Miracle-dz/UniFAR-FTUs huggingface dataset:
Species of Coccidia (Apicomplexa: Eimeriidae) in Shrews From Alaska, U.S.A., and Northeastern Siberia, Russia, with Description of Two New Species

Fecal samples (n = 636) from 10 species of shrews collected in Alaska (n = 540) and northeastern Siberia (n = 96) were examined for the presence of coccidia (Apicomplexa: Eimeriidae). Five distinct oocyst morphotypes were observed. Three types were consistent with oocysts of previously recognized coccidia species from other shrew hosts. These were Eimeria inyoni, E. vagrantis, and Isospora brevicauda, originally described from the inyo shrew (Sorex tenellus), dusky shrew (S. monticolus), and northern short-tailed shrew (Blarina brevicauda), respectively. We found 5 new host records for E. inyoni, 3 for E. vagrantis, and 3 for I. brevicauda. The 2 additional oocyst morphotypes, both from the tundra shrew (Sorex tundrensis), are putative new species. Sporulated oocysts of Eimeria beringiacea n. sp. are subspheroidal, 17.7 × 15.6 μm (14–24 × 13–20 μm) with a length (L)/width (W) ratio of 1.1 (1.0–1.4); these lack a micropyle (M), an oocyst residuum (OR), and a polar granule (PG). Sporocysts are ellipsoidal, 10.3 × 6.1 μm (7–14 × 4–8 μm), with a L/W ratio of 1.7 (1.3–2.3) and have a Stieda body (SB), Substieda body (SSB), and sporocyst residuum (SR). Oocysts of Eimeria tundraensis n. sp. are spheroidal to subspheroidal, 24.8 × 23.5 μm (23–26 × 22–25 μm), with a L/W ratio of 1.1 (1.0–1.2); these lack a M and OR, but a single PG is present. Sporocysts are elongate ellipsoidal, 15.4 × 8.3 μm (13–17 × 7–9 μm), with a L/W ratio of 1.9 (1.4–2.1) and have a SB, SSB, and SR.
Elizabethkingia anophelis: Molecular Manipulation and Interactions with Mosquito Hosts

ABSTRACT Flavobacteria (members of the family Flavobacteriaceae) dominate the bacterial community in the Anopheles mosquito midgut. One such commensal, Elizabethkingia anophelis, is closely associated with Anopheles mosquitoes through transstadial persistence (i.e., from one life stage to the next); these and other properties favor its development for paratransgenic applications in control of malaria parasite transmission. However, the physiological requirements of E. anophelis have not been investigated, nor has its capacity to perpetuate despite digestion pressure in the gut been quantified. To this end, we first developed techniques for genetic manipulation of E. anophelis, including selectable markers, reporter systems (green fluorescent protein [GFP] and NanoLuc), and transposons that function in E. anophelis. A flavobacterial expression system based on the promoter PompA was integrated into the E. anophelis chromosome and showed strong promoter activity to drive GFP and NanoLuc reporter production. Introduced, GFP-tagged E. anophelis associated with mosquitoes at successive developmental stages and propagated in Anopheles gambiae and Anopheles stephensi but not in Aedes triseriatus mosquitoes. Feeding NanoLuc-tagged cells to A. gambiae and A. stephensi in the larval stage led to infection rates of 71% and 82%, respectively. In contrast, a very low infection rate (3%) was detected in Aedes triseriatus mosquitoes under the same conditions. Of the initial E. anophelis cells provided to larvae, 23%, 71%, and 85% were digested in A. stephensi, A. gambiae, and Aedes triseriatus, respectively, demonstrating that E. anophelis adapted to various mosquito midgut environments differently. Bacterial cell growth increased up to 3-fold when arginine was supplemented in the defined medium. Furthermore, the number of NanoLuc-tagged cells in A. stephensi significantly increased when arginine was added to a sugar diet, showing it to be an important amino acid for E. anophelis. Animal erythrocytes promoted E. anophelis growth in vivo and in vitro, indicating that this bacterium could obtain nutrients by participating in erythrocyte lysis in the mosquito midgut.
Spectral Efficiency of Joint Multiple Cell-Site Processors for Randomly Spread DS-CDMA Systems

A chip-interleaved randomly spread direct-sequence code-division multiple-access (DS-CDMA) scheme is considered, employed in two variants of Wyner's infinite linear cell-array model with flat fading. Focusing on the asymptotic setup in which both the number of users per cell and the processing gain go to infinity, while their ratio (the ldquocell loadrdquo) goes to some finite constant, the spectral efficiencies of the optimum and linear minimum mean-squared error (MMSE) joint multicell receivers are investigated. A dramatic performance enhancement as compared to single-cell-site processing is demonstrated. The asymptotic behavior of the two receivers in extreme signal-to-noise ratio (SNR) regimes and in a high cell-load regime are analyzed as well. The impact of chip interleaving versus symbol interleaving is also investigated. Chip-level interleaving is found beneficial in several cases of interests, and is conjectured to be beneficial in general.
Antigenic variation (mar mutations) in herpes simplex virus glycoprotein B can induce temperature-dependent alterations in gB processing and virus production

Monoclonal antibody-resistant (mar) mutants altered in the antigenic structure of glycoprotein B (gB) of herpes simplex virus type 1, strain KOS-321, were selected by neutralization with each of six independently derived gB-specific monoclonal antibodies. Analysis of the reactivity patterns of these mar mutants with a panel of 16 virus-neutralizing monoclonal antibodies identified at least five nonoverlapping epitopes on this antigen, designated groups I through V. Multiple mar mutations were also introduced into the gB structural gene by recombination and sequential antibody selection to produce a set of mar mutants with double, triple, and quadruple epitope alterations. Group II (B2) and group III (B4) antibodies were used to select the corresponding mutants, mar B2.1 and mar B4.1, which in addition to carrying the mar phenotype were temperature sensitive (ts) for processing of the major partially glycosylated precursor of gB, pgB (Mr = 107,000), to mature gB (Mr = 126,000) and showed reduced levels of gB on the cell surface at high temperature (39 degrees C). These mutants were not, however, ts for production of infectious progeny. A recombinant virus, mar B2/4.1, carrying both of these alterations was ts for virus production and failed to produce and transport any detectable mature gB to the cell surface at 39 degrees C. Rather, pgB accumulated in the infected cell. Revertants of the ts phenotype, isolated from virus plaques at 39 degrees C, regained the B2 but not the B4 epitope and were phenotypically indistinguishable from the mar B4.1 parent. Finally, it was shown that group II (B5) and group III (B4) antibodies failed to immunoprecipitate pgB (39 degrees C) produced by ts gB mutants of herpes simplex virus type 1 which were not selected with monoclonal antibodies. Taken together, our findings indicate that (i) mar mutations can alter antigenic as well as other functional domains of gB, namely, the domain(s) involved in processing and infectivity, and (ii) group II and group III epitopes lie within an essential functional domain of gB which is a target for ts gB mutations.
Manifold-Learning Based API Recommendation for Mashup Creation

With the wide adoption of Service-Oriented Architecture (SOA), the number of web accessible services and their compositions is increasing rapidly. Among huge number of services, how to recommend appropriate ones for automatic composition satisfying users' need is challenging. We investigate services and their compositions in Programmable Web which characterize services as APIs and their compositions as mashups. We study the problem of recommending suitable APIs satisfying users' need for mash up creation. To this end, we propose a manifold ranking framework for API recommendation. First, we categorize existing mashups into functionally similar clusters. Then we recommend APIs for each mash up cluster using manifold ranking algorithm which incorporate the relationships between mashups, between APIs and between mashups and APIs. Intuitively, we take three factors into consideration: (1) We recommend APIs that are in functionally similar mashups. (2) We recommend APIs that are popular in the mashups. (3) We recommend APIs that are similar to each other. Finally, we map a user's requirement for mash up creation to a mash up cluster and recommend APIs generated by the algorithm to user. Experiments based on real dataset crawled from Programmble Web demonstrate the effectiveness of the proposed approach in terms of precision, recall, and NDCG.
β-Catenin is essential for pancreatic acinar but not islet development

Despite our increasingly sophisticated understanding of transcriptional regulation in pancreas development, we know relatively little about the extrinsic signaling pathways involved in this process. We show here that the early pancreatic epithelium exhibits a specific enrichment in unphosphorylatedβ -catenin protein, a hallmark of activation of the canonical Wnt signaling pathway. To determine if this pathway is functionally required for normal pancreas development, we have specifically deleted the β-catenin gene in these cells. Pancreata developing without β-catenin are hypoplastic, although their early progenitors appear normal and exhibit no premature differentiation or death. Surprisingly, and in marked contrast to its role in the intestine, loss of β-catenin does not significantly perturb islet endocrine cell mass or function. The major defect of theβ -catenin-deficient pancreas is an almost complete lack of acinar cells, which normally comprise the majority of the organ. β-Catenin appears to be cell-autonomously required for the specification of acinar cells, rather than for their survival or maintenance, as deletion of β-catenin specifically in differentiated acinar cells has no effect. Thus, our data are consistent with a crucial role for canonical Wnt signals in acinar lineage specification and differentiation.
Constitutional Thinness and Anorexia Nervosa: A Possible Misdiagnosis?

Clinical and biological aspects of restrictive anorexia nervosa (R-AN) are well documented. More than 10,000 articles since 1911 and more than 600 in 2013 have addressed R-AN psychiatric, somatic, and biological aspects. Genetic background, ineffectiveness of appetite regulating hormones on refeeding process, bone loss, and place of amenorrhea in the definition are widely discussed and reviewed. Oppositely, constitutional thinness (CT) is an almost unknown entity. Only 32 articles have been published on this topic since 1953. Similar symptoms associating low body mass index, low fat, and bone mass are reported in both CT and R-AN subjects. Conversely, menses are preserved in CT women and almost the entire hormonal profile is normal, except for leptin and PYY. The aim of the present review is to alert the clinician on the confusing clinical presentation of these two situations, a potential source of misdiagnosis, especially since R-AN definition has changed in DSM5.
Predicting faults using the complexity of code changes

Predicting the incidence of faults in code has been commonly associated with measuring complexity. In this paper, we propose complexity metrics that are based on the code change process instead of on the code. We conjecture that a complex code change process negatively affects its product, i.e., the software system. We validate our hypothesis empirically through a case study using data derived from the change history for six large open source projects. Our case study shows that our change complexity metrics are better predictors of fault potential in comparison to other well-known historical predictors of faults, i.e., prior modifications and prior faults.
An exploration of L2 cache covert channels in virtualized environments

Recent exploration into the unique security challenges of cloud computing have shown that when virtual machines belonging to different customers share the same physical machine, new forms of cross-VM covert channel communication arise. In this paper, we explore one of these threats, L2 cache covert channels, and demonstrate the limits of these this threat by providing a quantification of the channel bit rates and an assessment of its ability to do harm. Through progressively refining models of cross-VM covert channels from the derived maximums, to implementable channels in the lab, and finally in Amazon EC2 itself we show how a variety of factors impact our ability to create effective channels. While we demonstrate a covert channel with considerably higher bit rate than previously reported, we assess that even at such improved rates, the harm of data exfiltration from these channels is still limited to the sharing of small, if important, secrets such as private keys.
Cardinality Bundling with Spence-Mirrlees Reservation Prices Jianqing “ Fisher ”

Abstract We study the pricing of cardinality bundles, where firms set prices that depend only on the size of the purchased bundle, a practice that is increasingly being adopted by industry. The model we study, where consumer choices are discrete, was originally proposed by Hitt and Chen (2005) and it requires that consumers’ preferences obey Spence-Mirrlees Single Crossing Property (SCP). We correct prior approaches and develop various structural and managerial insights. We develop a fast combinatorial technique to obtain the optimal prices. We extend our analysis to address a quantity discount problem originally proposed in Spence (1980). We provide examples that demonstrate that the proposed approach of Spence (1980) only identifies local optima without providing guidance on selecting the globally optimal pricing function. Our insights from the discrete model are extended to this context to develop a scheme that provides solutions within an arbitrary pre-specified tolerance. Consequently, we also solve the continuous version of the cardinality bundling problem.
Bioinspiring an Interest in STEM

Attracting K-12 students to pursue careers in science, technology, engineering, and mathematics (STEM) is viewed as a critical element for benefiting both the economy and society. This paper describes an outreach program, conducted in a Brooklyn, NY, USA, public middle school, aimed at educating students in mechatronics, biology, and bioinspiration. The program is designed to foster student interest in STEM subjects, especially engineering-related concepts, by actively demonstrating their application in solving tangible real-world problems. It consists of a series of lectures and practical activities that culminate with a hands-on bioinspiration-based event at the New York Aquarium. Survey results show that students who participated in the program have a better understanding of the relationship between engineering and nature, demonstrate improved knowledge of select STEM topics, and are more interested in pursuing STEM careers.
Soluble Fiber Dextrin and Soluble Corn Fiber Supplementation Modify Indices of Health in Cecum and Colon of Sprague-Dawley Rats

The objective of this study was to evaluate health outcomes resulting from dietary supplementation of novel, low-digestible carbohydrates in the cecum and colon of Sprague-Dawley rats randomly assigned to one of four treatment groups for 21 days: 5% cellulose (Control), Pectin, soluble fiber dextrin (SFD), or soluble corn fiber (SCF). Rats fed Pectin had a higher average daily food intake, but no differences in final body weights or rates of weight gain among treatments were observed. No differences were observed in total short-chain fatty acid (SCFA) or branched-chain fatty acid (BCFA) concentrations in the cecum and colon of rats fed either SFD or SCF. The SFD and SCF treatments increased cecal propionate and decreased butyrate concentrations compared to Control or Pectin. Pectin resulted in increased BCFA in the cecum and colon. Supplementation of SFD and SCF had no effect on cecal microbial populations compared to Control. Consumption of SFD and SCF increased total and empty cecal weight but not colon weight. Gut histomorphology was positively affected by SFD and SCF. Increased crypt depth, goblet cell numbers, and acidic mucin were observed in both the cecum and colon of rats supplemented with SFD, SCF, and Pectin. These novel, low-digestible carbohydrates appear to be beneficial in modulating indices of hindgut morphology when supplemented in the diet of the rat.
Antibody to Aquaporin 4 in the Diagnosis of Neuromyelitis Optica

Background Neuromyelitis optica (NMO) is a demyelinating disease of the central nervous system (CNS) of putative autoimmune aetiology. Early discrimination between multiple sclerosis (MS) and NMO is important, as optimum treatment for both diseases may differ considerably. Recently, using indirect immunofluorescence analysis, a new serum autoantibody (NMO-IgG) has been detected in NMO patients. The binding sites of this autoantibody were reported to colocalize with aquaporin 4 (AQP4) water channels. Thus we hypothesized that AQP4 antibodies in fact characterize NMO patients. Methods and Findings Based on these observations we cloned human water channel AQP4, expressed the protein in a eukaryotic transcription/translation system, and employed the recombinant AQP4 to establish a new radioimmunoprecipitation assay (RIPA). Indeed, application of this RIPA showed that antibodies against AQP4 exist in the majority of patients with NMO (n = 37; 21 positive) as well as in patients with isolated longitudinally extensive transverse myelitis (n = 6; six positive), corresponding to a sensitivity of 62.8% and a specificity of 98.3%. By contrast, AQP4 antibodies were virtually absent in 291 other participants, which included patients with MS (n = 144; four positive), patients with other inflammatory and noninflammatory neurological diseases (n = 73; one positive), patients with systemic autoimmune diseases (n = 45; 0 positive), and healthy participants (n = 29; 0 positive). Conclusions In the largest series reported so far to our knowledge, we quantified AQP4 antibodies in patients with NMO versus various other diseases, and showed that the aquaporin 4 water channel is a target antigen in a majority of patients with NMO. The newly developed assay represents a highly specific, observer-independent, and easily reproducible detection method facilitating clinically relevant discrimination between NMO, MS, and other inflammatory diseases.
Interleukin 15: biology and relevance to human disease.

Since the cloning of interleukin (IL)-15 six years ago, there have been numerous studies examining the molecular and cellular biology of this cytokine. IL-15 and IL-2 have similar biologic properties in vitro, consistent with their shared receptor (R) signaling components (IL-2/15Rβγc). However,
The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin: mechanism and evidence for two M species

The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin is investigated both for the native pigment and its D96N mutant. The experimental setup is based on creating the M intermediate by a first pulse, followed by a (blue) laser pulse which drives the back photoreaction of M. Experiments are carried out varying the delay between the two pulses, as well as the temperature over the -25 degrees C-20 degrees C range. It is found that the kinetic patterns of the M back photoreaction change with time after the generation of this intermediate. The data provide independent evidence for the suggestion of a photocycle mechanism based on two distinct M intermediates. They are thus in keeping with the consecutive model of Varo and Lanyi (Biochemistry 30, 5016-5022; 1991), although they cannot exclude other models such as those based on branched or parallel cycles. More generally, we offer a "photochemical" approach to discriminating between intermediate stages in the photocycle which does not depend on spectroscopic and/or kinetic data. While markedly affecting the rate of the M --> N transition in the photocycle, the rate of the thermal step in back photoreaction of M, at both room and low temperatures, is not significantly affected by the D96N mutation. It is proposed that while Asp 96 is the Schiff-base protonating moiety in the M --> N transition, another residue (most probably Asp 85) reprotonates the Schiff base following light absorption by M.
Full-gene sequencing analysis of NAT2 and its relationship with isoniazid pharmacokinetics in Venezuelan children with tuberculosis.

BACKGROUND Genetic variants in NAT2 are associated with pharmacokinetic variation of isoniazid, the cornerstone of antituberculosis treatment. We investigated the acetylator genotype and phenotype in children on antituberculosis treatment that were previously shown to have low plasma isoniazid levels. MATERIALS & METHODS NAT2 genotyping and phenotyping, represented as metabolic ratio of acetylisoniazid over isoniazid and as isoniazid half-life, were performed in 30 Venezuelan children. RESULTS Most children carried genotypes resulting in an intermediate or low enzyme activity (43 and 40%, respectively). Isoniazid exposure differed between genotypically slow and rapid acetylators (13.3 vs 4.5 h×mg/l, p < 0.01). Both the metabolic ratio as well as the half-life of isoniazid distinguished genotypically slow from genotypically rapid or intermediate acetylators (all p ≤ 0.01). CONCLUSION In Venezuelan children a clear difference in isoniazid pharmacokinetics and acetylator phenotype between genotypically slow and genotypically intermediate or rapid acetylating children was observed. Original submitted 31 July 2013; Revision submitted 11 November 2013.
Disentangling opposing effects of motivational states on pain perception

Abstract Introduction: Although the motivation to avoid injury and pain is central to human and animal behavior, this goal compete priority with other homeostatic goals. Animal studies have shown that competing motivational states, such as thirst, reduce pain. However, such states may also induce negative mood, which in humans has been found to increase pain. These opposing effects complicate study of the effects of motivational states in humans. Objectives: To evaluate concurrent effects of motivational state competition and mood on pain ratings. Methods: We compared a thirst challenge against a control group and measured thirst and mood as potential mediators. Pain induced through contact heat stimulation on the left forearm and was tested at 3 time points: before group randomization, after thirst induction, and after rehydration. Results: Overall, the thirst group reported more pain when thirsty compared with baseline and controls. Mediation analyses showed evidence for two opposing effects. First, the thirst challenge increased negative mood and thirstiness, which was related to increased pain. Second, the thirst challenge produced a direct, pain-reducing effect. Conclusion: Competing motivational states reduce pain but also induce concurrent mood changes that can mask motivational state-related effects.