Miracle-dz/UniFAR-FTUs huggingface dataset:
Psoriatic arthritis epidemiology

Psoriatic arthritis (PsA) is a chronic inﬂammatory arthritis that can cause severe joint deformities and disability. The expected prevalence of inﬂammatory arthritis among patients with psoriasis has varied from 7% to 40%. Early diagnosis and treatment of PsA is recommended to discourage from disease associated disability and breakdown of work place efficiency. The epidemiological studies are quite limited because of small and selective study populations, limited follow-up, and absence of validated PsA classification criteria. The epidemiology of psoriatic arthritis has been reviewed in this manuscript by summarizing incidence and prevalence estimates up to date and epidemiological studies indicating the degree of genetic load of PsA. Potential risk factors like demographic features, characteristics of psoriasis lesions and the effect of environmental and hormonal factors in epidemiological spectrum of psoriatic arthritis are analyzed.
Carcinosarcoma of the Stomach: A Case Report

Carcinosarcoma is a rare malignant, biphasic tumor comprised of carcinoma and sarcoma components. In the gastrointestinal tract, carcinosarcoma is most frequently seen in the esophagus and rarely in the stomach. We report a 51-year-old female patient with 2-month-history of epigastric pain and dyspepsia. Endoscopic finding revealed a huge ulcerative lesion that infiltrated from the antrum to the mid-body. An endoscopically taken biopsy revealed poorly differentiated malignant round cell neoplasm. After the palliative subtotal gastrectomy, immunohistochemical studies showed two positive reactions for the epithelial marker and mesenchymal marker. Based on the above findings, the patient was diagnosed with gastric carcinosarcoma. The immunohistochemical analysis is a critical method in making an accurate diagnosis of carcinosarcoma.
Memory Impairment in Transgenic Alzheimer Mice Requires Cellular Prion Protein

Soluble oligomers of the amyloid-β (Aβ) peptide are thought to play a key role in the pathophysiology of Alzheimer's disease (AD). Recently, we reported that synthetic Aβ oligomers bind to cellular prion protein (PrPC) and that this interaction is required for suppression of synaptic plasticity in hippocampal slices by oligomeric Aβ peptide. We hypothesized that PrPC is essential for the ability of brain-derived Aβ to suppress cognitive function. Here, we crossed familial AD transgenes encoding APPswe and PSen1ΔE9 into Prnp−/− mice to examine the necessity of PrPC for AD-related phenotypes. Neither APP expression nor Aβ level is altered by PrPC absence in this transgenic AD model, and astrogliosis is unchanged. However, deletion of PrPC expression rescues 5-HT axonal degeneration, loss of synaptic markers, and early death in APPswe/PSen1ΔE9 transgenic mice. The AD transgenic mice with intact PrPC expression exhibit deficits in spatial learning and memory. Mice lacking PrPC, but containing Aβ plaque derived from APPswe/PSen1ΔE9 transgenes, show no detectable impairment of spatial learning and memory. Thus, deletion of PrPC expression dissociates Aβ accumulation from behavioral impairment in these AD mice, with the cognitive deficits selectively requiring PrPC.
A Taxonomy for Abstract Environments.

AbstractA wide range of problems can be abstractly expressed in terms of two systems inter-acting over time with the second system providing feedback to the ﬂrst on its successin achieving some goal. The agent{environment model in reinforment learning and thecontroller{plant model from control theory are both examples of this framework. Problemswhich can be expressed in terms of this framework include statistical sampling processes,prediction problems, classiﬂcation problems, decision problems, games and function opti-misation problems. While these problem classes are very common and strong relationshipsbetween them are apparent, they are not usually considered in toto . Here we formallydeﬂne many of these common problem classes as environments using the chronological sys-tem formalism. From this we establish the elementary relationships between the problemclasses giving a taxonomy of abstract environments. 1 Agent-Environment Model 1.1 Introduction The agent-environment model is very simple and yet surprisingly general. It consists of twoentities called the
Entropy-driven partitioning of the hierarchical protein space

Motivation: Modern protein sequencing techniques have led to the determination of >50 million protein sequences. ProtoNet is a clustering system that provides a continuous hierarchical agglomerative clustering tree for all proteins. While ProtoNet performs unsupervised classification of all included proteins, finding an optimal level of granularity for the purpose of focusing on protein functional groups remain elusive. Here, we ask whether knowledge-based annotations on protein families can support the automatic unsupervised methods for identifying high-quality protein families. We present a method that yields within the ProtoNet hierarchy an optimal partition of clusters, relative to manual annotation schemes. The method’s principle is to minimize the entropy-derived distance between annotation-based partitions and all available hierarchical partitions. We describe the best front (BF) partition of 2 478 328 proteins from UniRef50. Of 4 929 553 ProtoNet tree clusters, BF based on Pfam annotations contain 26 891 clusters. The high quality of the partition is validated by the close correspondence with the set of clusters that best describe thousands of keywords of Pfam. The BF is shown to be superior to naïve cut in the ProtoNet tree that yields a similar number of clusters. Finally, we used parameters intrinsic to the clustering process to enrich a priori the BF’s clusters. We present the entropy-based method’s benefit in overcoming the unavoidable limitations of nested clusters in ProtoNet. We suggest that this automatic information-based cluster selection can be useful for other large-scale annotation schemes, as well as for systematically testing and comparing putative families derived from alternative clustering methods. Availability and implementation: A catalog of BF clusters for thousands of Pfam keywords is provided at http://protonet.cs. huji.ac.il/bestFront/ Contact: michall@cc.huji.ac.il
Complete Chemical Synthesis , Assembly , and Cloning of a Mycoplasma genitalium Genome

www.sciencemag. org (this information is current as of April 13, 2008 ): The following resources related to this article are available online at http://www.sciencemag. org/cgi/content/full/319/5867/1215 version of this article at: including high-resolution figures, can be found in the online Updated information and services, http://www.sciencemag. org/cgi/content/full/1151721/DC1 can be found at: Supporting Online Material found at: can be related to this article A list of selected additional articles on the Science Web sites http://www.sciencemag. org/cgi/content/full/319/5867/1215#related-content http://www.sciencemag. org/cgi/content/full/319/5867/1215#otherarticles , 16 of which can be accessed for free: cites 29 articles This article http://www.sciencemag. org/cgi/collection/genetics Genetics : subject collections This article appears in the following http://www.sciencemag. org/about/permissions.dtl in whole or in part can be found at: this article permission to reproduce of this article or about obtaining reprints Information about obtaining
IBM System z10 processor cache subsystem microarchitecture

With the introduction of the high-frequency IBM System z10™ processor design, a new, robust cache hierarchy was needed to enable up to 80 of these processors aggregated into a tightly coupled symmetric multiprocessor (SMP) system to reach their performance potential. Typically, each time the processor frequency increases by a significant factor, as did the z10™ processor over the predecessor IBM System z9® processor, the access time of data, as measured by the number of processor cycles beyond the level 1 cache on an identical processor cache subsystem, would increase proportionally as well because the flight time on the chip interconnects across multiple hardware packaging levels has stayed relatively constant in nanoseconds. To address the latency scaling problem and the increased demand of the larger 80-way SMP size, the z10 processor cache subsystem introduces new innovative concepts and solutions.
NK Cells and Other Innate Lymphoid Cells in Hematopoietic Stem Cell Transplantation

Natural killer (NK) cells play a major role in the T-cell depleted haploidentical hematopoietic stem cell transplantation (haplo-HSCT) to cure high-risk leukemias. NK cells belong to the expanding family of innate lymphoid cells (ILCs). At variance with NK cells, the other ILC populations (ILC1/2/3) are non-cytolytic, while they secrete different patterns of cytokines. ILCs provide host defenses against viruses, bacteria, and parasites, drive lymphoid organogenesis, and contribute to tissue remodeling. In haplo-HSCT patients, the extensive T-cell depletion is required to prevent graft-versus-host disease (GvHD) but increases risks of developing a wide range of life-threatening infections. However, these patients may rely on innate defenses that are reconstituted more rapidly than the adaptive ones. In this context, ILCs may represent important players in the early phases following transplantation. They may contribute to tissue homeostasis/remodeling and lymphoid tissue reconstitution. While the reconstitution of NK cell repertoire and its role in haplo-HSCT have been largely investigated, little information is available on ILCs. Of note, CD34+ cells isolated from different sources of HSC may differentiate in vitro toward various ILC subsets. Moreover, cytokines released from leukemia blasts (e.g., IL-1β) may alter the proportions of NK cells and ILC3, suggesting the possibility that leukemia may skew the ILC repertoire. Further studies are required to define the timing of ILC development and their potential protective role after HSCT.
ISOFT at QALD-4: Semantic Similarity-based Question Answering System over Linked Data

We present a question answering system over linked data. We use natural language processing tools to extract slots and SPARQL templates from the question. Then, we use semantic similarity to map a natural language question to a SPARQL query. We combine important words to avoid loss of meaning, and compare combined words with uniform resource identifiers (URIs) from a knowledgebase (KB). This process is more powerful than comparing each word individually. Using our method, the problem of mapping a phrase of a user question to URIs from a KB can be more easily solved than without our method; this method improves the F-measure of the system.
Linear Growth and Child Development in Low- and Middle-Income Countries: A Meta-Analysis

BACKGROUND AND OBJECTIVE: The initial years of life are critical for physical growth and broader cognitive, motor, and socioemotional development, but the magnitude of the link between these processes remains unclear. Our objective was to produce quantitative estimates of the cross-sectional and prospective association of height-for-age z score (HAZ) with child development. METHODS: Observational studies conducted in low- and middle-income countries (LMICs) presenting data on the relationship of linear growth with any measure of child development among children <12 years of age were identified from a systematic search of PubMed, Embase, and PsycINFO. Two reviewers then extracted these data by using a standardized form. RESULTS: A total of 68 published studies conducted in 29 LMICs were included in the final database. The pooled adjusted standardized mean difference in cross-sectional cognitive ability per unit increase in HAZ for children ≤2 years old was +0.24 (95% confidence interval [CI], 0.14–0.33; I2 = 53%) and +0.09 for children >2 years old (95% CI, 0.05–0.12; I2 = 78%). Prospectively, each unit increase in HAZ for children ≤2 years old was associated with a +0.22-SD increase in cognition at 5 to 11 years after multivariate adjustment (95% CI, 0.17–0.27; I2 = 0%). HAZ was also significantly associated with earlier walking age and better motor scores (P < .05). CONCLUSIONS: Observational evidence suggests a robust positive association between linear growth during the first 2 years of life with cognitive and motor development. Effective interventions that reduce linear growth restriction may improve developmental outcomes; however, integration with environmental, educational, and stimulation interventions may produce larger positive effects.
Submillimeter Array Observations of Infrared Dark Clouds: A Tale of Two Cores

We present high angular resolution submillimeter continuum images and molecular line spectra obtained with the Submillimeter Array toward two massive cores that lie within infrared dark clouds (IRDCs), one actively star-forming (G034.43+00.24 MM1) and the other more quiescent (G028.53–00.25 MM1). The high angular resolution submillimeter continuum image of G034.43+00.24 MM1 reveals a compact (~0.03 pc) and massive (~29 M☉) structure, while the molecular line spectrum shows emission from numerous complex molecules. Such a rich molecular line spectrum from a compact region indicates that G034.43+00.24 MM1 contains a hot molecular core, an early stage in the formation of a high-mass protostar. Moreover, the velocity structure of its 13CO (3-2) emission indicates that this B0 protostar may be surrounded by a rotating circumstellar envelope. In contrast, the submillimeter continuum image of G028.53–00.25 MM1 reveals three compact (≲0.06 pc), massive (9-21 M☉) condensations, but there are no lines detected in its spectrum. We suggest that the core G028.53–00.25 MM1 is in a very early stage in the high-mass star formation process; its size and mass are sufficient to form at least one high-mass star, yet it shows no signs of localized heating. Because the combination of high-velocity line wings with a large IR-to-millimeter bolometric luminosity (~102 L☉) indicates that this core has already begun to form accreting protostars, we speculate that the condensations may be in the early phase of accretion and may eventually become high-mass protostars. Therefore, we have found the possible existence of two high-mass star-forming cores: one in a very early phase of star formation and one in the later hot-core phase. Together, the properties of these two cores support the idea that the earliest stages of high-mass star formation occur within IRDCs.
Local Symmetry Detection in Natural Images Using a Particle Filtering Approach

In this paper, we propose an algorithm to detect smooth local symmetries and contours of ribbon-like objects in natural images. The detection is formulated as a spatial tracking task using a particle filtering approach, extracting one part of a structure at a time. Using an adaptive local geometric model, the method can detect straight reflection symmetries in perfectly symmetrical objects as well as smooth local symmetries in curved elongated objects. In addition, the proposed approach jointly estimates spine and contours, making it possible to generate back ribbon objects. Experiments for local symmetry detection have been conducted on a recent extension of the Berkeley segmentation data sets. We also show that it is possible to retrieve specific geometrical objects using intuitive prior structural information.
Calanoid copepods:linking lower-higher trophic levels by linking lower-higher Reynolds numbers

The copepods are said to be the most abundant multicellular animals on earth, with an estimated species number of 11 500+ (Humes 1994). The most typical form of planktonic copepods in the oceans is the calanoids, which makes up >? Or% of all net-collected zooplankton (e.g. Lalli & Parsons 1993). Why are the calanoids so abundant and successful? A clue to the answer to this question is the size (and the moving speed) of the calanoids, as shown in the life strategies of many animals (e.g. McMahon 1973, Schmidt-Nielsen 1984). The size of ca1anoi.d~ ranges roughly from 0.5 to 5 mm, and lies on the border that separates the aquatic habitats into 2 parallel worlds: the inertial and vlscous worlds (Purcell 1977; Fig. 1 ) . In the inertial world, the combat between prey and predators is primarily a matter of speed in escape and attack (Kerfoot 1978). By contrast, viscosity predominates over speed in the viscous world, where a moving object drags water and a water current drags objects. The inertial and viscous worlds are described by the Reynolds number (Re), which is the dimensionless ratio of inertial and viscous forces as follows:
Time-scale modification of speech using an incremental time-frequency approach with waveform structure compensation

The authors try to identify the primary sources of distortion in a non-recursive time-scale modification (TSM) algorithm which is based on the short-time Fourier transform (STFT). A simpler version of this TSM algorithm is then proposed for processing speech, where incremental estimators eliminate the need for explicit linear time-scaling operations. Also featured in the design is a waveform structure compensation stage to prevent excessive deterioration of the rate-changed output. A polar (i.e., magnitude-phase) synthesis equation is used for increased efficiency. The TSM method is capable of generating high-quality rate-changed speech at a reasonable computational cost. <<ETX>>
Long-Run Cultural Divergence: Evidence from the Neolithic Revolution

This paper investigates the long-run influence of the Neolithic Revolution on contemporary cultural norms as reflected in the dimension of collectivism–individualism. We present a theory of agricultural origins of cultural divergence, where we claim that the advent of farming in a core region was characterized by collectivist values and eventually triggered the out-migration of individualistic farmers towards more and more peripheral areas. This migration pattern caused the initial cultural divergence, which remained persistent over generations. Using detailed data on the date of adoption of Neolithic agriculture among Western regions and countries, the empirical findings show that the regions which adopted agriculture early also value obedience more and feel less in control of their lives. The findings add to the literature by suggesting the possibility of extremely long-lasting norms and beliefs influencing today's socioeconomic outcomes.
Geographical Inequalities and Social and Environmental Risk Factors for Under-Five Mortality in Ghana in 2000 and 2010: Bayesian Spatial Analysis of Census Data

Background Under-five mortality is declining in Ghana and many other countries. Very few studies have measured under-five mortality—and its social and environmental risk factors—at fine spatial resolutions, which is relevant for policy purposes. Our aim was to estimate under-five mortality and its social and environmental risk factors at the district level in Ghana. Methods and Findings We used 10% random samples of Ghana’s 2000 and 2010 National Population and Housing Censuses. We applied indirect demographic methods and a Bayesian spatial model to the information on total number of children ever born and children surviving to estimate under-five mortality (probability of dying by 5 y of age, 5q0) for each of Ghana’s 110 districts. We also used the census data to estimate the distributions of households or persons in each district in terms of fuel used for cooking, sanitation facility, drinking water source, and parental education. Median district 5q0 declined from 99 deaths per 1,000 live births in 2000 to 70 in 2010. The decline ranged from <5% in some northern districts, where 5q0 had been higher in 2000, to >40% in southern districts, where it had been lower in 2000, exacerbating existing inequalities. Primary education increased in men and women, and more households had access to improved water and sanitation and cleaner cooking fuels. Higher use of liquefied petroleum gas for cooking was associated with lower 5q0 in multivariate analysis. Conclusions Under-five mortality has declined in all of Ghana’s districts, but the cross-district inequality in mortality has increased. There is a need for additional data, including on healthcare, and additional environmental and socioeconomic measurements, to understand the reasons for the variations in mortality levels and trends.
Comparing the Similarity of Different Groups of Bacteria to the Human Proteome

Numerous aspects of the relationship between bacteria and human have been investigated. One aspect that has recently received attention is sequence overlap at the proteomic level. However, there has not yet been a study that comprehensively characterizes the level of sequence overlap between bacteria and human, especially as it relates to bacterial characteristics like pathogenicity, G-C content, and proteome size. In this study, we began by performing a general characterization of the range of bacteria-human similarity at the proteomic level, and identified characteristics of the most- and least-similar bacterial species. We then examined the relationship between proteomic similarity and numerous other variables. While pathogens and nonpathogens had comparable similarity to the human proteome, pathogens causing chronic infections were found to be more similar to the human proteome than those causing acute infections. Although no general correspondence between a bacterium’s proteome size and its similarity to the human proteome was noted, no bacteria with small proteomes had high similarity to the human proteome. Finally, we discovered an interesting relationship between similarity and a bacterium’s G-C content. While the relationship between bacteria and human has been studied from many angles, their proteomic similarity still needs to be examined in more detail. This paper sheds further light on this relationship, particularly with respect to immunity and pathogenicity.
The effects of Splenectomy on Lipid Peroxidation and Neuronal Loss in experimental Spinal Cord Ischemia/Reperfusion Injury Deneysel Omurilik İskemi/Reperfüzyon Hasarinda Splenektominin Lipit Peroksidasyonu ve Nöronal Kayip Üzerindeki Etkileri

AIm: The aim of this study is to investigate the effects of prior splenectomy on oxidative stress and neuronal loss following spinal cord ischemia and reperfusion injury. mAterIAl and methOds: Twenty-one Sprague Dawley rats were randomly divided into three groups as sham laparatomy (n=7), spinal cord ischemia/reperfusion (SCIR) injury (n=7) and splenectomy+spinal cord ischemia/reperfusion (SSCIR) injury (n=7). In the latter group, splenectomy was performed 3 days before the SCIR injury. The activity of lipid peroxidation in the spinal cord was assessed by malondialdehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GPx) and catalase (CAT) activities. The difference between the 3 groups was compared using Kruskal-Wallis test. The histological differences were assessed by counting the viable neurons. results: SCIR injury resulted in a decrease of tissue lipid peroxidation activities. There was statistically significance between the three groups (p 0.05). The number of viable neurons was higher in SSCIR group when comparing with SCIR group (p<0.05). COnClusIOn: SCIR injury affects lipid peroxidation in rats. Prior splenectomy does not attenuate lipid peroxidation, but prevents neuronal loss after SCIR injury.