Miracle-dz/UniFAR-FTUs huggingface dataset:
A Phylogeographic Investigation of African Monkeypox

Monkeypox is a zoonotic disease caused by a virus member of the genus Orthopoxvirus and is endemic to Central and Western African countries. Previous work has identified two geographically disjuct clades of monkeypox virus based on the analysis of a few genomes coupled with epidemiological and clinical analyses; however, environmental and geographic causes of this differentiation have not been explored. Here, we expand previous phylogenetic studies by analyzing a larger set of monkeypox virus genomes originating throughout Sub-Saharan Africa to identify possible biogeographic barriers associated with genetic differentiation; and projected ecological niche models onto environmental conditions at three periods in the past to explore the potential role of climate oscillations in the evolution of the two primary clades. Analyses supported the separation of the Congo Basin and West Africa clades; the Congo Basin clade shows much shorter branches, which likely indicate a more recent diversification of isolates within this clade. The area between the Sanaga and Cross Rivers divides the two clades and the Dahomey Gap seems to have also served as a barrier within the West African clade. Contraction of areas with suitable environments for monkeypox virus during the Last Glacial Maximum, suggests that the Congo Basin clade of monkeypox virus experienced a severe bottleneck and has since expanded its geographic range.
Pregnancy and the Risk of Relapse in Patients Diagnosed With Hodgkin Lymphoma.

PURPOSE Many patients and clinicians are worried that pregnancy after the diagnosis of Hodgkin lymphoma (HL) may increase the risk of relapse despite a lack of empirical evidence to support such concerns. We investigated if an association exists between pregnancy and relapse in women with a diagnosis of HL. MATERIALS AND METHODS Using Swedish healthcare registers combined with medical records, we included 449 women who received a diagnosis of HL between 1992 and 2009 and who were age 18 to 40 years at diagnosis. Follow-up started 6 months after diagnosis, when the patients' condition was assumed to be in remission. Pregnancy-associated relapse was defined as a relapse during pregnancy or within 5 years after delivery. Hazard ratios (HRs) with 95% CIs were estimated by using the Cox proportional hazards model. RESULTS Among the 449 women, 144 (32%) became pregnant during follow-up. Overall, 47 relapses were recorded, of which one was a pregnancy-associated relapse. The adjusted HR for the comparison of the pregnancy-associated relapse rate to the non-pregnancy-associated relapse rate was 0.29 (95% CI, 0.04 to 2.18). The expected number of relapses in women with a recent pregnancy, given that they would experience the same relapse rate as that of women without a recent pregnancy, was 3.76; the observed-to-expected ratio was 0.27 (95% exact CI, 0.01 to 1.51). CONCLUSION We found no evidence that a pregnancy after diagnosis increases the relapse rate among women whose HL is in remission. Survivors of HL need to consider a range of factors when deciding about future reproduction. However, given the results of this study, the risk of pregnancy-associated relapse does not need to be considered.
Carbonyl J Acid Derivatives Block Protein Priming of Hepadnaviral P Protein and DNA-Dependent DNA Synthesis Activity of Hepadnaviral Nucleocapsids

ABSTRACT Current treatments for chronic hepatitis B are effective in only a fraction of patients. All approved directly antiviral agents are nucleos(t)ide analogs (NAs) that target the DNA polymerase activity of the hepatitis B virus (HBV) P protein; resistance and cross-resistance may limit their long-term applicability. P protein is an unusual reverse transcriptase that initiates reverse transcription by protein priming, by which a Tyr residue in the unique terminal protein domain acts as an acceptor of the first DNA nucleotide. Priming requires P protein binding to the ε stem-loop on the pregenomic RNA (pgRNA) template. This interaction also mediates pgRNA encapsidation and thus provides a particularly attractive target for intervention. Exploiting in vitro priming systems available for duck HBV (DHBV) but not HBV, we demonstrate that naphthylureas of the carbonyl J acid family, in particular KM-1, potently suppress protein priming by targeting P protein and interfering with the formation of P-DHBV ε initiation complexes. Quantitative evaluation revealed a significant increase in complex stability during maturation, yet even primed complexes remained sensitive to KM-1 concentrations below 10 μM. Furthermore, KM-1 inhibited the DNA-dependent DNA polymerase activity of both DHBV and HBV nucleocapsids, including from a lamivudine-resistant variant, directly demonstrating the sensitivity of human HBV to the compound. Activity against viral replication in cells was low, likely due to low intracellular availability. KM-1 is thus not yet a drug candidate, but its distinct mechanism of action suggests that it is a highly useful lead for developing improved, therapeutically applicable derivatives.
Economic evaluation of integrated care: an introduction

Abstract Background Integrated care has emerged in a variety of forms in industrialised countries during the past decade. It is generally assumed that these new arrangements result in increased effectiveness and quality of care, while being cost-effective or even cost-saving at the same time. However, systematic evaluation, including an evaluation of the relative costs and benefits of these arrangements, has largely been lacking. Objectives To stimulate fruitful dialogue and debate about the need for economic evaluation in integrated care, and to outline possibilities for undertaking economic appraisal studies in this relatively new field. Theory Key concepts, including e.g. scarcity and opportunity costs, are introduced, followed by a brief overview of the most common methods used in economic evaluation of health care programmes. Then a number of issues that seem particularly relevant for economic evaluation of integrated care arrangements are addressed in more detail, illustrated with examples from the literature. Conclusion and discussion There is a need for well-designed economic evaluation studies of integrated care arrangements, in particular in order to support decision making on the long-term financing of these programmes. Although relatively few studies have been done to date, the field is challenging from a methodological point of view, offering analysts a wealth of opportunities. Guidance to realise these opportunities is provided by the general principles for economic evaluation, which can be tailored to the requirements of this particular field.
Complementary and alternative medicine in back pain utilization report.

OBJECTIVES This systematic review was undertaken to evaluate which complementary and alternative medicine (CAM) therapies are being used for persons with back pain in the United States. DATA SOURCES MEDLINE, CINHAHL, EMBASE, and Cochrane Central, and a variety of CAM specific databases were searched from 1990 to November 2007. A grey literature search was also undertaken, particularly for clinical practice guidelines (CPG) related to CAM. REVIEW METHODS Standard systematic review methodology was employed. Eligibility criteria included English studies of adults with back pain, and a predefined list of CAM therapies. RESULTS A total of 103 publications were evaluated; of these 29 did not present CAM therapy use stratified for back pain. There were a total of 65 utilization studies, 43 of which were American. Four publications evaluated the concurrent use of four or more CAM therapies and these suggest that chiropractic/manipulation is the most frequently used modality followed by massage and acupuncture. A limited number of publications evaluated utilization rates within multiple regions of the back and show that CAM was used least for treating the thoracic spine and most for the low back. However, rates of the use of massage were similar for neck and lower back regions. Concurrent use of different CAM or conventional therapies was not well reported. From 11 eligible CPG, only one (for electro-acupuncture) provided recommendations for frequency of use for low back pain of all acuity levels. Eighteen cost publications were reviewed and all but one publication (cost-effectiveness) were cost identification studies. There is limited information on the impact of insurance coverage on costs and utilization specific to back pain. CONCLUSIONS There are a few studies evaluating the relative utilization of various CAM therapies for back pain. For those studies evaluating utilization of individual CAM therapies, the specific characteristics of the therapy, the providers, and the clinical presentation of the back pain patients were not adequately detailed; nor was the overlap with other CAM or conventional treatments.
Distinct Chromatin Configurations Regulate the Initiation and the Maintenance of hGH Gene Expression

ABSTRACT For many mammalian genes, initiation of transcription during embryonic development must be subsequently sustained over extensive periods of adult life. It remains unclear whether maintenance of gene expression reflects the same set of pathways as are involved in initial gene activation. The human pituitary growth hormone (hGH-N) locus is activated in the differentiating somatotrope midway through embryogenesis by a multicomponent locus control region (LCR). DNase I-hypersensitive site I (HSI) of the LCR is essential to full developmental activation of the hGH-N locus. Here we demonstrate that conditional deletion of HSI from the active hGH locus in the adult pituitary effectively silences hGH-N expression. Analyses of chromatin structure and locus positioning demonstrate that a specific subset of the HSI functions active in the embryo retain their HSI dependence in the adult pituitary. These functions sustain engagement of the hGH locus with polymerase II (Pol II) factories, histone acetylation at the hGH-N promoter, and looping of the LCR to its target promoter. These data reveal that HSI is essential to both the maintenance and the initiation phases of gene expression. These observations contribute to our mechanistic understanding of how stable patterns of mammalian gene expression are established in a terminally differentiated cell.
Gender comparisons of function-related dependence pain and insecurity in geriatric rehabilitation.

OBJECTIVE To evaluate possible gender differences regarding the effect of intervention in geriatric rehabilitation, expressed in terms of change in function-related dependence, pain and insecurity. DESIGN Comparative study. PARTICIPANTS A total of 110 women and 44 men undergoing geriatric rehabilitation. METHODS Performance-based assessments with use of the General Motor Function assessment scale. Non-parametric statistics were mainly used. RESULTS The women showed higher degrees of function-related dependence, pain and insecurity on admission than the men. Both women and men displayed significant improvement in all 3 variables during the rehabilitation period. However, the positive changes regarding pain and insecurity were according to the analyses of systematic group changes, at a low degree among the men, probably because of the low levels on admission. Gender comparisons of proportions with positive intervention outcome indicated that a significantly larger proportion of the women showed a positive treatment effect after intervention, with a difference in recovery of 19% in dependence, 23% in pain and 33% in insecurity (p<0.05). CONCLUSIONS Gender differences in disability, with higher degrees of function-related dependence, pain and insecurity among women on admission for geriatric rehabilitation, can be diminished during the rehabilitation period. These promising results may have relevance for the public health of the elderly population.
Linear Local Models for Monocular Reconstruction of Deformable Surfaces

Recovering the 3D shape of a nonrigid surface from a single viewpoint is known to be both ambiguous and challenging. Resolving the ambiguities typically requires prior knowledge about the most likely deformations that the surface may undergo. It often takes the form of a global deformation model that can be learned from training data. While effective, this approach suffers from the fact that a new model must be learned for each new surface, which means acquiring new training data, and may be impractical. In this paper, we replace the global models by linear local models for surface patches, which can be assembled to represent arbitrary surface shapes as long as they are made of the same material. Not only do they eliminate the need to retrain the model for different surface shapes, they also let us formulate 3D shape reconstruction from correspondences as either an algebraic problem that can be solved in closed form or a convex optimization problem whose solution can be found using standard numerical packages. We present quantitative results on synthetic data, as well as qualitative results on real images.
Experiment mimics fishing on parrotfish: insights on coral reef recovery and alternative attractors

Dominance shifts in ecosystems can occur rapidly, resulting in alternative stable states. While some coral reef ecosystems shift and recover relatively quickly, others recover slowly or not at all over periods of centuries. We explore the role of large (fishing-susceptible) parrotfish in triggering algal phase shifts as alternative attractors that may lock reefs into coral-depleted alternative stable states. We designed an experiment to modestly reduce herbivory only from large parrotfish in the immediate vicinity of experimental coral settlement nursery habitats. We used vertical pegs ('parrotfish deterrents' or PDs) around coral settlement plates on 2 Belizean fore reefs. Time-lapse videos and a year's accumulation of bite-marks on plates confirmed that only herbivory from large parrotfish declined significantly due to PDs. Patches of macroalgae developed around PDs reducing coral recruitment in this treatment only. Two dominant reefdwelling coral genera (Porites and Agaricia) recruited to our settlement plates. The fast-growing, high-light requiring, reef-building coral Porites was more negatively affected by phase shifts; this coral failed to recruit at and above mid-levels of algal abundance. We illustrate the direct roles eco logical processes such as herbivory from large parrotfish play in regulating algal abundance, which in turn reduces the recruitment potential of reefs and thus the ecosystem's capacity to recover. Combining our empirical results with an individually-based ecological simulation model, we determined that these processes cascade to drive alternative states and create a 'hysteresis' effect delaying or preventing recovery of the coral reef ecosystem.
Fast list Viterbi decoding and application for source-channel coding of images

A list Viterbi algorithm (LVA) finds the n best paths in a trellis. We propose a new implementation of the tree-trellis LVA. Instead of storing all paths in a single sorted list, we show that it is more efficient to use several lists, where all paths of the same list have the same metric. For an integer metric, both the time and space complexity of our implementation are linear in n. Experimental results show that our implementation is much faster than all previous LVAs. This allows us to consider a large number of paths in acceptable time, which significantly improves the performance of a popular progressive source-channel coding system that protects embedded data with a concatenation of an outer error detecting code and an inner error correcting convolutional code.
Enabling and measuring electronic customer relationship management readiness

This work provides a comprehensive customer-focused evaluation framework that businesses can use to assess their electronic customer relationship management (e-CRM) readiness. The framework is intended to provide a big picture of the overall composition of e-CRM, to facilitate gap analysis, and to support a monitoring and feedback process. Knowledge management, trust, and technology are identified as key enablers of e-CRM. Finally, we propose weighting and rating scales to aid in assessing customer relationship management readiness, and provide examples of their use.
SSCC TD: A Serial and Simultaneous Configural-Cue Compound Stimuli Representation for Temporal Difference Learning

This paper presents a novel representational framework for the Temporal Difference (TD) model of learning, which allows the computation of configural stimuli – cumulative compounds of stimuli that generate perceptual emergents known as configural cues. This Simultaneous and Serial Configural-cue Compound Stimuli Temporal Difference model (SSCC TD) can model both simultaneous and serial stimulus compounds, as well as compounds including the experimental context. This modification significantly broadens the range of phenomena which the TD paradigm can explain, and allows it to predict phenomena which traditional TD solutions cannot, particularly effects that depend on compound stimuli functioning as a whole, such as pattern learning and serial structural discriminations, and context-related effects.
Reassortment between avian H5N1 and human H3N2 influenza viruses creates hybrid viruses with substantial virulence

The spread of avian H5N1 influenza viruses around the globe has become a worldwide public health concern. To evaluate the pathogenic potential of reassortant viruses between currently cocirculating avian H5N1 and human H3N2 influenza viruses, we generated all the 254 combinations of reassortant viruses between A/chicken/South Kalimantan/UT6028/06 (SK06, H5N1) and A/Tokyo/Ut-Sk-1/07 (Tok07, H3N2) influenza viruses by reverse genetics. We found that the presence of Tok07 PB2 protein in the ribonucleoprotein (RNP) complex allowed efficient viral RNA transcription in a minigenome assay and that RNP activity played an essential role in the viability and replicative ability of the reassortant viruses. When the pathogenicity of 75 reassortant H5 viruses was tested in mice, 22 were more pathogenic than the parental SK06 virus, and three were extremely virulent. Strikingly, all 22 of these viruses obtained their PB2 segment from Tok07 virus. Further analysis showed that Tok07 PB1 alone lacked the ability to enhance the pathogenicity of the reassortant viruses but could do so by cooperating with Tok07 PB2. Our data demonstrate that reassortment between an avian H5N1 virus with low pathogenicity in mice and a human virus could result in highly pathogenic viruses and that the human virus PB2 segment functions in the background of an avian H5N1 virus, enhancing its virulence. Our findings highlight the importance of surveillance programs to monitor the emergence of human H5 reassortant viruses, especially those containing a PB2 segment of human origin.
A qualitative study

Objective: Very little research has been conducted that examines men, sport, masculinities, and disability in the context of health. Readdressing this absence, this paper examines the health narratives told by spinal injured men and the work narratives do on, in, and for them. Methods: In-depth life history interviews and fieldwork observations with men (n=17) who sustained a spinal injury through playing sport and are now disabled were conducted. Qualitative data were analyzed using a dialogical narrative analysis. Results: Stories told about health characterized a style of embodied actions choices that anticipated a certain type of narrative, that is, an emergent narrative. The men’s narrative habitus, fashioned through the process rehabilitation, predisposed them to be interpellated to care about health. To uphold hegemonic masculinities the men also did not care too much about health. The analysis also reveals the work narratives do on, in, and for health behavior, masculine identities, resilience, leisure time physical activity, and body-self relationships. Implications for health promotion work are highlighted. Conclusions: The paper advances knowledge by revealing the emergent narrative of health. It reveals too for the first time the way certain contexts and masculine identities create a new subject of health that cares about doing health work, but not too much. Building on the theoretical knowledge advanced here, this paper contributes to practical understandings of men’s health and disability by highlighting the potential of narrative for changing human lives and behavior.
A New Reference Frame Recompression Algorithm and Its VLSI Architecture for UHDTV Video Codec

Video encoders and decoders for HEVC-like compression standards require huge external memory bandwidth, which occupies a significant portion of the codec power consumption. To reduce the memory bandwidth, this paper presents a new lossless reference frame recompression algorithm along with a high-throughput hardware architecture. Firstly, hybrid spatial -domain prediction is proposed to combine the merits of DPCM scanning and averaging. The prediction is then enhanced with multiple modes to accommodate various image characteristics. Finally, efficient residual regrouping based on semi-fixed-length (SFL) coding is used to improve the compression performance. Compared to no compression, the proposed scheme can reduce data traffic by an average of 57.6% with no image quality degradation. The average compression ratio is 2.49, an improvement of at least 12.2-13.2%, relative to the state-of-the-art algorithms. By applying a reordered two-step architecture and the two optimizations, residual reuse and simplified coding mode decision, the hardware cost is similar to that of previous reference frame recompression architectures. The computational complexity increase caused by multi-mode prediction affects the HW cost slightly. This work can be implemented with 45.1 k gates for the compressor and 34.5 k gates for the decompressor at 300 MHz, enough to support a 3840 ×2160@60fps video encoder and decoder.