no effect on cell-mediated immunity. The suppressive effect of food restriction on reproductive and immune function was overcome by maintaining animals in short days. However, short-day, food-restricted mice maintained at low ambient temperatures displayed reduced reproductive and immune function compared to animals maintained at mild temperatures. Taken together, these results suggest that short-day enhancement of immune function can counteract some, but not all, of the immunosuppressive effects of winter stressors. These data are consistent with the hypothesis that immune function is enhanced in short days to counteract stress-mediated immune suppression occurring during winter.
Project REDEAM : models for historical horizontal deformation

provides Government-wide leadership in the improvement of geodetic surveying methods and instrumentation, c o o r d i n a t e s o p e r a t i o n s t o a s s u r e network development, and provides specifications and criteria for survey operations by Federal, State, and other agencies. NGS engages in research and development for the improvement of knowledge of the figure of the Earth and its gravity field, and has the responsibility to procure geodetic data from all sources, process these data, and make them.generally available to users through a central data base.
TNFR2 Stimulation Promotes Mitochondrial Fusion via Stat3- and NF-kB–Dependent Activation of OPA1 Expression

Rationale: Mitochondria are important cellular organelles and play essential roles in maintaining cell structure and function. Emerging evidence indicates that in addition to having proinflammatory and proapoptotic effects, TNF&agr; (tumor necrosis factor &agr;) can, under certain circumstances, promote improvements in mitochondrial integrity and function, phenomena that can be ascribed to the existence of TNFR2 (TNF&agr; receptor 2). Objective: The present study aimed to investigate whether and how TNFR2 activation mediates the effects of TNF&agr; on mitochondria. Methods and Results: Freshly isolated neonatal mouse cardiac myocytes treated with shRNA targeting TNFR1 were used to study the effects of TNFR2 activation on mitochondrial function. Neonatal mouse cardiac myocytes exhibited increases in mitochondrial fusion, a change that was associated with increases in mitochondrial membrane potential, intracellular ATP levels, and oxygen consumption capacity. Importantly, TNFR2 activation–induced increases in OPA1 (optic atrophy 1) protein expression were responsible for the above enhancements, and these changes could be attenuated using siRNA targeting OPA1. Moreover, both Stat3 and RelA bound to the promoter region of OPA1 and their interactions synergistically upregulated OPA1 expression at the transcriptional level. Stat3 acetylation at lysine 370 or lysine 383 played a key role in the ability of Stat3 to form a supercomplex with RelA. Meanwhile, p300 modulated Stat3 acetylation in HEK293T (human embryonic kidney 293T) cells, and p300-mediated Stat3/RelA interactions played an indispensable role in OPA1 upregulation. Finally, TNFR2 activation exerted beneficial effects on OPA1 expression in an in vivo transverse aortic constriction model, whereby TNFR1-knockout mice exhibited better outcomes than in mice with both TNFR1 and TNFR2 knocked out. Conclusions: TNFR2 activation protects cardiac myocytes against stress by upregulating OPA1 expression. This process was facilitated by p300-mediated Stat3 acetylation and Stat3/RelA interactions, leading to improvements in mitochondrial morphology and function.
Description of an intensive residential aphasia treatment program: rationale, clinical processes, and outcomes.

PURPOSE The purpose of this article is to describe the rationale, clinical processes, and outcomes of an intensive comprehensive aphasia program (ICAP). METHOD Seventy-three community-dwelling adults with aphasia completed a residentially based ICAP. Participants received 5 hr of daily 1:1 evidence-based cognitive-linguistically oriented aphasia therapy, supplemented with weekly socially oriented and therapeutic group activities over a 23-day treatment course. Standardized measures of aphasia severity and communicative functioning were obtained at baseline, program entry, program exit, and follow-up. Results were analyzed using a Bayesian latent growth curve model with 2 factors representing (a) the initial level and (b) change over time, respectively, for each outcome measure. RESULTS Model parameter estimates showed reliable improvement on all outcome measures between the initial and final assessments. Improvement during the treatment interval was greater than change observed across the baseline interval, and gains were maintained at follow-up on all measures. CONCLUSIONS The rationale, clinical processes, and outcomes of a residentially based ICAP have been described. ICAPs differ with respect to treatments delivered, dosing parameters, and outcomes measured. Specifying the defining components of complex interventions, establishing their feasibility, and describing their outcomes are necessary to guide the development of controlled clinical trials.
Reaching movements to augmented and graphic objects in virtual environments

This work explores how the availability of visual and haptic feedback affects and kinematics of reaching performance in a tabletop virtual environment. Eight subjects performed reach-to-grasp movements toward target objects of various sites in conitions where visual and haptic feedback were either present or absent. It was found that movement time was slower when visual feedback of the moving limb was not available. Further MT varied systematically with target size when haptic feedback was available (i.e. augmented targets), and thus followed Fitts' law. However, movement times were constant regardless of target size when haptic feedback was removed. In depth analysis of the reaching kinematics revealed that subjects spent longer decelerating toward smaller targets in conditions where haptic feedback was available. In contrast, deceleration time was constant when haptic feedback was absent. These results suggest that visual feedback about the moving limb and veridical haptic feedback about object contract are extremely important for humans to effectively work in virtual environments.