Miracle-dz/UniFAR-FTUs huggingface dataset:
Inflammatory bowel disease aggregation in Utah kindreds

Background: The observed heritability of inflammatory bowel disease (IBD) is incompletely explained by known genetic risk factors. Kindred‐specific genetic variants that cause IBD may be a source of “missing heritability. ” Given that they have been previously difficult to identify, we sought to identify high‐risk IBD kindreds. Methods: We used a large population‐based database—the Utah Population Database (UPDB)—which contains genealogical and healthcare data to characterize the risk of Crohn's disease (CD), ulcerative colitis (UC), and IBD in kindreds. We identified CD and UC cases using ICD‐9 codes. We calculated the adjusted relative risk to relatives of affected individuals. We calculated the familial standardized incidence ratio (FSIR) to quantify the kindred‐specific disease risk. Results: In all, 3601 CD cases and 3976 UC cases met inclusion criteria. A total of 655 CD kindreds and 615 UC kindreds had a statistical excess of disease. Risk of disease varied among kindreds, with some kindreds demonstrating ≈20‐fold elevated risk. For CD, UC, and IBD, relative risks were significantly elevated for first‐ and second‐degree relatives and first cousins. The adjusted population attributable risks for familial CD, UC, and IBD were 0.20 (95% confidence interval [CI]: 0.17–0.23); 0.17 (0.14–0.21); and 0.19 (0.17–0.22), respectively. Conclusions: We identified multiple kindreds with a statistical excess of CD, UC, and IBD, and validated the UPDB as a resource for family studies in IBD. Given the need for novel genetic mapping strategies to explain the apparent missing heritability in IBD, further studies of these high‐risk kindreds is justified. (Inflamm Bowel Dis 2011)
Computer-aided detection in screening CT for pulmonary nodules.

OBJECTIVE Our objective was to evaluate the performance of a computer-aided detection (CAD) system for pulmonary nodule detection using low-dose screening CT images. MATERIALS AND METHODS One hundred fifty consecutive low-dose screening CT examinations were independently evaluated by a radiologist and a CAD pulmonary nodule detection system (R2 Technology) designed to identify nodules larger than 4 mm in maximum long-axis diameter. All discrepancies between the two techniques were reviewed by one of another two radiologists working in consensus with the initial interpreting radiologist, and a "true" nodule count was determined. Detected nodules were classified by size, density, and location. The performance of the initial radiologist and the CAD system were compared. RESULTS The radiologist detected 518 nodules and the CAD system, 934 nodules. Of the 1,106 separate nodules detected using the two techniques, 628 were classified as true nodules on consensus review. Of the true nodules present, the radiologist detected 518 (82%) of 628 nodules and the CAD, 456 (73%) of 628 nodules. All 518 radiologist-detected nodules were true nodules, and 456 (49%) of 934 of CAD-detected nodules were true nodules. The radiologist missed 110 true nodules that were only detected by CAD. In six patients, these were the only nodules detected in the examination, changing the imaging follow-up protocol. CAD identified 478 lesions that on consensus review were false-positive nodules, a rate of 3.19 (478/150) per patient. CONCLUSION CAD detected 72.6% of true nodules and detected nodules in six (4%) patients not identified by radiologists, changing the imaging follow-up protocol of these subjects. In this study, the combined review of low-dose CT scans by both the radiologist and CAD was necessary to identify all nodules.
Cholesterol-fed and casein-fed rabbit models of atherosclerosis. Part 1: Differing lesion area and volume despite equal plasma cholesterol levels.

One-month-old male New Zealand White rabbits were fed either a cholesterol-free casein diet (CAS; n = 10); low-level cholesterol-supplemented (0.125% to 0.5% by weight) chow (CH; n = 10); or standard laboratory rabbit chow (n = 3) for 24 weeks, during which total plasma cholesterol (TPC) levels were matched for the two experimental groups (TPCCAS = 475 +/- 39 mg/dL; TPCCH = 515 +/- 70 mg/dL). The percentage of cholesterol partitioned into each of the lipoprotein fractions except high-density lipoprotein (HDL) was significantly different for the experimental groups: casein-fed rabbits had a primarily low-density lipoprotein (LDL) hypercholesterolemia while cholesterol-fed rabbits had approximately equal levels of very-low-density lipoprotein (VLDL), intermediate-density lipoprotein (IDL), and LDL cholesterol. Despite matched TPC, lesions in CH animals covered twice the luminal surface area (as detected by oil red O staining; P < .05) and had three times the total volume compared with lesions in the CAS group (P < .05). Lesion volume was positively correlated with TPC and IDL and LDL cholesterol for the CAS group and with TPC and IDL cholesterol for the CH group. When the experimental groups were combined, TPC and VLDL and IDL cholesterol were positively correlated with the lesion volume. Probability of occurrence maps revealed, however, that both groups were virtually identical with respect to the topographic distribution of lesions in the thoracic and abdominal aortas. The data suggested that the differential partitioning of cholesterol into the lipoprotein fractions seen in CAS and CH rabbits influenced lesion area and volume but not topographic distribution.
Flexible and energy-efficient duty cycling in wireless networks with MacZ

In wireless networks formed of battery-powered nodes, energy consumption is a major concern. On the communication side, energy can be saved by switching transceivers to idle or power-down mode when not needed. To this end, duty cycling protocols located at MAC level have been devised. These protocols have in common that they define modified CSMA/CA schemes, and that they assume the availability of some time synchronization mechanism. This strongly limits their potential to reduce energy consumption, as well as their flexibility regarding activity phases. In this paper, we propose a more flexible and energy-efficient solution for duty cycling, which is based on our experimental wireless MAC protocol MacZ. Flexibility is strengthened by the possibility to define weakly periodic activity periods. Energy-efficiency is improved by the possibility to reserve and use exclusive transmission slots, thereby switching transceivers to active mode only when needed. Both measures are supported by an underlying protocol for accurate, deterministic tick and time synchronization. We assess our solution and compare it to a well-known duty cycling protocol based on real-life scenarios.
CLINICAL SIGNIFICANCE OF PROTEIN BINDING OF THE PENICILLINS

The clinical significance of serum protein binding of penicillins has not been clearly established by trial in patients. Furthermore, it is difficult to conceive how a properly conducted comparative dose-response curve study can be constructed in view of ethical considerations inherent in the management of seriously ill patients. For this reason, indirect means of obtaining evidence of antimicrobial activity and distribution of active drug in tissues must be relied on for guidance. Useful information required in comparing drugs with similar mode of action include 1 ) relative antimicrobial potency, 2 ) extent of serum binding, 3 ) relative rate of gastrointestinal absorption, 4) tissue distribution, 5 ) rate of removal by liver, kidneys and other organs, and 6) rate of inactivation. No one factor, considered alone, is sufficient to judge potential value in infection (Kunin, 1964). The phenomenon of serum binding has been amply reviewed in the general pharmacologic literature (Goldstein, 1949; Thorp, 1964; Gillette, 1965) and for the penicillins by Verwey (1966) and Rolinson (1967). This literature may be summarized as follows: Binding of small molecules to serum proteins is a normal physiologic process which solubilizes and sequesters metabolites and hormones and permits their slow release to meet tissue requirements. It may also be considered as a defense mechanism which retains potentially toxic substances in an inactive form until their disposal by the liver or kidneys. Albumin is the best known of the binding proteins, because of the wide variety of substances that bind to it. Normal metabolites that bind to albumin include such diverse substances as fatty acids, bilirubin, calcium and various hormones. Transcortin, transferrin, thyroxinbinding globulins and ceruloplasmin are more specialized serum proteins that selectively bind cortisol, iron, thyroxin and copper, respectively. This reversible form of binding is not adequate for induction of antibody formation. In penicillin allergy, for example, a rearrangement product of the penicillin molecule binds irreversibly to a serum protein to form an antigen. Binding by albumin should be viqwed as a dynamic process in which a constant proportion of drug exists in the unbound or free state. This is shown in the following equation:
EFFECTS OF INITIAL RAT CAPTURES ON SUBSEQUENT CAPTURE SUCCESS OF TRAPS

Author(s): Tobin, Mark E. ; Sugihara, Robert T. ; Engeman, Richard M. | Abstract: Trapping records from studies conducted in Hawaiian sugarcane fields were analyzed to determine the effects of rat captures on subsequent capture success of Rattus norvegicus, R. rattus, and R. exulans. Traps that captured rats were subsequently more likely to capture another rat of the same species. We detected no differences in trap responses of males and females, nor did we observe any evidence that capture success of Polynesian rats and roof rats was affected by previous captures of Norway rats. This increased trap success may have been due to residual trap odors, or to greater success of traps set in optimal locations. Researchers should exercise caution in interpreting trapping results, and take precautions to eliminate residual trap odors due to previous captures. A better understanding of the effects of congeneric odors on the trapability of rats could lead to the development of more attractive and selective bait formulations, improved trapping techniques, and better interpretation of research results.
Beech cupules as keystone structures for soil fauna

Facilitative or positive interactions are ubiquitous in nature and play a fundamental role in the configuration of ecological communities. In particular, habitat modification and niche construction, in which one organism locally modifies abiotic conditions and favours other organisms by buffering the effects of adverse environmental factors, are among the most relevant facilitative interactions. In line with this, ‘keystone structures’, which provide resources, refuge, or advantageous services decisive for other species, may allow the coexistence of various species and thus considerably contribute to diversity maintenance. Beech cupules are woody husks harbouring beech fruits that remain in the forest soil for relatively long periods of time. In this study, we explored the potential role of these cupules in the distribution and maintenance of the soil fauna inhabiting the leaf litter layer. We experimentally manipulated cupule availability and soil moisture in the field to determine if such structures are limiting and can provide moist shelter to soil animals during drought periods, contributing to minimize desiccation risks. We measured invertebrate abundances inside relative to outside the cupules, total abundances in the leaf litter and animal body sizes, in both dry and wet experimental plots. We found that these structures are preferentially used by the most abundant groups of smaller soil animals—springtails, mites and enchytraeids—during droughts. Moreover, beech cupules can be limiting, as an increase in use was found with higher cupule densities, and are important resources for many small soil invertebrates, driving the spatial structure of the soil community and promoting higher densities in the leaf litter, probably through an increase in habitat heterogeneity. We propose that fruit woody structures should be considered ‘keystone structures’ that contribute to soil community maintenance. Therefore, beech trees may indirectly facilitate soil fauna activities through their decaying fruit husks, hence acting as ecosystem engineers.
Influenza Vaccination and Associated Factors among Korean Cancer Survivors : A Cross-Sectional Analysis of the Fourth & Fifth Korea National Health and Nutrition Examination Surveys

Influenza vaccination is important for cancer survivors, a population with impaired immunity. This study was designed to assess influenza vaccination patterns among Korean cancer survivors. In this cross-sectional analysis, data were obtained from standardized questionnaires from 943 cancer survivors and 41,233 non-cancer survivors who participated in the Fourth and Fifth Korea National Health and Nutrition Examination Surveys (2007-2011). We identified the adjusted influenza vaccination rates and assessed factors associated with influenza vaccination using multivariate logistic regression. Cancer survivors tended to have a higher adjusted influenza vaccination rate than the general population. The rates for influenza vaccination in specific cancer types such as stomach, hepatic, colon, and lung cancers were significantly higher than non-cancer survivors. Among all cancer survivors, those with chronic diseases, elderly subjects, and rural dwellers were more likely to receive influenza vaccination; those with cervical cancer were less likely to receive influenza vaccination. Cancer survivors were more likely to receive influenza vaccinations than non-cancer survivors, but this was not true for particular groups, especially younger cancer survivors. Cancer survivors represent a sharply growing population; therefore, immunization against influenza among cancer survivors should be concerned as their significant preventative healthcare services. Graphical Abstract
Downregulation of the Drosophila Immune Response by Peptidoglycan-Recognition Proteins SC1 and SC2

Peptidoglycan-recognition proteins (PGRPs) are evolutionarily conserved molecules that are structurally related to bacterial amidases. Several Drosophila PGRPs have lost this enzymatic activity and serve as microbe sensors through peptidoglycan recognition. Other PGRP family members, such as Drosophila PGRP-SC1 or mammalian PGRP-L, have conserved the amidase function and are able to cleave peptidoglycan in vitro. However, the contribution of these amidase PGRPs to host defense in vivo has remained elusive so far. Using an RNA-interference approach, we addressed the function of two PGRPs with amidase activity in the Drosophila immune response. We observed that PGRP-SC1/2–depleted flies present a specific over-activation of the IMD (immune deficiency) signaling pathway after bacterial challenge. Our data suggest that these proteins act in the larval gut to prevent activation of this pathway following bacterial ingestion. We further show that a strict control of IMD-pathway activation is essential to prevent bacteria-induced developmental defects and larval death.
The association between imitation recognition and socio-communicative competencies in chimpanzees (Pan troglodytes)

Imitation recognition provides a viable platform from which advanced social cognitive skills may develop. Despite evidence that non-human primates are capable of imitation recognition, how this ability is related to social cognitive skills is unknown. In this study, we compared imitation recognition performance, as indicated by the production of testing behaviors, with performance on a series of tasks that assess social and physical cognition in 49 chimpanzees. In the initial analyses, we found that males were more responsive than females to being imitated and engaged in significantly greater behavior repetitions and testing sequences. We also found that subjects who consistently recognized being imitated performed better on social but not physical cognitive tasks, as measured by the Primate Cognitive Test Battery. These findings suggest that the neural constructs underlying imitation recognition are likely associated with or among those underlying more general socio-communicative abilities in chimpanzees. Implications regarding how imitation recognition may facilitate other social cognitive processes, such as mirror self-recognition, are discussed.
Social Ideology and Taxes in a Differentiated Candidates Framework

How does ideological polarization on non-economic matters influence the size of government? We analyze this question using a differentiated candidates framework: Two office-motivated candidates differ in their (fixed) ideological position and their production function for public goods, and choose which tax rate to propose. We provide conditions under which a unique equilibrium exists. In equilibrium, candidates propose different tax rates, and the extent of economic differentiation is influenced by the distribution and intensity of non-economic preferences in the electorate. In turn, the extent of economic differentiation influences whether parties divide the electorate primarily along economic or social lines.
22 . Enceladus : An Active Cryovolcanic Satellite

Enceladus is one of the most remarkable satellites in the solar system, as revealed by Cassini’s detection of active plumes erupting from warm fractures near its south pole. This discovery makes Enceladus the only icy satellite known to exhibit ongoing internally-driven geological activity. The activity is presumably powered by tidal heating maintained by Enceladus’ 2:1 mean-motion resonance with Dione, but many questions remain. For instance, it appears difficult or impossible to maintain the currently observed radiated power (probably at least 6 GW) in steady state. It is also not clear how Enceladus first entered its current self-maintaining warm and dissipative stateinitial heating from non-tidal sources is probably required. There are also many unanswered questions about Enceladus’ interior. The silicate fraction inferred from its density of 1.68 g cm is probably differentiated into a core, though we have not direct evidence for differentiation. Above the core there is probably a global or regional water layer, inferred from several models of tidal heating, and an ice shell thick enough to support the ~1 km amplitude topography seen on Enceladus. It is possible that dissipation is largely localized beneath the south polar region. Enceladus’ surface geology, ranging from moderately cratered terrain to the virtually crater-free active south polar region, is highly diverse, tectonically complex, and remarkably symmetrical about the rotation axis and the direction to Saturn. South polar activity is concentrated along the four “tiger stripe” fractures, which radiate heat at temperatures up to at least 167 K and are the source of multiple plumes ejecting ~200 kg s of H2O vapor along with significant N2 (or C2H4), CO2, CH4, NH3, and higher-mass hydrocarbons. The escaping gas maintains Saturn’s neutral gas torus, and the plumes also eject a large number of micron-sized H2O ice grains that populate Saturn’s E-ring. The mechanism that powers the plumes is not well understood, and whether liquid water is involved is a subject of active debate. Enceladus provides perhaps the most promising potential habitat for life in the outer solar system, and the active plumes allow the unique opportunity for direct
When Guardians Matter Most: Exploring the Conditions Under Which Electoral Management Body Institutional Design Affects Election Integrity

Abstract Problems with election fraud and election integrity are of increasing interest in both established and transitional democracies. In many transitional democracies, independent electoral management bodies (EMBs) have been championed as a key institutional reform measure to successfully strengthen election integrity. However, empirical findings regarding the impact of EMB institutional design on election integrity are mixed. While regional studies have found a positive impact of independent EMBs on election integrity in Latin America and Africa, global comparative studies appear to show that EMB institutional design is either negatively, or only very weakly related to election integrity. In this paper, we examine the effects of EMB institutional design on election integrity using the new Varieties of Democracy dataset and data from the International IDEA. We find that the mixed findings on EMB institutional design are due to the differences between transitional and established democracies on the one hand, and regimes with low and high quality of government on the other. The paper concludes with a reflection on results and a discussion of implications of these findings for the debate on electoral reform in Ireland.
Transient solutions for one-dimensional problems with strain softening

Closed-form solutions are presented for the transient response of rods in which strain softening occurs and the stress-strain laws exhibit nonvanishing stresses after the strain-softening regime. It is found that the appearance of any strain softening results in an infinite strain rate if the material is inviscid. For a stress-strain law with a monotonically decreasing stress the strains are infinite also. If the stress increases after the strain-softening portion, the strains remain finite and the strain-softening point moves through the rod.
Multiuser Diversity - Multiplexing Tradeoff in MIMO Broadcast Channels with Limited Feedback

We consider joint scheduling and beamforming in a broadcast channel with multiple antennas at the transmitter and a single antenna at the mobile receiver. Perfect channel knowledge is assumed to be available at the receiver while the transmitter is provided with partial channel state information (CSIT) through a limited rate feedback channel. Each user feeds back quantized information regarding the channel vector direction (from a codebook) and a quantized (scalar) channel quality indicator. We identify the tradeoff between multiuser diversity and spatial multiplexing gain given a limited amount of feedback bits. Scaling laws of the above parameters are derived in order to achieve a target rate performance. Our results reveal useful design guidelines for the split of feedback bits for channel quantization and channel quality.