Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain Connectivity in Ateles geoffroyi: Resting-State Functional Magnetic Resonance Imaging of Working Memory and Executive Control

The objective of this research was to describe the organization and connectivity of the working memory (WM) and executive control (EC) networks in Ateles geoffroyi in resting-state conditions. Recent studies have shown that resting-state activity may underlie rudimentary brain functioning, showing that several brain regions can be tonically active at rest, maximizing the efficiency of information transfer while preserving a low physical connection cost. Whole-brain resting-state images were acquired from three healthy adult Ateles monkeys (2 females, 1 male; mean age 10.5 ± SD 2.5 years). Data were analyzed with independent component analysis, and results were grouped together using the GIFT software. The present study compared the EC and WM networks obtained with human data and with results found in the literature in other primate species. Nine resting-state networks were found, which were similar to resting networks found in healthy human adults in the prefrontal basal portion and frontopolar area. Additionally, components of the WM network were found to be extending into the hypothalamus and the olfactory areas. A key finding was the discovery of connections in the WM and EC networks to the hypothalamus, the motor cortex, and the entorhinal cortex, suggesting that information is integrated from larger brain areas. The correlated areas suggest that many elements of WM and EC may be conserved across primate species. Characterization of these networks in resting-state conditions in nonhuman primate brains is a fundamental prerequisite for understanding of the neural bases underlying the evolution and function of this cognitive system.
Kaposi’s Sarcoma-Associated Herpesvirus K3 and K5 Proteins Down Regulate Both DC-SIGN and DC-SIGNR

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of multicentric Castleman’s disease, primary effusion lymphoma and Kaposi’s sarcoma. In this study, we show that like the C-type lectin DC-SIGN, the closely related DC-SIGNR can also enhance KSHV infection. Following infection, they are both targeted for down modulation and our data indicate that the KSHV MARCH-family ubiquitin ligase K5 is mediating this regulation and subsequent targeting for degradation of DC-SIGN and DC-SIGNR in the context of the virus. The closely related viral K3 protein, is also able to target these lectins in exogenous expressions studies, but only weakly during viral infection. In addition to requiring a functional RING-CH domain, several protein trafficking motifs in the C-terminal region of both K3 and K5 are important in regulation of DC-SIGN and DC-SIGNR. Further exploration of this modulation revealed that DC-SIGN is endocytosed from the cell surface in THP-1 monocytes, but degraded from an internal location with minimal endocytosis in HEK-293 cells. Pull-down data indicate that both K3 and K5 preferentially associate with immature forms of the lectins, mediating their ubiquitylation and degradation. Together, these data emphasize the molecular complexities of K3 and K5, while expanding the repertoire of targets of these two viral proteins.
Activity and Mechanism of Action of HDVD, a Novel Pyrimidine Nucleoside Derivative with High Levels of Selectivity and Potency against Gammaherpesviruses

ABSTRACT A novel nucleoside analogue, 1-[(2S,4S-2-(hydroxymethyl)-1,3-dioxolan-4-yl]5-vinylpyrimidine-2,4(1H,3H)-dione, or HDVD, was evaluated against a wide variety of herpesviruses and was found to be a highly selective inhibitor of replication of the gammaherpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV). HDVD had also a pronounced inhibitory activity against murine herpesvirus 68 (MHV-68) and herpes simplex virus 1 (HSV-1). In contrast, replication of herpesvirus saimiri (HVS), HSV-2, and varicella-zoster virus (VZV) was weakly inhibited by the compound, and no antiviral activity was determined against human cytomegalovirus (HCMV) and rhesus rhadinovirus (RRV). The HDVD-resistant virus phenotype contained point mutations in the viral thymidine kinase (TK) of HSV-1, MHV-68, and HVS isolates. These mutations conferred cross-resistance to other TK-dependent drugs, with the exception of an MHV-68 mutant (E358D) that exhibited resistance only to HDVD. HSV-1 and HVS TK-mutants isolated under selective pressure with bromovinyldeoxyuridine (BVDU) also showed reduced sensitivity to HDVD. Oral treatment with HDVD and BVDU was assessed in an intranasal model of MHV-68 infection in BALB/c mice. In contrast to BVDU treatment, HDVD-treated animals showed a reduction in viral DNA loads and diminished viral gene expression during acute viral replication in the lungs in comparison to levels in untreated controls. The valyl ester prodrug of HDVD (USS-02-71-44) suppressed the latent infection in the spleen to a greater extent than HDVD. In the present study, HDVD emerged as a highly potent antiviral with a unique spectrum of activity against herpesviruses, in particular, gammaherpesviruses, and may be of interest in the treatment of virus-associated diseases.
Assessment of the burden of human African trypanosomiasis by rapid participatory appraisal in three high-risk villages in Urambo District, Northwest Tanzania.

BACKGROUND The public health and socio-economic burden of Human African Trypanosomiasis (HAT) in East Africa is not well documented. Understanding the epidemiology and impact of HAT in such settings is difficult due to a lack of robust surveillance and reporting systems, restricting evidence-based policy development and contributing to the continued neglect of this disease. OBJECTIVE To investigate the burden of HAT in Urambo District, Tanzania in order to inform future public health policy. METHODS A rapid participatory appraisal (RPA) using a combination of qualitative and quantitative methods was conducted, that included key informant interviews, hospital record analysis, and tools adapted from participatory learning and action. RESULTS Three villages adjacent to Ugala Game Reserve appeared to be the most affected. High levels of under-reporting were noted due to a lack of diagnostic tools at peripheral health care facilities and limited access to specialist services. Community stakeholders perceived the health and socio-economic burden of HAT to be similar to that of malaria. CONCLUSION The burden of HAT in remote rural communities is difficult to capture through routine surveillance systems alone. The RPA represents an efficient mechanism for engaging communities in public health action for trypanosomiasis control in northwest Tanzania.
Laconic Schema Mappings: Computing the Core with SQL Queries

A schema mapping is a declarative specification of the relationship between instances of a source schema and a target schema. The data exchange (or data translation) problem asks: given an instance over the source schema, materialize an instance (or solution) over the target schema that satisfies the schema mapping. In general, a given source instance may have numerous different solutions. Among all the solutions, universal solutions and core universal solutions have been singled out and extensively studied. A universal solution is a most general one and also represents the entire space of solutions, while a core universal solution is the smallest universal solution and is unique up to isomorphism (hence, we can talk about the core). The problem of designing efficient algorithms for computing the core has attracted considerable attention in recent years. In this paper, we present a method for directly computing the core by SQL queries, when schema mappings are specified by source-to-target tuple-generating dependencies (s-t tgds). Unlike prior methods that, given a source instance, first compute a target instance and then recursively minimize that instance to the core, our method avoids the construction of such intermediate instances. This is done by rewriting the schema mapping into a laconic schema mapping that is specified by first-order s-t tgds with a linear order in the active domain of the source instances. A laconic schema mapping has the property that a "direct translation" of the source instance according to the laconic schema mapping produces the core. Furthermore, a laconic schema mapping can be easily translated into SQL, hence it can be optimized and executed by a database system to produce the core. We also show that our results are optimal: the use of the linear order is inevitable and, in general, schema mappings with constraints over the target schema cannot be rewritten to a laconic schema mapping.
Large displacement optical flow computation withoutwarping

We propose an algorithm for large displacement optical flow estimation which does not require the commonly used coarse-to-fine warping strategy. It is based on a quadratic relaxation of the optical flow functional which decouples data term and regularizer in such a way that the non-linearized variational problem can be solved by an alternation of two globally optimal steps, one imposing optimal data consistency, the other imposing discontinuity-preserving regularity of the flow field. Experimental results confirm that the proposed algorithmic implementation outperforms the traditional warping strategy, in particular for the case of large displacements of small scale structures.
Lookup table based simulation and statistical modeling of sigma-delta ADCs

Sigma-delta (EA) ADCs have been widely adopted in data conversion applications due to the good performance. However, oversampling and complex circuit behavior render the simulation of these designs prohibitively time consuming. In this paper, a lookup table (LUT) based modeling technique is presented for efficient analysis of SigmaDelta ADCs. In the proposed approach, various transistor-level circuit non-idealities are systematically characterized at the building-block level and the complete ADC is simulated much more efficiently using these table models. As such, our approach can provide up to four orders of magnitude runtime speedup over SPICE-like simulators, hence significantly shortening the CPU time required for evaluating system performances such as SNDR (signal-noise-distortion-ratio). The proposed LUT modeling technique is further extended to assess performance variations due to parameter fluctuations. The resulting parameterized LUT modeling technique not only facilitates scalable performance variation analysis of complex SigmaDelta ADC designs, but also allows us to feasibly extract statistical performance correlation models for low-cost test solutions
Tunable Sensitivity to Large Errors in Neural Network Training

When humans learn a new concept, they might ignore examples that they cannot make sense of at first, and only later focus on such examples, when they are more useful for learning. We propose incorporating this idea of tunable sensitivity for hard examples in neural network learning, using a new generalization of the cross-entropy gradient step, which can be used in place of the gradient in any gradient-based training method. The generalized gradient is parameterized by a value that controls the sensitivity of the training process to harder training examples. We tested our method on several benchmark datasets. We propose, and corroborate in our experiments, that the optimal level of sensitivity to hard example is positively correlated with the depth of the network. Moreover, the test prediction error obtained by our method is generally lower than that of the vanilla cross-entropy gradient learner. We therefore conclude that tunable sensitivity can be helpful for neural network learning.
Enforcing Network-Wide Policies in the Presence of Dynamic Middlebox Actions using FlowTags

Middleboxes provide key security and performance guarantees in networks. Unfortunately, the dynamic traffic modifications they induce make it difficult to reason about network management tasks such as access control, accounting, and diagnostics. This also makes it difficult to integrate middleboxes into SDN-capable networks and leverage the benefits that SDN can offer. In response, we develop the FlowTags architecture. FlowTags-enhanced middleboxes export tags to provide the necessary causal context (e.g., source hosts or internal cache/miss state). SDN controllers can configure the tag generation and tag consumption operations using new FlowTags APIs. These operations help restore two key SDN tenets: (i) bindings between packets and their "origins," and (ii) ensuring that packets follow policy-mandated paths. We develop new controller mechanisms that leverage FlowTags. We show the feasibility of minimally extending middleboxes to support FlowTags. We also show that FlowTags imposes low overhead over traditional SDN mechanisms. Finally, we demonstrate the early promise of FlowTags in enabling new verification and diagnosis capabilities.
How Often and under Which Circumstances Do Mexican Pharmacy Vendors Recommend Misoprostol to Induce an Abortion?

and the information they provide to clients who request it. Simulated clients have been widely used in pharmacy-based studies; 6 the methodology has advantages over interviews because it reduces observation bias. 7 Posing as clients and presenting a particular scenario, trained field-workers engage providers to seek information in a situation similar to what the provider might be expected to encounter on any given day of routine service. Providers are unaware that these clients are involved in research. According to three studies using simulated clients conducted in Latin American countries, pharmacy vendors are aware of the abortifacient properties of misoprostol, but have limited knowledge about effective doses and do not provide sufficient counseling or follow-up instructions. 8–10 A study conducted in Mexico City in 2003 reported that pharmacy vendors recommended misoprostol in 39% of the scenarios in which a simulated client asked for a drug to " induce menstruation, " but that in only 17% of those interactions did pharmacy workers actually provide correct information about an effective dosage. 8 In a 2006 study conducted in one Mexican state, 90% of pharmacy vendors discussed misoprostol either spontaneously or after being prompted by a simulated client, but the majority of these vendors did not provide accurate information about dosage, mode of administration or what women should CONTEXT: Misoprostol was used by women across Mexico to induce abortion even before 2007, when first-trimester abortion was legalized in Mexico City. Pharmacy vendors' misoprostol recommendation practices across subregions of Mexico after abortion legalization warrant examination. METHODS: Overall, 192 pharmacies in four regions of Mexico were randomly selected and visited by simulated clients presenting three scenarios (a young woman, an adult woman and a male partner). Bivariate and multivariate analyses were used to explore associations between pharmacy, vendor and client characteristics and drug access. RESULTS: In 558 encounters with simulated clients, 78% of vendors provided information about misoprostol—18% recommended it spontaneously and 60% recommended it only after the client asked specifically for the drug. Fifteen percent of vendors recommended a potentially effective misoprostol dosing regimen. Mexico City–based pharmacies and those in the Central region were significantly less likely than those in the North region to require a prescription to sell misoprostol (odds ratios, 0.2 and 0.3, respectively). Independent pharmacies and those from low-income areas were significantly more likely to sell misoprostol by the pill than chain pharmacies and those in medium-income areas (3.2 and 2.7, respectively). …
Sunscreen use before and after transplantation and assessment of risk factors associated with skin cancer development in renal transplant recipients.

OBJECTIVE To determine the degree of compliance with sunscreen use among renal transplant recipients before and after transplantation and to determine risk factors associated with skin carcinogenesis. DESIGN Single-observer study with structured interview using a standardized questionnaire. Medical records and histology reports were examined for details of prior skin cancer. Cox proportional hazards regression was used for analysis of risk factors for developing skin cancer after transplantation. SETTING Patients attending Beaumont Hospital, the national renal transplantation center in Dublin, Ireland. PATIENTS The study population comprised 270 patients (182 male and 88 female). MAIN OUTCOME MEASURES Patients' use of sunscreens before and after transplantation relative to known skin cancer risk factors and subsequent skin carcinogenesis. RESULTS Prior to transplantation, 68.5% of patients never applied sunscreen on a sunny day compared with 25.9% after transplantation. Patients 50 years or younger were more likely to always apply sunscreen both before and after transplantation (P = .01), as were female patients prior to transplantation (P = .02). Those patients who participated in an outdoor recreation were more likely to subsequently develop nonmelanoma skin cancer (P = .04), as were those older than 50 years (P<.001) and those with a history of 2 or more painful sunburns (P = .03). CONCLUSIONS Transplant recipients are poorly compliant with the use of sunscreens both before and after transplantation. Compliance is poorest in those groups at higher risk of nonmelanoma skin cancer.
PRRS Virus-Induced Damage to Intravascular Macrophages

and Implications The results of this research suggest: (1) PRRSV has a detrimental effect on the uptake of copper particles by pulmonary intravascular macrophages (PIMs), (2) the severity of PRRSV-induced damage to PIMs differs among PRRSV isolates, and (3) PRRSV-induced decreased pulmonary clearance supports the hypothesis that PRRSV infection makes pigs more susceptible to bacterial septicemia.
Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs

Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the Late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum. Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species' responses to past climate fluctuations. We apply this approach to multi-locus sequence data from five co-distributed frog species endemic to the Wet Tropics rainforests of northeast Australia. Our results demonstrate at least two episodes of vicariance owing to climate-driven forest contractions: one in the Early Pleistocene and the other considerably older. Understanding how repeated cycles of rainforest contraction and expansion differentially affected lineage divergence among co-distributed species provides a framework for identifying evolutionary processes that underlie population divergence and speciation.
Minimum Fuel Control Strategy in Automated Car-Following Scenarios

Fuel consumption of traditional ground vehicles is significantly affected by how the vehicles are driven. This paper focuses on the servo-loop control design of a Pulse-and-Gliding (PnG) strategy to minimize fuel consumption in automated car following. A switching-based framework is proposed for real-time implementation. The corresponding controller was synthesized for ideal conditions and subsequently enhanced to compensate for practical factors such as powertrain dynamics, speed variations, and plant uncertainties. Simulations in both uniform and naturalistic traffic flows demonstrate that, compared with a linear quadratic (LQ)-based benchmark controller, the PnG controller improves fuel economy up to 20%. The significant fuel saving is achieved while maintaining precise range bounds so that the negative impact on safety/traffic flow is contained. The developed algorithm can potentially be embedded in adaptive cruise control systems to achieve fuel-saving function.
Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths

This study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA. Groundwater of different ages was sampled along hydrogeologic paths or loops, in three contrasting hard-rock aquifers in Brittany (France). Microbial community composition was driven by groundwater residence time and hydrogeologic loop position. In recent groundwater, in the upper section of the aquifers or in their recharge zone, surface water inputs caused high nitrate concentration and the predominance of putative denitrifiers. Although denitrification does not seem to fully decrease nitrate concentrations due to low dissolved organic carbon concentrations, nitrate input has a major effect on microbial communities. The occurrence of taxa possibly associated with the application of organic fertilizers was also noticed. In ancient isolated groundwater, an ecosystem based on Fe(II)/Fe(III) and S/SO4 redox cycling was observed down to several 100 of meters below the surface. In this depth section, microbial communities were dominated by iron oxidizing bacteria belonging to Gallionellaceae. The latter were associated to old groundwater with high Fe concentrations mixed to a small but not null percentage of recent groundwater inducing oxygen concentrations below 2.5 mg/L. These two types of microbial community were observed in the three sites, independently of site geology and aquifer geometry, indicating hydrogeologic circulation exercises a major control on microbial communities.
Characteristics of HIV‐1 non‐B subtype infections in Northwest Poland

The number of non‐B subtype HIV‐1 infections in Europe has been increasing even though major regional differences have been observed. This trend was investigated in northwestern Poland using sequence and epidemiological data from a cohort of 102 HIV‐1‐infected patients from Szczecin, Poland. HIV‐1 subtypes were defined by phylogenetic analysis of viral reverse transcriptase‐ and protease‐partial coding regions, and results were compared with online subtyping by Standford and REGA tools. Subtype analysis using on‐line subtyping methods produced varying results if compared to phylogenesis, with concordant variant assignment obtained for 98% (100/102) of sequences by Stanford and 85% (87/102) by REGA. In the population studied, non‐B subtype infections comprised 21% of the infections and consisted of subtype D (57%, n = 12), CRF01_AE (19%, n = 4), A and C clades (9.5%, n = 2), and the CRF13_cpx recombinant isolate (4.8%, n = 1). Patients carrying non‐B subtypes were predominantly heterosexuals with high percentage (57%) of women observed in the group. All HIV‐1 non‐B women were Caucasian with majority (83%) of infections acquired in Poland; however, among 12 travelers included in the study a higher proportion of non‐B infections was noted (50%, P = 0.01). Moreover, lower baseline lymphocyte CD4 counts (P = 0.01), higher baseline HIV‐1 viremia (P = 0.08), and a more advanced stage of the disease (P = 0.03) were observed among individuals infected with non‐B subtypes. The data indicated that the proportion of HIV‐1 non‐B subtype infections was higher than previously reported in Poland consisting of a high subtype D prevalence. Furthermore, subtype D transmission occurred primarily between heterosexual Caucasian individuals from this region. J. Med. Virol. 82:1306–1313, 2010. © 2010 Wiley‐Liss, Inc.