bluuebunny/crossref_metadata_2025 huggingface dataset:
The Two-Step Purification of Ribosomal RNA and Plant Viral RNA by Polyacrylamide Slab Gel Electrophoresis
Authors: H Symons Robert
Published: July 2016

The requirement for purified plant viral RNAs for sequence characterization by hybridization analysis using complementary DNA led to the development of a routine two-step procedure for their purification. The method was worked out using Escherichia coli ribosomal RNAs and then applied to four plant viral RNAs, all of which contain four major RNA components. The first of the two steps involves the electrophoresis of native RNA on 2�8 % polyacrylamide slab gels, the location of the RNA bands by brief staining and the recovery of the RNA from each gel band by electrophoretic elution. The eluted RNA, concentrated by ethanol precipitation, was then run on a second gel after a denaturation step to release nicked and aggregated RNA fragments. Each RNA band was again located by staining and recovered by electrophoretic elution and ethanol precipitation. The 16-S and 23-S ribosomal RNAs and the plant viral RNAs were obtained in overall yields of 40 and 8-16 % respectively. RNAs so purified have been successfully used for the preparation of complementary DNA by two different methods.
The Effect of Cryptorchidism on the Quantitative Histology, Histochemistry and Hydrolytic Enzyme Activity of the Rat Testis
Authors: Blackshaw AW , Massey PF
Published: July 2016

Cryptorchidism of the mature rat testis led to degeneration of the seminiferous tubules and changes in enzyme patterns and activities. Spermatogenic stages 1--4, containing pachytene primary spermatocytes in late meiotic prophase, and stage 5, containing recently formed round spermatids, were damaged by 48 h. Within 96 h stages showed a loss of germinal cells into the lumen and this was almost complete by 192 h.
Production of Enniatin as a Criterion for Confirming the Identity of Fusarium lateritium Isolates
Authors: Bishop GC , Ilsley AH
Published: July 2016

The use of an organic metabolite as an aid in confirming the identity of isolates of Fusarium thought to be F. lateritium has been investigated.
Of rats and pathogens: pathogens transmitted by urban rats with an emphasis on hantaviruses.
Authors: Pépin M. , Dupinay T. , Zilber A. L. , McElhinney L. M.
Published: July 2016

Rats (brown- or Norway- and black:
Rattus norvegicus
and
Rattus rattus
, respectively) are very invasive rodents. They are originated from Southeast Asia and are present now everywhere in the world, exploiting their extraordinary capacity to proliferate in close contact with human populations. Rats, and particularly the brown rat, take advantage of conditions raised by overpopulation in cities, lack of hygiene and poverty. Beside the significant damage caused by their presence in rural and urban ecosystems, rats are also dangerous carriers of numerous pathogens transmissible to humans. Among these pathogens, leptospira and hantaviruses (particularly Seoul virus or SEOV) are the most important. Seoul virus belongs to the virus family
Bunyaviridae
and genus Hantavirus, has a worldwide distribution, and causes haemorrhagic fever with renal syndrome (HFRS) in humans. Leptospira and particularly
Leptospira interrogans
, serogroup Icterohaemorrhagiae, are zoonotic bacteria very frequently borne and excreted by rats and cause severe disease - leptospirosis - both in humans and domestic animals. Next-generation sequencing confirmed that rats can carry many other microbes and parasites for which the zoonotic capacity is not always determined. The importance of rats as pests and carriers of numerous pathogens demands the fight against their proliferation, especially in urban environments. The use of rodenticides such as anticoagulants is one pillar of prevention. However, increasing levels of rodenticide resistance can often render this means of control as ineffective. The second and absolutely necessary pillar of prevention involves the control of all environmental factors, which favour the establishment and proliferation of rats: age of housing, density of dwellings, defective drains/sewers, poor structural maintenance, proximity to food sources and poor hygiene.
Mammalian wildlife diversity in rubber and oil palm plantations.
Authors: Harich F. K. , Treydte A. C.
Published: July 2016

In the face of globally diminishing natural habitats in biodiversity-rich regions, agricultural landscapes around protected areas have increasingly gained importance as extended habitat for wildlife species. Rubber (
Hevea brasiliensis
) and oil palm (
Elais guineensis
) plantations are two of the dominant land-use systems in Southeast Asia that have seen a tremendous expansion over the last decades. Despite far-reaching ecological consequences of these intensively cropped monocultures on natural ecosystems, relatively little is known about their utilization by wildlife populations. With this review we want to give an overview of mammalian diversity in rubber and oil palm plantations with reference to human-wildlife conflicts occurring as a result of overlapping resource use. We searched the literature for studies on wild mammalian diversity in rubber and oil palm plantations and found 17 publications. We considered 29 additional publications that provided information on single species in such plantations. We discuss the potential of 'wildlife-friendly' farming for mammalian assemblages in plantations and its importance in the case of rubber and oil palm production. Our review showed that most wild mammal species found in these plantations were likely to be visitors that use cultivated landscapes as fringe habitat but some adapted well to plantations and few even became resident. We conclude that although plantations in the tropics and subtropics cannot substitute for forests and the preservation of natural habitats is indispensable, the reality of ongoing forest degradation and transformation into plantations will make wildlife-friendly farming a key strategy in maintaining mammalian diversity, particularly in land-use matrices surrounding natural habitats.
Preliminary Findings for a Relationship between Instream Flow and Shoal Chub Recruitment in the Lower Brazos River, Texas
Authors: Rodger Anthony W. , Mayes Kevin B. , Winemiller Kirk O.
Published: July 2016

Seasonal flow pulses in rivers facilitate spawning, dispersal, and early life stage survival of many fish species. To evaluate the effectiveness of current flow standards to sustain threatened fish populations, we investigated the relationship between hydrology and recruitment of the Shoal Chub Macrhybopsis hyostoma, a broadcast‐spawning minnow in the Brazos River, Texas. From March 2013 to March 2014, we collected metalarval and juvenile Shoal Chub bimonthly at night using arrays of stationary drift nets. Otoliths were examined to estimate age, and the relationship between hatch date and discharge was analyzed. Shoal Chub recruited under both base‐flow and pulse‐flow conditions, including intervals of increasing, decreasing, and stable discharge. However, hatch dates of surviving fish indicated greater levels of recruitment during flow pulses, particularly on the rising limb. Greatest recruitment occurred during flow pulses of a magnitude defined as two per season according to the method of hydrological analysis adopted by the state's environmental flow program. Our findings imply that the state's current environmental flow standards for the lower Brazos River may be insufficient to sustain Shoal Chub populations and additional research on this issue is warranted.

Received October 11, 2015; accepted March 30, 2016 Published online July 28, 2016
Arctic Grayling Movements through a Nature‐Like Fishpass in Northern Canada
Authors: Cahill Christopher L. , Howland Kimberly L. , Hulsman Mark F. , Noddin Fred , Tonn William M. , Courtice Gregory , Zhu David Z.
Published: July 2016

Using a PIT detection system and two in‐stream, swim‐through antennas, we examined the movements of Arctic Grayling Thymallus arcticus through a low‐gradient (<1%), nature‐like fishpass that connected two small lakes in the Barrenlands region of northern Canada. We used an ensemble of generalized linear mixed models to evaluate whether passage events (1) were related to fish FL, water depth in the fishpass, and/or temperature in the fishpass; and (2) exhibited any diel patterns. During two seasons, passage events were not related to fish FL or fishpass water temperature; however, the probability of a passage event occurring increased with increases in fishpass depth, which likely served as a proxy for velocity and/or discharge. Most notably, 95% (n = 193/204) of Arctic Grayling passages occurred at night (1800–0559 hours) throughout our study. Although the cause(s) of this diel pattern were not examined directly, we hypothesized that it represented a response to avian predation given the shallow depth of the fishpass and given our observations of daytime avian predation events on Arctic Grayling in the littoral zones of the study lakes. Our results offer novel insights into correlates of Arctic Grayling passage through a fishpass and lay the foundation for future studies to address the hypotheses supported herein with well‐designed experiments to determine the mechanisms behind the patterns we observed.

Received September 8, 2015; accepted April 7, 2016 Published online July 28, 2016
Forward thinking: correlates of posttreatment outcome expectation among depressed outpatients / Pensamiento prospectivo: correlatos de las expectativas de resultados post-tratamiento de pacientes ambulatorios que sufren depresión
Authors: Constantino Michael J. , Vîslă Andreea , Ogrodniczuk John S. , Coyne Alice E. , Söchting Ingrid
Published: July 2016

Although patients’ expectation about a treatment’s efficacy correlate with beneficial therapy processes and outcomes, scant research addresses patients’ expectation for lasting improvement at treatment’s end. Given the influence of beliefs on psychological functioning, posttreatment outcome expectation reflects an important acute treatment outcome. In this study, we examined patient characteristics, treatment processes and clinical change factors in relation to the posttreatment outcome expectation of 65 depressed outpatients completing group cognitive-behavioural therapy. Less than 1% of variability in posttreatment outcome expectation was due to group effects; thus, we conducted single-level regressions. Patients with less severe baseline depression, higher session 3 outcome expectation, more during-treatment hope and a greater reduction in interpersonal problems reported greater posttreatment outcome expectancy. Various patient characteristics and change factors can help clinicians forecast, and respond to, those patients who will possess stronger or weaker belief in their ability to maintain therapy gains at treatment’s end.
Determinants of approval of the work of truth commissions in the southern cone: a comparative study / Determinantes de la aprobación del trabajo realizado por las Comisiones de Verdad y Reconciliación en el cono sur: un estudio comparativo
Authors: Cárdenas Manuel , Zubieta Elena , Páez Darío , Arnoso Maitane , Espinosa Agustín
Published: July 2016

The socio-demographic and psychosocial approval determinants of the work conducted by the truth and reconciliation commissions (TRC) are analysed based on original survey data from Chilean, Argentinian and Peruvian samples ( N = 2,947). A linear multiple regression analysis was carried out ( R 2 between .28 and .44; f 2 between .45 and .78) which reveals the positive effect of commission functions perceived achievement, mainly the knowledge of truth (β = .28), justice (β = .15) and the contribution in creating a common history (β = .15). An analysis by country reveals in Chile salient variables such as institutional trust, political ideas, institutional apologies and hope and sadness emotions. In Argentina, together with TRC functions, the degree of information about the work of the commission and the perception of a negative social climate appear as relevant predictors. As regards Peru, the degree of exposure to violence appears as a good predictor of TRC’s work support. The results show the relevance of TRC functions’ fulfillment, as well as the role of institutional variables in the approval of the work they have done.
A MHD invariant and the confinement regimes in a tokamak
Authors: Spineanu F. , Vlad M.
Published: July 2016

Fundamental Lagrangian, frozen-in and topological invariants can be useful to explain systematic connections between plasma parameters. At high plasma temperature the dissipation is small and the robust invariances are manifested. We invoke a frozen-in invariant which is an extension of Ertel’s theorem, and connects the vorticity of the large scale motions with the profile of the safety factor and of particle density. Assuming ergodicity of the small scale turbulence we consider the approximative preservation of the invariant for changes of the vorticity in an annular region of finite radial extension (i.e. poloidal rotation). We find that the ionization-induced rotation triggered by a pellet requires a reversed-q profile. In the H-mode, the invariance requires an accumulation of the current density in the rotation layer. Then this becomes a vorticity-current sheet which may explain experimental observations related to the penetration of the resonant magnetic perturbation and the filamentation during the edge localized modes.
Fast particle loss channels in Wendelstein 7-X
Authors: Faustin J.M. , Cooper W.A. , Graves J.P. , Pfefferlé D. , Geiger J.
Published: July 2016

One of the main goals of Wendelstein 7-X (W7-X) is to demonstrate the fast particle confinement properties of the quasi-isodynamic stellarator concept. Fast particle populations will be produced either by Neutral Beam Injection (NBI) or by minority Ion Cyclotron Resonant Heating (ICRH). A fraction of these particles are expected to be lost (even without collisions), despite the optimisation procedure used for the W7-X design. Confinement properties of NBI particles in W7-X were presented in the paper of Drevlak et al (2014 Nucl. Fusion
54 073002). A detailed study is presented here where the loss patterns of an NBI population are described. In particular, focussing on a high-mirror equilibrium, the confinement of fast ions with varying energy injection is studied under collisional conditions. It is found that collisions are not only responsible for classical transport losses but also enhance drift induced losses caused by trapped particles. Moreover, an asymmetry is found in the toroidal position of particle losses which can be explained by local variation in the equilibrium field. The effects of a neoclassically resolved radial electric field are also investigated. Fast particle confinement is significantly improved by the associated

E
×
B

drift. In particular, an increasing radial electric field helps to reduce and even stop the losses due to the 3D equilibrium structure for times comparable to slowing down time.
To Invest or Sell? The Impacts of Ontario’s Greenbelt on Farm Exit and Investment Decisions
Authors: Li Na , Vyn Richard J. , McEwan Ken
Published: July 2016

This article examines the impact that Ontario’s Greenbelt legislation, a farmland preservation policy implemented in 2005 that permanently protects over 1.8 million acres of land from non‐agricultural development, has on farmers’ exit and investment decisions. There are conflicting hypotheses regarding the impacts that farmland preservation could have on farmers’ management decisions with respect to investment or disinvestment, and there is a lack of evidence in the literature regarding the nature of such impacts. To address this issue, this article uses a farm‐level panel data set to estimate the impacts of the Greenbelt policy on farm exit and on farm investment. The Greenbelt policy is found to have influenced both farm exit and farm investment decisions, with the impact varying depending on location within the Greenbelt. In particular, the results indicate evidence of a negative impact on farm investment, which is contrary to one of the objectives of the Greenbelt policy.
Reduced Efficacy of Praziquantel Against Schistosoma mansoni Is Associated With Multiple Rounds of Mass Drug Administration
Authors: Crellen Thomas , Walker Martin , Lamberton Poppy H. L. , Kabatereine Narcis B. , Tukahebwa Edridah M. , Cotton James A. , Webster Joanne P.
Published: July 2016

Background.  Mass drug administration (MDA) with praziquantel is the cornerstone of schistosomiasis control in sub-Saharan Africa. The effectiveness of this strategy is dependent on the continued high efficacy of praziquantel; however, drug efficacy is rarely monitored using appropriate statistical approaches that can detect early signs of wane.

Methods.  We conducted a repeated cross-sectional study, examining children infected with Schistosoma mansoni from 6 schools in Uganda that had previously received between 1 and 9 rounds of MDA with praziquantel. We collected up to 12 S. mansoni egg counts from 414 children aged 6–12 years before and 25–27 days after treatment with praziquantel. We estimated individual patient egg reduction rates (ERRs) using a statistical model to explore the influence of covariates, including the number of prior MDA rounds.

Results.  The average ERR among children within schools that had received 8 or 9 previous rounds of MDA (95% Bayesian credible interval [BCI], 88.23%–93.64%) was statistically significantly lower than the average in schools that had received 5 rounds (95% BCI, 96.13%–99.08%) or 1 round (95% BCI, 95.51%–98.96%) of MDA. We estimate that 5.11%, 4.55%, and 16.42% of children from schools that had received 1, 5, and 8–9 rounds of MDA, respectively, had ERRs below the 90% threshold of optimal praziquantel efficacy set by the World Health Organization.

Conclusions.  The reduced efficacy of praziquantel in schools with a higher exposure to MDA may pose a threat to the effectiveness of schistosomiasis control programs. We call for the efficacy of anthelmintic drugs used in MDA to be closely monitored.
Currency, Conversation, and Control: Political Discourse and the Coinage in Mid-Tudor England
Authors: Bishop Jennifer
Published: July 2016

In 1542, Henry VIII authorised the first of a series of debasements of the English silver coinage which would collectively come to be known as the ‘great debasement’ of the mid-sixteenth century. The debasement was accompanied by a period of inflation and political change, and for contemporary observers these phenomena were inextricably linked. The coinage became the subject of a growing critical discourse, and governors feared that popular discontent threatened to spill over into riot and disorder—and perhaps even the subversion of the commonwealth. Moving away from the details of mint policy and quantitative assessments of the circulating medium that have previously occupied historians, this article explores the coinage as a topic of political discourse in the mid-Tudor period. As a matter of state, the coinage was a topic on which ordinary subjects were supposed to be silent and even Crown agents had to be circumspect, as criticising the coinage could be classed as sedition and mishandling it was a treasonous offence. But because of its status as common currency, the coinage was always in the public sphere, and was subject to the vagaries of popular opinion. This article recovers a range of contemporary perceptions and discussions of the coinage, from royal proclamations, government documents, and formal treatises, to correspondence, diary entries, court cases, and rumours. In so doing, it shows that the Crown’s efforts to control the coinage were consonant with its attempts to control political discourse and the discussion of matters of state in the mid-sixteenth century.
Therapeutic Jurisprudence
Authors: Chesser Brianna
Published: July 2016

Therapeutic jurisprudence is an interdisciplinary method of legal scholarship that aims to reform the law in order to positively impact the psychological well-being of the accused person. In 1990, law professors David Wexler and Bruce Winick coined the term “therapeutic jurisprudence” to acknowledge the sociopsychological consequences of any legal action and that these consequences can be impacted by the interpretation of substantive legal rules and procedures. Therapeutic Jurisprudence: The Law as a Therapeutic Agent by David Wexler (Wexler 1990, cited under General Overviews) asserts that the law is capable of operating as a therapeutic agent. In essence, therapeutic jurisprudence examines the extent to which substantive rules, legal procedures, the roles of court personnel such as lawyers, judges, and court administrators combine to produce therapeutic or nontherapeutic consequences, by taking a non-adversarial approach to the administration of justice. The key stakeholders in court proceedings combine their efforts to create a strategy that will assist the offender to take responsibility for making positive changes in their own lives. The use of this approach is becoming more widespread, and principles of therapeutic jurisprudence have also been discussed in light of family law, employment law, torts, and in personal injury law. Although therapeutic jurisprudence has been largely well received, some academics and practitioners have questioned its unfettered implementation. The therapeutic jurisprudential approach argues that any anti-therapeutic consequence of a legal decision should be avoided and where possible, a holistic solution should be found that addresses the behavioral, emotional, psychological, or situational issues of the accused person. However, the use of this approach should not impinge on the operation of the court nor interfere with the administration of justice. Although therapeutic jurisprudence has been largely well received, some academics and practitioners have questioned its unfettered implementation. The rapid dissemination of therapeutic jurisprudence without the accompanying evaluative research has led to varying opinions of the effectiveness of this problem-solving model within the courts and has led some commentators to misinterpret this approach by labeling it paternalistic and coercive. The therapeutic jurisprudential approach is aligned closely with the subsequent development of the mental health court and is also relied heavily upon in other problem-solving court models including drug and other specialist courts.
Modern Dynastic Rule
Authors: Yates Douglas A.
Published: July 2016

Dynasty comes from the Greek word for family and is used for a family that rules or simply reigns. One quarter of all states in the contemporary world system have a family dynast as their head of state or government. Some are constitutional monarchs; others are absolute monarchs. Some are republics temporarily ruled by democratic political families who win and lose power in elections. Others are tyrants born to rule oxymoronic dynastic republics. One thing is certain. Dynasty is no archaism on the verge of extinction. Every historical era and geographical region breeds its own kind of dynasty. So the question is why do we accept to be ruled by families? What kind of atavistic behavior is this? Does dynastic style really provide a comparative advantage? How should we study these omnipresent phenomena? No modern textbook in comparative politics is available on modern dynastic rule per se, so we tend to borrow from the classics of Antiquity or from sociology’s theory of patrimonialism, anthropological theories of kinship, psychological theories of personality, political and social histories, biographies, and journalism. This leads to an eclectic bibliography, if it is intended for political scientists. Before diving into thick biographies or attempting to read national histories about very different peoples and cultures, it is important to have some understanding of the debated anthropological concept of family kinship and sociological theories of patrimonial rule, as well as some grounding in psychological theories of family influence on individual personality. Empirical cases of modern dynasties are limited here to contemporary families still currently in power, divided into four fundamental categories: two authoritarian (Absolute Monarchies, Dynastic Republics) and two democratic (Constitutional Monarchies, Democratic Political Families) in order to distinguish those regime types and to differentiate monarchy from republic. The life-span of a dynasty is a subject of political science. One theory is that a dynasty lasts on average three generations, which is useful in making predictive statements of the some of the world’s most despotic regimes, but this will require more testing by scholars in the future.
The British Army of the Rhine
Authors: Moody Simon
Published: July 2016

The British Army of the Rhine (BAOR) began life in 1945 as a postwar administrative headquarters deployed in support of the civilian authority of the British zone of occupation, northern Germany. With the activation of a NATO unified command structure in 1951, BAOR became an integral part, along with Belgian, Canadian, and Dutch army units, of the Northern Army Group (NORTHAG). Deployed on the European Central Front with its NORTHAG sister formations, BAOR was a significant feature of NATO’s forward shield of ground forces to deter or, if deterrence failed, to repel a major Warsaw Pact offensive on the Continent. To improve its combat effectiveness BAOR was equipped since the early 1960s with tactical nuclear weapons, and in so doing, became the first formation of the British army trained to fight and prevail on a nuclear battlefield. The deployment of BAOR on the European Central Front was symbolic of British political intent vis-à-vis European security and was the military means by which Britain sought to deter a conventional or nuclear Warsaw Pact attack. The history of BAOR, then, is not simply a history of an army formation. It is a history of British European security commitments, of NATO military strategy, and of the changing character of land warfare after 1945. This annotated bibliography presents the best quality scholarship relating to BAOR, from its inception until its replacement under the conditions of the 1994 Options for Change defense review with the twenty-five-thousand strong British Forces Germany.
Deuteronomy
Authors: Levinson Bernard
Published: July 2016

Deuteronomy, the fifth book of the Bible and last book of the Pentateuch, presents itself as a valedictory address by Moses, spoken to the Israelites forty years after their escape from slavery in Egypt, just as Moses is about to die, and just as the Israelites are about to enter the promised land of Canaan without him. In a series of three speeches, Moses reminisces about the Israelites’ collective past, expounds upon their laws, and instructs them about the importance of loyalty to God. He also swears the nation to uphold this combination of law and theological instruction as a covenant upon the plains of Moab, one that supplements the covenant previously sworn at Horeb. In literary terms, the core of Deuteronomy is found in the legal corpus (chapters 12–26), which contains a blend of religious, political, civil, and criminal law. That legislation is embedded in a literary frame, in which chapters 1–11 recall the events of the Exodus, including the proclamation of the Ten Commandments, or Decalogue (Ten Words). Following the legal corpus, chapters 27–34 conclude with ceremonies to ratify Israel’s covenant with God, the commissioning of Joshua as the successor of Moses, a poetic blessing by Moses of the twelve tribes of Israel, and a prose account of Moses’ death. Striking similarities exist between the distinctive religious and legal requirements of Deuteronomy and the account in 2 Kings 22–23 of a religious reform carried out by King Josiah in 622 bce. Josiah restricted all sacrificial worship of God to Jerusalem, removed foreign elements from the system of sacrificial worship (technically, the “cultus”), and ordered the celebration of the first nationally centralized Passover at the Temple in Jerusalem. According to the narrative, Josiah’s reform was inspired by the discovery in the Temple of a “book of the law” (2 Kings 22:8). So strongly do these royal initiatives correspond to the distinctive requirements of Deuteronomy that scholars have long identified the “book [or more accurately, scroll] of the law” discovered in Josiah’s temple as Deuteronomy. The implications of this conclusion for the Origin, Purpose, and Dating and the Composition and Redaction of Deuteronomy, as well as its relation to Near Eastern literature, remain issues for ongoing scholarly debate.
Estimate of disease heritability using 7.4 million familial relationships inferred from electronic health records
Authors: Polubriaginof Fernanda , Vanguri Rami , Quinnies Kayla , Belbin Gillian M. , Yahi Alexandre , Salmasian Hojjat , Lorberbaum Tal , Nwankwo Victor , Li Li , Shervey Mark , Glowe Patricia , Ionita-Laza Iuliana , Simmerling Mary , Hripcsak George , Bakken Suzanne , Goldstein David , Kiryluk Krzysztof , Kenny Eimear E. , Dudley Joel , Vawdrey David K. , Tatonetti Nicholas P.
Published: July 2016

Heritability is essential for understanding the biological causes of disease, but requires laborious patient recruitment and phenotype ascertainment. Electronic health records (EHR) passively capture a wide range of clinically relevant data and provide a novel resource for studying the heritability of traits that are not typically accessible. EHRs contain next-of-kin information collected via patient emergency contact forms, but until now, these data have gone unused in research. We mined emergency contact data at three academic medical centers and identified millions of familial relationships while maintaining patient privacy. Identified relationships were consistent with genetically-derived relatedness. We used EHR data to compute heritability estimates for 500 disease phenotypes. Overall, estimates were consistent with literature and between sites. Inconsistencies were indicative of limitations and opportunities unique to EHR research. These analyses provide a novel validation of the use of EHRs for genetics and disease research.

One Sentence Summary

We demonstrate that next-of-kin information can be used to identify familial relationships in the EHR, providing unique opportunities for precision medicine studies.
Each cell needs long double-stranded RNA for silencing by feeding RNAi inC. elegans
Authors: Raman Pravrutha , Zaghab Soriayah M , Traver Edward C , Jose Antony M
Published: July 2016

Long double-stranded RNA (dsRNA) can silence genes of matching sequence upon ingestion in many invertebrates and is therefore being developed as a pesticide. Such feeding RNA interference (RNAi) is best understood in the wormC. elegans, where it is thought that derivatives of ingested dsRNA, including short dsRNAs, move between cells and cause systemic silencing. Movement of short dsRNAs has been inferred using tissue-specific rescue of the long dsRNA-binding protein RDE-4 by expressing it from repetitive transgenes. We found that the use of repetitive transgenes for the tissue-specific rescue of a gene could inhibit RNAi within that tissue and could result in misexpression of the gene in other tissues. Both inhibition and misexpression were not detectable when a single-copy transgene was used for tissue-specific rescue. In animals with single-copy rescue of RDE-4, RNAi was restricted to the tissue with RDE-4 expression. Thus, unlike previous observations using repetitive transgenes, these results suggest that binding of long dsRNA by RDE-4 in each silenced cell is required for systemic RNAi. Taken together with the requirement for long dsRNA to trigger RNAi in insects, these results suggest that the entry of long dsRNA is a necessary first step for feeding RNAi in animal cells.
Projected spread of Zika virus in the Americas
Authors: Zhang Qian , Sun Kaiyuan , Chinazzi Matteo , Pastore-Piontti Ana , Dean Natalie E. , Rojas Diana Patricia , Merler Stefano , Mistry Dina , Poletti Piero , Rossi Luca , Bray Margaret , Halloran M. Elizabeth , Longini Ira M. , Vespignani Alessandro
Published: July 2016

We use a data-driven global stochastic epidemic model to project past and future spread of the Zika virus (ZIKV) in the Americas. The model has high spatial and temporal resolution, and integrates real-world demographic, human mobility, socioeconomic, temperature, and vector density data. We estimate that the first introduction of ZIKV to Brazil likely occurred between August 2013 and April 2014 (90% credible interval). We provide simulated epidemic profiles of incident ZIKV infections for several countries in the Americas through February 2017. The ZIKV epidemic is characterized by slow growth and high spatial and seasonal heterogeneity, attributable to the dynamics of the mosquito vector and to the characteristics and mobility of the human populations. We project the expected timing and number of pregnancies infected with ZIKV during the first trimester, and provide estimates of microcephaly cases assuming different levels of risk as reported in empirical retrospective studies. Our approach represents an early modeling effort aimed at projecting the potential magnitude and timing of the ZIKV epidemic that might be refined as new and more accurate data from the region become available.
de novoassembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
Authors: Istace Benjamin , Friedrich Anne , d’Agata Léo , Faye Sébastien , Payen Emilie , Beluche Odette , Caradec Claudia , Davidas Sabrina , Cruaud Corinne , Liti Gianni , Lemainque Arnaud , Engelen Stefan , Engelen Stefan , Wincker Patrick , Schacherer Joseph , Aury Jean-Marc
Published: July 2016

Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small and low-cost single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments. The Oxford Nanopore technology is truly disruptive and can sequence small genomes in a matter of seconds. It has the potential to revolutionize genomic applications due to its portability, low-cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Here, we resequenced the genome of theSaccharomyces cerevisiaeS288C strain to evaluate the performance of nanopore-only assemblers. Then wede novosequenced and assembled the genomes of 21 isolates representative of theS. cerevisiaegenetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65% of the chromosomes. This high continuity allowed us to accurately detect large structural variations across the 21 studied genomes. Moreover, because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy.
A single double-strand break system reveals repair dynamics and mechanisms in heterochromatin and euchromatin
Authors: Janssen Aniek , Breuer Gregory A. , Brinkman Eva K. , van der Meulen Annelot I. , Borden Sean V. , van Steensel Bas , Bindra Ranjit S. , LaRocque Jeannine R. , Karpen Gary H.
Published: July 2016

Repair of DNA double-strand breaks (DSBs) must be properly orchestrated in diverse chromatin regions to maintain genome stability. The choice between two main DSB repair pathways, nonhomologous end-joining (NHEJ) and homologous recombination (HR), is regulated by the cell cycle as well as chromatin context.

Pericentromeric heterochromatin forms a distinct nuclear domain that is enriched for repetitive DNA sequences that pose significant challenges for genome stability. Heterochromatic DSBs display specialized temporal and spatial dynamics that differ from euchromatic DSBs. Although HR is thought to be the main pathway used to repair heterochromatic DSBs, direct tests of this hypothesis are lacking. Here, we developed an in vivo single DSB system for both heterochromatic and euchromatic loci in Drosophila melanogaster. Live imaging of single DSBs in larval imaginal discs recapitulates the spatio–temporal dynamics observed for irradiation (IR)-induced breaks in cell culture. Importantly, live imaging and sequence analysis of repair products reveal that DSBs in euchromatin and heterochromatin are repaired with similar kinetics, employ both NHEJ and HR, and can use homologous chromosomes as an HR template. This direct analysis reveals important insights into heterochromatin DSB repair in animal tissues and provides a foundation for further explorations of repair mechanisms in different chromatin domains.
Nucleolar organizer regions: genomic ‘dark matter’ requiring illumination
Authors: McStay Brian
Published: July 2016

Nucleoli form around tandem arrays of a ribosomal gene repeat, termed nucleolar organizer regions (NORs). During metaphase, active NORs adopt a characteristic undercondensed morphology. Recent evidence indicates that the HMG-box-containing DNA-binding protein UBF (upstream binding factor) is directly responsible for this morphology and provides a mitotic bookmark to ensure rapid nucleolar formation beginning in telophase in human cells. This is likely to be a widely employed strategy, as UBF is present throughout metazoans. In higher eukaryotes, NORs are typically located within regions of chromosomes that form perinucleolar heterochromatin during interphase. Typically, the genomic architecture of NORs and the chromosomal regions within which they lie is very poorly described, yet recent evidence points to a role for context in their function. In Arabidopsis, NOR silencing appears to be controlled by sequences outside the rDNA (ribosomal DNA) array. Translocations reveal a role for context in the expression of the NOR on the X chromosome in Drosophila. Recent work has begun on characterizing the genomic architecture of human NORs. A role for distal sequences located in perinucleolar heterochromatin has been inferred, as they exhibit a complex transcriptionally active chromatin structure. Links between rDNA genomic stability and aging in Saccharomyces cerevisiae are now well established, and indications are emerging that this is important in aging and replicative senescence in higher eukaryotes. This, combined with the fact that rDNA arrays are recombinational hot spots in cancer cells, has focused attention on DNA damage responses in NORs. The introduction of DNA double-strand breaks into rDNA arrays leads to a dramatic reorganization of nucleolar structure. Damaged rDNA repeats move from the nucleolar interior to form caps at the nucleolar periphery, presumably to facilitate repair, suggesting that the chromosomal context of human NORs contributes to their genomic stability. The inclusion of NORs and their surrounding chromosomal environments in future genome drafts now becomes a priority.
Metabolites: messengers between the microbiota and the immune system
Authors: Levy Maayan , Thaiss Christoph A. , Elinav Eran
Published: July 2016

The mammalian intestine harbors one of the largest microbial densities on Earth, necessitating the implementation of control mechanisms by which the host evaluates the state of microbial colonization and reacts to deviations from homeostasis. While microbial recognition by the innate immune system has been firmly established as an efficient means by which the host evaluates microbial presence, recent work has uncovered a central role for bacterial metabolites in the orchestration of the host immune response. In this review, we highlight examples of how microbiota-modulated metabolites control the development, differentiation, and activity of the immune system and classify them into functional categories that illustrate the spectrum of ways by which microbial metabolites influence host physiology. A comprehensive understanding of how microbiota-derived metabolites shape the human immune system is critical for the rational design of therapies for microbiota-driven diseases.
A conserved virus-induced cytoplasmic TRAMP-like complex recruits the exosome to target viral RNA for degradation
Authors: Molleston Jerome M. , Sabin Leah R. , Moy Ryan H. , Menghani Sanjay V. , Rausch Keiko , Gordesky-Gold Beth , Hopkins Kaycie C. , Zhou Rui , Jensen Torben Heick , Wilusz Jeremy E. , Cherry Sara
Published: July 2016

RNA degradation is tightly regulated to selectively target aberrant RNAs, including viral RNA, but this regulation is incompletely understood. Through RNAi screening in Drosophila cells, we identified the 3′-to-5′ RNA exosome and two components of the exosome cofactor TRAMP (Trf4/5–Air1/2–Mtr4 polyadenylation) complex, dMtr4 and dZcchc7, as antiviral against a panel of RNA viruses. We extended our studies to human orthologs and found that the exosome as well as TRAMP components hMTR4 and hZCCHC7 are antiviral. While hMTR4 and hZCCHC7 are normally nuclear, infection by cytoplasmic RNA viruses induces their export, forming a cytoplasmic complex that specifically recognizes and induces degradation of viral mRNAs. Furthermore, the 3′ untranslated region (UTR) of bunyaviral mRNA is sufficient to confer virus-induced exosomal degradation. Altogether, our results reveal that signals from viral infection repurpose TRAMP components to a cytoplasmic surveillance role where they selectively engage viral RNAs for degradation to restrict a broad range of viruses.
Crystal structure of 5-[(4-carboxybenzyl)oxy]isophthalic acid
Authors: Faizi Md. Serajul Haque , Ahmad Musheer , Ali Akram , Potaskalov Vadim A.
Published: July 2016

The molecular shape of the title compound, C16H12O7, is bent around the central CH2—O bond. The two benzene rings are almost perpendicular to one another, making a dihedral angle of 87.78 (7)°. In the crystal, each molecule is linked to three others by three pairs of O—H...O hydrogen bonds, forming undulating sheets parallel to thebcplane and enclosingR22(8) ring motifs. The sheets are linked by C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional network.
Crystal structures offac-tricarbonylchlorido(6,6′-dihydroxy-2,2′-bipyridine)rhenium(I) tetrahydrofuran monosolvate andfac-bromidotricarbonyl(6,6′-dihydroxy-2,2′-bipyridine)manganese(I) tetrahydrofuran monosolvate
Authors: Lense Sheri , Piro Nicholas A. , Kassel Scott W. , Wildish Andrew , Jeffery Brent
Published: July 2016

The structures of two facially coordinated Group VII metal complexes,fac-[ReCl(C10H8N2O2)(CO)3]·C4H8O (I·THF) andfac-[MnBr(C10H8N2O2)(CO)3]·C4H8O (II·THF), are reported. In both complexes, the metal ion is coordinated by three carbonyl ligands, a halide ligand, and a 6,6′-dihydroxy-2,2′-bipyridine ligand in a distorted octahedral geometry. Both complexes co-crystallize with a non-coordinating tetrahydrofuran (THF) solvent molecule and exhibit intermolecular but not intramolecular hydrogen bonding. In both crystal structures, chains of complexes are formed due to intermolecular hydrogen bonding between a hydroxy group from the 6,6′-dihydroxy-2,2′-bipyridine ligand and the halide ligand from a neighboring complex. The THF molecule is hydrogen bonded to the remaining hydroxy group.
Different cation-protonation patterns in molecular salts of unsymmetrical dimethyhydrazine: C2H9N2·Br and C2H9N2·H2PO3
Authors: Katinaitė Judita , Harrison William T. A.
Published: July 2016

We describe the syntheses and crystal structures of two molecular salts containing the 1,1-dimethylhydrazinium cation, namely 1,1-dimethylhydrazin-1-ium bromide, C2H9N2+·Br−, (I), and 2,2-dimethylhydrazin-1-ium dihydrogen phosphite, C2H9N2+·H2PO3−, (II). In (I), the cation is protonated at the methylated N atom and N—H...Br hydrogen bonds generate [010] chains in the crystal. In (II), the cation is protonated at the terminal N atom and cation-to-anion N—H...O and anion-to-anion O—H...O hydrogen bonds generate (001) sheets.
Redetermination of the crystal structure of NbF4
Authors: Bandemehr Jascha , Conrad Matthias , Kraus Florian
Published: July 2016

Single crystals of NbF4, niobium(IV) tetrafluoride, were synthesized by disproportionation of Nb2F5at 1273 K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4were based on X-ray powder diffraction data and the observed isotypicity to SnF4[Gortsema & Didchenko (1965).Inorg. Chem.4, 182–186; Schäferet al.(1965).J. Less Common Met.9, 95–104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6octahedra, leading to a layer structure extending parallel to theabplane.
Isotypic one-dimensional coordination polymers:catena-poly[[dichloridocadmium]-μ-5,6-bis(pyridin-2-yl)pyrazine-2,3-dicarboxylato-κ2N5:N6] andcatena-poly[[dichloridomercury(II)]-μ-5,6-bis(pyridin-2-yl)pyrazine-2,3-dicarboxylato-κ2N5:N6]
Authors: Alfonso Montserrat , Stoeckli-Evans Helen
Published: July 2016

The isotypic title one-dimensional coordination polymers, [CdCl2(C18H14N4O4)]n, (I), and [HgCl2(C18H14N4O4)]n, (II), are, respectively, the cadmium(II) and mercury(II) complexes of the dimethyl ester of 5,6-bis(pyridin-2-yl)pyrazine-2,3-dicarboxylic acid. In both compounds, the metal ions are located on a twofold rotation axis and a second such axis bisects the Car—Carbonds of the pyrazine ring. The metal ions are bridged by binding to the N atoms of the two pyridine rings and have anMN2Cl2bisphenoidal coordination geometry. The metal–Npyrazinedistances are much longer than the metal–Npyridinedistances; the difference is 0.389 (2) Å for the Cd—N bonds but only 0.286 (5) Å for the Hg—N bond lengths. In the crystals of both compounds, the polymer chains are linkedviapairs of C—H...Cl hydrogen bonds, forming corrugated slabs parallel to theacplane.
Zwitterionic 4-bromo-6-methoxy-2-{[tris(hydroxymethyl)methyl]iminiumylmethyl}phenolate: crystal structure and Hirshfeld surface analysis
Authors: Lee See Mun , Lo Kong Mun , Tan Sang Loon , Tiekink Edward R. T.
Published: July 2016

In the solid state, the title compound, C12H16BrNO5[systematic name: 4-bromo-2-((1E)-{[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]iminiumyl}methyl)-6-methoxybenzen-1-olate], C12H16BrNO5, is found in the keto–amine tautomeric form, with an intramolecular iminium-N—H...O(phenolate) hydrogen bond and anEconformation about the C=N bond. Bothgauche(two) andantirelationships are found for the methylhydroxy groups. In the crystal, a supramolecular layer in thebcplane is formedviahydroxy-O—H...O(hydroxy) and charge-assisted hydroxy-O—H...O(phenolate) hydrogen-bonding interactions; various C—H...O interactions provide additional cohesion to the layers, which stack along theaaxis with no directional interactions between them. A Hirshfeld surface analysis confirms the lack of specific interactions in the inter-layer region.
(3S,4S)-4-Phenyl-1,5-bis(prop-2-en-1-yl)-3-(prop-2-en-1-yloxy)-2,3,4,5-tetrahydro-1H-1,5-benzodiazepin-2-one
Authors: Rida Mohammed , El Bakri Youness , Sebbar Nada Kheira , Essassi El Mokhtar , Mague Joel T
Published: July 2016

In the title compound, C24H26N2O2, the dihedral angle between the benzene rings is 45.69 (7)°. In the crystal, the molecules form helical supramolecular chains running parallel to thebaxisviaweak C—H...O hydrogen bonds.
4-Chloro-1-[2-(2-chlorophenyl)ethyl]-2-nitrobenzene
Authors: Yeshwanthkumar H. S. , Nagendra P. , Siddaraju B. P. , Chaluvaraju K. C. , Byrappa K. , Lokanath N. K. , Madan Kumar S.
Published: July 2016

In the title compound, C14H11Cl2NO2, the dihedral angle between the phenyl rings is 8.60 (17)° and the nitro group makes a dihedral anle of 29.4 (4)° with its attached ring. The crystal structure features C—H...O hydrogen bonds and π–π interactions.