Miracle-dz/UniFAR-FTUs huggingface dataset:
Discrimination between six species of Theileria using oligonucleotide probes which detect small subunit ribosomal RNA sequences

SUMMARY The complete small subunit ribosomal RNA (srRNA) gene of Theileria parva was cloned and sequenced. Two primers were designed which permitted the specific amplification of part of the Theileria srRNA gene from Theileria-infected cell line samples which were predominantly (> 95%) bovine DNA. The sequence of the central (variable) region of the srRNA genes of T. annulata, T. taurotragi, T. mutans and two unidentified parasites referred to as Theileria sp. (buffalo) and Theileria sp. (Marula) were obtained. An alignment of the sequences was generated from which 6 oligonucleotide probes, corresponding to species-specific regions, were designed. These probes were demonstrated to provide unequivocal identification of each of the 6 species either by direct detection of parasite srRNA or by hybridization to amplified parasite srRNA genes. The probes were not able to distinguish buffalo-derived T. parva, the causal agent of Corridor disease, from cattle-derived T. parva, the causal agent of East Coast fever.
Understanding failures in petascale computers

With petascale computers only a year or two away there is a pressing need to anticipate and compensate for a probable increase in failure and application interruption rates. Researchers, designers and integrators have available to them far too little detailed information on the failures and interruptions that even smaller terascale computers experience. The information that is available suggests that application interruptions will become far more common in the coming decade, and the largest applications may surrender large fractions of the computer's resources to taking checkpoints and restarting from a checkpoint after an interruption. This paper reviews sources of failure information for compute clusters and storage systems, projects failure rates and the corresponding decrease in application effectiveness, and discusses coping strategies such as application-level checkpoint compression and system level process-pairs fault-tolerance for supercomputing. The need for a public repository for detailed failure and interruption records is particularly concerning, as projections from one architectural family of machines to another are widely disputed. To this end, this paper introduces the Computer Failure Data Repository and issues a call for failure history data to publish in it.
Structural origin of dynamic heterogeneity in three-dimensional colloidal glass formers and its link to crystal nucleation

The physical understanding of glass transition remains a major challenge of physics and materials science. Among various glass-forming liquids, a colloidal liquid interacting with hard-core repulsion is now regarded as one of the most ideal model systems. Here we study the structure and dynamics of three-dimensional polydisperse colloidal liquids by Brownian dynamics simulations. We reveal that medium-range crystalline bond orientational order of the hexagonal close packed structure grows in size and lifetime with increasing packing fraction. We show that dynamic heterogeneity may be a direct consequence of this transient structural ordering, which suggests its origin is thermodynamic rather than kinetic. We also reveal that nucleation of crystals preferentially occurs in regions of high medium-range order, reflecting the low crystal–liquid interfacial energy there. These findings may shed new light not only on the fundamental nature of the glass transition, but also the mechanism of crystal nucleation.
Antitumor Activity and Mechanism of Action of the Cyclopenta[b]benzofuran, Silvestrol

Background Flavaglines are a family of natural products from the genus Aglaia that exhibit anti-cancer activity in vitro and in vivo and inhibit translation initiation. They have been shown to modulate the activity of eIF4A, the DEAD-box RNA helicase subunit of the eukaryotic initiation factor (eIF) 4F complex, a complex that stimulates ribosome recruitment during translation initiation. One flavagline, silvestrol, is capable of modulating chemosensitivity in a mechanism-based mouse model. Methodology/Principal Findings Among a number of flavagline family members tested herein, we find that silvestrol is the more potent translation inhibitor among these. We find that silvestrol impairs the ribosome recruitment step of translation initiation by affecting the composition of the eukaryotic initiation factor (eIF) 4F complex. We show that silvestrol exhibits significant anticancer activity in human breast and prostate cancer xenograft models, and that this is associated with increased apoptosis, decreased proliferation, and inhibition of angiogenesis. We demonstrate that targeting translation by silvestrol results in preferential inhibition of weakly initiating mRNAs. Conclusions/Significance Our results indicate that silvestrol is a potent anti-cancer compound in vivo that exerts its activity by affecting survival pathways as well as angiogenesis. We propose that silvestrol mediates its effects by preferentially inhibiting translation of malignancy-related mRNAs. Silvestrol appears to be well tolerated in animals.
The WEB Book experiments in electronic textbook design

This paper describes a series of three evaluations of electronic textbooks on the Web, which focused on assessing how appearance and design can affect users’ sense of engagement and directness with the material. The EBONI Project's methodology for evaluating electronic textbooks is outlined and each experiment is described, together with an analysis of results. Finally, some recommendations for successful design are suggested, based on an analysis of all experimental data. These recommendations underline the main findings of the evaluations: that users want some features of paper books to be preserved in the electronic medium, while also preferring electronic text to be written in a scannable style.
Effects of enzymatic degradation on the subunit composition and biologic properties of human factor VIII.

Human factor VIII was purified from cryoprecipitate and subjected to enzymatic degradation with plasmin, trypsin, chymotrypsin, and thrombin. The reactions were monitored by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis and by measurement of four biologic properties, namely, procoagulant activity, ristocetin cofuctor activity, precipitation by heterologous antibody, and neutralization of a human factor VIII inhibitor. The dcctrophoretic patterns of reduced digests showed a reproducible sequence of degradation of the 215,000 molecular weight subunit by plasmin, trypsin, and chymotrypsin, each with well-defined intermediate and enzyme-resistant chain remnants. There were striking similarities in the sizes of several intermediate chain remnants produced by these three enzymes, suggesting the presence of regions on the factor VIII molecule that are espedolly susceptible to enzymatic degradation, but each enzyme also produced distinctive proteolytic derivatives. The most obvious differences included (1) a singlechained 40,000 molecular weight remnant cleaved by plasmin and trypsin which was either absent or degraded in chymotryptic digests, (2) large intermediate chain remnants of 1 76,000 and 1 57,000 molecular weight which were produced only by trypsin, and (3) differences in size and content of nonreduced fragments in the final digests. Thrombin caused no detectable change in electrophoretic patterns. The immunoprecipitation reaction was sensitive to minor degrees of proteolytic cleavage, showing a marked increase in rocket size even when the SDS-treated subunit chains showed virtually no change in dcctrophoretic mobility. Procoagulant and inhibitor neutralizing activities were rapidly destroyed by trypsin and plasmin, but this destruction did not correlate with specific changes in electrophoretic patterns. Both thrombin and chymotrypsin caused an increase in procoagulant activity prior to destruction of activity; changes in this property were therefore unrelated to changes in the protein visualized by gel electrophoresis. Ristocetin cofactor activity was considerably more resistant to plasmm than to trypsin or chymotrypsin, and roughly paralleled the persistence of highly aggregated forms in the digests.
New Methods in Automatic Extracting

This paper describes new methods of automatically extracting documents for screening purposes, i.e. the computer selection of sentences having the greatest potential for conveying to the reader the substance of the document. While previous work has focused on one component of sentence significance, namely, the presence of high-frequency content words (key words), the methods described here also treat three additional components: pragmatic words (cue words); title and heading words; and structural indicators (sentence location). The research has resulted in an operating system and a research methodology. The extracting system is parameterized to control and vary the influence of the above four components. The research methodology includes procedures for the compilation of the required dictionaries, the setting of the control parameters, and the comparative evaluation of the automatic extracts with manually produced extracts. The results indicate that the three newly proposed components dominate the frequency component in the production of better extracts.
Improved enrichment broth for cultivation of fastidious organisms

An enrichment broth developed in our laboratory, fastidious broth (FB), was compared with two commercially available broth media, supplemented thioglycolate broth and enriched eugonic broth. FB supported the growth of a number of organisms that were not cultivatable in either of the other two media, including Corynebacterium jeikeium, Haemophilus influenzae, Neisseria gonorrhoeae, and Streptococcus pneumoniae. In addition, for several organisms that were able to grow in all three broths, including Neisseria meningitidis, Nocardia asteroides, and Actinomyces spp. , both the time of incubation and the starting inoculum necessary to enable detection of growth were decreased significantly by using FB.
Maximal values of sniff nasal inspiratory pressure in healthy subjects.

BACKGROUND--Inspiratory muscle strength is often better reflected by oesophageal pressure during a maximal sniff (sniff POES) than by maximal inspiratory pressure (PImax). Sniff POES can be estimated non-invasively by measuring the sniff nasal inspiratory pressure (SNIP). The aim was to establish maximal normal values for the SNIP and to compare them with PImax. METHODS--One hundred and sixty healthy subjects (80 men) aged 20-80 years were recruited. All subjects had a forced vital capacity (FVC) of > 80%, a forced expiratory volume in one second (FEV1)/FVC of > 85% predicted value, and a body mass index of 18-31 kg/m2. Because PImax is known to be reduced in the supine posture, the SNIP was measured in both the sitting and the supine positions. PImax sustained over one second was measured from functional residual capacity (FRC) in the sitting position with a standard flanged mouthpiece during four manoeuvres. SNIP was measured from FRC in the sitting and supine positions using a catheter through a plug occluding one nostril during 10 maximal sniffs through the contralateral nostril. For each test the largest pressure measured in cm H2O was taken into account. RESULTS--For both men and women maximal SNIP was negatively correlated with age, and was similar in the sitting and the supine positions. In the sitting position maximal SNIP was greater or equal to PImax in 107 of 160 subjects. The mean (SD) ratio SNIP/PImax was 1.08 (0.22) in men and 1.17 (0.29) in women. CONCLUSIONS--Normal values of maximal SNIP can be predicted from age and sex. Maximal SNIP is similar in the sitting and the supine position and is significantly higher than PImax in healthy subjects. The low level of agreement between maximal SNIP and PImax indicates that the two manoeuvres are not interchangeable but complementary.
A centrifugal pathway to the mouse accessory olfactory bulb from the medial amygdala conveys gender‐specific volatile pheromonal signals

We previously found that female mice exhibited Fos responses in the accessory olfactory bulb (AOB) after exposure to volatile opposite‐sex, but not same‐sex, urinary odours. This effect was eliminated by lesioning the main olfactory epithelium, raising the possibility that the AOB receives information about gender via centrifugal inputs originating in the main olfactory system instead of from the vomeronasal organ. We asked which main olfactory forebrain targets send axonal projections to the AOB, and whether these input neurons express Fos in response to opposite‐sex urinary volatiles. Female mice received bilateral injections of the retrograde tracer cholera toxin B (CTB), into the AOB, and were exposed to either same‐ or opposite‐sex volatile urinary odours 1 week later. We found CTB‐labeled cell bodies in several forebrain sites including the bed nucleus of the accessory olfactory tract, the rostral portion of the medial amygdala (MeA) and the posteromedial cortical nucleus of the amygdala. A significant increase in the percentage of CTB/Fos co‐labeled cells was seen only in the MeA of female subjects exposed to male but not to female urinary volatiles. In Experiment 2, CTB‐injected females were later exposed to volatile odours from male mouse urine, food, or cat urine. Again, a significant increase in the percentage of CTB/Fos co‐labeled cells was seen in the MeA of females exposed to male mouse urinary volatiles but not to food or predator odours. Main olfactory–MeA–AOB signaling may motivate approach behaviour to opposite‐sex pheromonal signals that ensure successful reproduction.
The mediating role of affective commitment in the rewards-knowledge transfer relation

Purpose – The purpose of this paper is to assess the relative importance of intrinsic and extrinsic rewards as determinants of affective commitment and the influence of employees’ affective commitment on knowledge transfer in the context of a Spanish social firm. Design/methodology/approach – Using data from a sample of 227 employees working for a Spanish social firm, this study employs the partial least squares approach to test the research hypotheses. Findings – The research findings show that contrary to the findings of prior empirical studies, reward systems do not influence knowledge transfer in a direct way. Rather, reward systems act indirectly through the development of affective commitment, which is required to increase employees’ loyalty, reduce their turnover levels and improve their willingness to transfer their knowledge. Research limitations/implications – This research focuses on a Spanish social firm, and recommendations to other organizations should, therefore, be made with caution. Howev.
Nonparametric Triangular Simultaneous Equations Models with Weak Instruments

Instrumental variables are widely used to identify and estimate causal relationships in models with endogenous explanatory variables. The consequences of weak instruments have been extensively studied in the literature with linear simultaneous equations models. One might conjecture that the problem of weak instruments becomes even more important when studying endogenous explanatory variables in nonparametric models, as more exible models generally require stronger identi cation power, and hence plausibly stronger instruments. This paper is the rst to analyze the e¤ect of weak instruments on identi cation, estimation, and inference in a nonparametric setting. We consider a triangular simultaneous equations model, and follow the control function approach for identi cation and estimation. We derive a necessary and su¢ cient rank condition for identi cation, based on which weak identi cation is established. Then, nonparametric weak instruments are de ned as a sequence of reduced form functions that converges to a constant function. We characterize weak instruments as a multicollinearity problem or, more generally, as an inverse problem, which motivates the introduction of a regularization scheme. We propose a series estimation method with penalization to alleviate the e¤ects of weak instruments. We derive the rate of convergence of the resulting penalized series estimator. Consistency and asymptotic normality are achieved with mildlyweak instruments and a rapidly shrinking penalization parameter. Monte Carlo results show that the nite sample performance of the penalized estimator is appealing. The results of this paper are applied to an empirical example, where the e¤ect of class size on test scores is estimated nonparametrically. I am very grateful to my advisors, Donald Andrews and Edward Vytlacil, and committee members, Xiaohong Chen and Yuichi Kitamura for their inspiration, guidance and support. I am deeply indebted to Donald Andrews for his thoughtful advice throughout the project. This paper has bene ted from discussions with Joseph Altonji, Ivan Canay, Philip Haile, Keisuke Hirano, Han Hong, Joel Horowitz, Seokbae Simon Lee, Oliver Linton, Whitney Newey, Peter Phillips, Andres Santos, and Alex Torgovitsky. I gratefully acknowledge nancial support from a Carl Arvid Anderson Prize of the Cowles Foundation. yEmail: sukjin.han@yale.edu. Tel: 1-203-623-6736. Comments are welcome.
Design of a 79 dB 80 MHz 8X-OSR Hybrid Delta-Sigma/Pipelined ADC

A hybrid delta-sigma/pipelined modulator is presented in this paper. The proposed modulator takes advantage of the high resolution and distributed pipelined quantization, and combines it with the noise shaping property of a delta-sigma modulator. As a result, gain, swing, and slew requirements of the integrators are significantly reduced. The modulator also makes use of the latency in the pipelined quantization to enhance noise shaping. These advantages lead to less power dissipation, increased stability, and higher resolution. The prototype chip is implemented in a 0.18 ¿m CMOS process. With an 80 MHz clock, and an oversampling ratio of 8 (5 MHz bandwidth), the measured dynamic range and SNDR of this prototype IC are 79 dB and 75.4 dB.
Mechanisms of Toxin Inhibition and Transcriptional Repression by Escherichia coli DinJ-YafQ*

Background: Toxin-antitoxin complexes autoregulate transcription depending upon growth conditions. Results: DinJ-YafQ structure was determined, and minimal requirements for transcriptional autorepression were identified. Conclusion: The dinJyafQ operon is regulated in a novel manner by either DinJ-YafQ- or LexA-mediated repression. Significance: Our results reveal new mechanistic insights into the action of DinJ-YafQ as a transcriptional repressor. Bacteria encounter environmental stresses that regulate a gene expression program required for adaptation and survival. Here, we report the 1.8-Å crystal structure of the Escherichia coli toxin-antitoxin complex YafQ-(DinJ)2-YafQ, a key component of the stress response. The antitoxin DinJ dimer adopts a ribbon-helix-helix motif required for transcriptional autorepression, and toxin YafQ contains a microbial RNase fold whose proposed active site is concealed by DinJ binding. Contrary to previous reports, our studies indicate that equivalent levels of transcriptional repression occur by direct interaction of either YafQ-(DinJ)2-YafQ or a DinJ dimer at a single inverted repeat of its recognition sequence that overlaps with the −10 promoter region. Surprisingly, multiple YafQ-(DinJ)2-YafQ complexes binding to the operator region do not appear to amplify the extent of repression. Our results suggest an alternative model for transcriptional autorepression that may be novel to DinJ-YafQ.
Dwindling Wetland Ecosystems: A Survey of Impacts of Anthropogenic Activity on Marura Wetland, Kenya

Many developed and developing member States to the Ramsar Convention on conservation of Wetlands have developed their national policies on wetlands conservation and management. Management systems that, on the global extent involve community based approaches have been developed. Nevertheless, many challenges in wetland conservation and management continue to determine the existence and survival of these ecosystems. Several unlike and intensely bad threats including undesirable anthropogenic activities, within the wetland catchment areas and in the wetlands, are a threat to these delicate ecosystems. The main objective of this study was to monitor the water quality using limnological variables from different sampling points of a swamp during the flood and drought period of the wetland. Nutrients such as nitrogen and phosphates were determined. Dissolved oxygen (DO), pH, turbidity, temperature, total solids and conductivity were determined using standard analytical procedures. There were six sampling points, Sampling Original Research Article Wanjala et al.; JAERI, 14(4): 1-19, 2018; Article no.JAERI. 35588 2 point 1 was on Sergoit River before water enters Marura Wetland and acted as the control and the other five sampling points were within Marura Wetland, and were sampled in two seasons, wet and dry. The three replicas were collected four times in the dry season (December 2015 to March 2016) and four times during the wet season (April to July 2016). The findings revealed that there is a statistically significant difference between the control and test sample means of nitrates, phosphates, Dissolved oxygen, pH, Turbidity, Conductivity, and Total Solids. The results reveal that there is significance value of p = 0.000, which is below 0.05. , and therefore, there is a statistically significant difference among the different parameters in test samples and control. There is a statistically significant difference in turbidity between test samples and control samples as determined by one-way ANOVA (F (11, 36) = 82.340, p = 0.000). There was a statistically significant difference in phosphates between study areas and control samples as determined by one-way ANOVA (F (11, 36) = 39.020, p = 0.000). There was a statistically significant difference in conductivity among the study areas and control samples as determined by one-way ANOVA (F (11, 36) = 651.859, p = 0.000). This study concludes that Marura Wetland is a polluted ecosystem as indicated by phosphorous, turbidity and conductivity that were above specifications by the Kenya National Water Quality Standards (KNWQS). The findings of this study provide an important baseline or insight from which to monitor future change in water quality of Marura Wetland. This study recommends that further studies should be conducted to establish the actual potential of the site and actual points of source pollution and the types of electrolytes dissolved in the waters of Marura Wetland. The study also recommends intervention by local and national authorities to safeguard this dwindling ecosystem.
How Targeting Affects Customer Search: A Field Experiment

It has become common practice for retailers to personalize direct marketing efforts based on customer transaction histories as a tactic to increase sales. Targeted email offers featuring products in the same category as a customer's previous purchases generate higher purchase rates. However, a targeted offer emphasizing familiar products could result in curtailed search for unadvertised products, as a closely matched offer weakens a customer's incentives to search beyond the targeted items. In a field experiment using email offers sent by an online wine retailer, targeted offers resulted in decreased search activity on the retailer's website. This effect is driven by a lower rate of search by customers who visit the site, rather than a lower incidence of search. There are several ways this could potentially hurt retailers and consumers, such as reduced cross-selling and fewer opportunities for customers to explore new products.