bluuebunny/crossref_metadata_2025 huggingface dataset:
A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1
Authors: Hollander Dror , Donyo Maya , Atias Nir , Mekahel Keren , Melamed Zeev , Yannai Sivan , Lev-Maor Galit , Shilo Asaf , Schwartz Schraga , Barshack Iris , Sharan Roded , Ast Gil
Published: February 2016

Splicing aberrations are prominent drivers of cancer, yet the regulatory pathways controlling them are mostly unknown. Here we develop a method that integrates physical interaction, gene expression, and alternative splicing data to construct the largest map of transcriptomic and proteomic interactions leading to cancerous splicing aberrations defined to date, and identify driver pathways therein. We apply our method to colon adenocarcinoma and non-small-cell lung carcinoma. By focusing on colon cancer, we reveal a novel tumor-favoring regulatory pathway involving the induction of the transcription factor MYC by the transcription factor ELK1, as well as the subsequent induction of the alternative splicing factor PTBP1 by both. We show that PTBP1 promotes specific RAC1, NUMB, and PKM splicing isoforms that are major triggers of colon tumorigenesis. By testing the pathway's activity in patient tumor samples, we find ELK1, MYC, and PTBP1 to be overexpressed in conjunction with oncogenic KRAS mutations, and show that these mutations increase ELK1 levels via the RAS-MAPK pathway. We thus illuminate, for the first time, a full regulatory pathway connecting prevalent cancerous mutations to functional tumor-inducing splicing aberrations. Our results demonstrate our method is applicable to different cancers to reveal regulatory pathways promoting splicing aberrations.
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
Authors: Putnam Nicholas H. , O'Connell Brendan L. , Stites Jonathan C. , Rice Brandon J. , Blanchette Marco , Calef Robert , Troll Christopher J. , Fields Andrew , Hartley Paul D. , Sugnet Charles W. , Haussler David , Rokhsar Daniel S. , Green Richard E.
Published: February 2016

Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem, dramatically increasing the scaffold contiguity of assemblies. Here, we describe a simpler approach (“Chicago”) based on in vitro reconstituted chromatin. We generated two Chicago data sets with human DNA and developed a statistical model and a new software pipeline (“HiRise”) that can identify poor quality joins and produce accurate, long-range sequence scaffolds. We used these to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 20 Mbp. We also demonstrated the utility of Chicago for improving existing assemblies by reassembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kbp to 10 Mbp.
Mapping nucleosome positions using DNase-seq
Authors: Zhong Jianling , Luo Kaixuan , Winter Peter S. , Crawford Gregory E. , Iversen Edwin S. , Hartemink Alexander J.
Published: February 2016

Although deoxyribonuclease I (DNase I) was used to probe the structure of the nucleosome in the 1960s and 1970s, in the current high-throughput sequencing era, DNase I has mainly been used to study genomic regions devoid of nucleosomes. Here, we reveal for the first time that DNase I can be used to precisely map the (translational) positions of in vivo nucleosomes genome-wide. Specifically, exploiting a distinctive DNase I cleavage profile within nucleosome-associated DNA—including a signature 10.3 base pair oscillation that corresponds to accessibility of the minor groove as DNA winds around the nucleosome—we develop a Bayes-factor–based method that can be used to map nucleosome positions along the genome. Compared to methods that require genetically modified histones, our DNase-based approach is easily applied in any organism, which we demonstrate by producing maps in yeast and human. Compared to micrococcal nuclease (MNase)-based methods that map nucleosomes based on cuts in linker regions, we utilize DNase I cuts both outside and within nucleosomal DNA; the oscillatory nature of the DNase I cleavage profile within nucleosomal DNA enables us to identify translational positioning details not apparent in MNase digestion of linker DNA. Because the oscillatory pattern corresponds to nucleosome rotational positioning, it also reveals the rotational context of transcription factor (TF) binding sites. We show that potential binding sites within nucleosome-associated DNA are often centered preferentially on an exposed major or minor groove. This preferential localization may modulate TF interaction with nucleosome-associated DNA as TFs search for binding sites.
A t(5;16) translocation is the likely driver of a syndrome with ambiguous genitalia, facial dysmorphism, intellectual disability, and speech delay
Authors: Ozantürk Ayşegül , Davis Erica E. , Sabo Aniko , Weiss Marjan M. , Muzny Donna , Dugan-Perez Shannon , Sistermans Erik A. , Gibbs Richard A. , Özgül Köksal R. , Yalnızoglu Dilek , Serdaroglu Esra , Dursun Ali , Katsanis Nicholas
Published: February 2016

Genetic studies grounded on monogenic paradigms have accelerated both gene discovery and molecular diagnosis. At the same time, complex genomic rearrangements are also appreciated as potent drivers of disease pathology. Here, we report two male siblings with a dysmorphic face, ambiguous genitalia, intellectual disability, and speech delay. Through quad-based whole-exome sequencing and concomitant molecular cytogenetic testing, we identified two copy-number variants (CNVs) in both affected individuals likely arising from a balanced translocation: a 13.5-Mb duplication on Chromosome 16 (16q23.1 → 16qter) and a 7.7-Mb deletion on Chromosome 5 (5p15.31 → 5pter), as well as a hemizygous missense variant inCXorf36(also known asDIA1R). The 5p terminal deletion has been associated previously with speech delay, whereas craniofacial dysmorphia and genital/urinary anomalies have been reported in patients with a terminal duplication of 16q. However, dosage changes in either genomic region alone could not account for the overall clinical presentation in our family; functional testing ofCXorf36in zebrafish did not induce defects in neurogenesis or the craniofacial skeleton. Notably, literature and database analysis revealed a similar dosage disruption in two siblings with extensive phenotypic overlap with our patients. Taken together, our data suggest that dosage perturbation of genes within the two chromosomal regions likely drives the syndromic manifestations of our patients and highlight how multiple genetic lesions can contribute to complex clinical pathologies.
Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer
Authors: Bova G. Steven , Kallio Heini M.L. , Annala Matti , Kivinummi Kati , Högnäs Gunilla , Häyrynen Sergei , Rantapero Tommi , Kivinen Virpi , Isaacs William B. , Tolonen Teemu , Nykter Matti , Visakorpi Tapio
Published: February 2016

We report the first combined analysis of whole-genome sequence, detailed clinical history, and transcriptome sequence of multiple prostate cancer metastases in a single patient (A21). Whole-genome and transcriptome sequence was obtained from nine anatomically separate metastases, and targeted DNA sequencing was performed in cancerous and noncancerous foci within the primary tumor specimen removed 5 yr before death. Transcriptome analysis revealed increased expression of androgen receptor (AR)-regulated genes in liver metastases that harbored an AR p.L702H mutation, suggesting a dominant effect by the mutation despite being present in only one of an estimated 16 copies per cell. The metastases harbored several alterations to the PI3K/AKT pathway, including a clonal truncal mutation in PIK3CG and present in all metastatic sites studied. The list of truncal genomic alterations shared by all metastases included homozygous deletion of TP53, hemizygous deletion of RB1 and CHD1, and amplification of FGFR1. If the patient were treated today, given this knowledge, the use of second-generation androgen-directed therapies, cessation of glucocorticoid administration, and therapeutic inhibition of the PI3K/AKT pathway or FGFR1 receptor could provide personalized benefit. Three previously unreported truncal clonal missense mutations (ABCC4 p.R891L, ALDH9A1 p.W89R, and ASNA1 p.P75R) were expressed at the RNA level and assessed as druggable. The truncal status of mutations may be critical for effective actionability and merit further study. Our findings suggest that a large set of deeply analyzed cases could serve as a powerful guide to more effective prostate cancer basic science and personalized cancer medicine clinical trials.
A comparison of X-ray stress measurement methods based on the fundamental equation
Authors: Miyazaki Toshiyuki , Sasaki Toshihiko
Published: February 2016

Stress measurement methods using X-ray diffraction (XRD) methods are based on so-called fundamental equations. The fundamental equation is described in the coordinate system that best suits the measurement situation, and so making a comparison between different XRD methods is not straightforward. However, by using the diffraction vector representation, the fundamental equations of different methods become identical. Furthermore, the differences between the various XRD methods reside in the choice of diffraction vectors and the way of calculating the stress from the measured data. The stress calculation methods can also be unified using the general least-squares method, which is a common least-squares method of multivariate analysis. Thus, the only difference between these methods turns out to be in the choice of the set of diffraction vectors. In the light of these ideas, three commonly used XRD methods are compared: the sin2ψ method, the XRD2 method and the cosα method, using the estimation of the measurement errors. The XRD2 method with 33 frames (data acquisitions) shows the best accuracy. On the other hand, the accuracy of the cosα method with three frames is comparable to that of the XRD2 method.
Aurore: new software for neutron reflectivity data analysis. Corrigendum
Authors: Gerelli Yuri
Published: February 2016

An incorrect statement in the paper by Gerelli [J. Appl. Cryst. (2016), 49, 330–339] is corrected.
Crystal structure of maize serine racemase with pyridoxal 5′-phosphate
Authors: Zou Lingling , Song Yang , Wang Chengliang , Sun Jiaqi , Wang Leilei , Cheng Beijiu , Fan Jun
Published: February 2016

Serine racemase (SR) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that is responsible for D-serine biosynthesisin vivo. The first X-ray crystal structure of maize SR was determined to 2.1 Å resolution and PLP binding was confirmed in solution by UV–Vis absorption spectrometry. Maize SR belongs to the type II PLP-dependent enzymes and differs from the SR of a vancomycin-resistant bacterium. The PLP is bound to each monomer by forming a Schiff base with Lys67. Structural comparison with rat and fission yeast SRs reveals a similar arrangement of active-site residues but a different orientation of the C-terminal helix.
Crystal structure of human GDF11
Authors: Padyana Anil K. , Vaidialingam Bhamini , Hayes David B. , Gupta Priyanka , Franti Michael , Farrow Neil A.
Published: February 2016

Members of the TGF-β family of proteins are believed to play critical roles in cellular signaling processes such as those involved in muscle differentiation. The extent to which individual family members have been characterized and linked to biological function varies greatly. The role of myostatin, also known as growth differentiation factor 8 (GDF8), as an inhibitor of muscle differentiation is well understood through genetic linkages. In contrast, the role of growth differentiation factor 11 (GDF11) is much less well understood. In humans, the mature forms of GDF11 and myostatin are over 94% identical. In order to understand the role that the small differences in sequence may play in the differential signaling of these molecules, the crystal structure of GDF11 was determined to a resolution of 1.50 Å. A comparison of the GDF11 structure with those of other family members reveals that the canonical TGF-β domain fold is conserved. A detailed structural comparison of GDF11 and myostatin shows that several of the differences between these proteins are likely to be localized at interfaces that are critical for the interaction with downstream receptors and inhibitors.
Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human C1ORF123 protein
Authors: Rahaman Siti Nurulnabila A. , Mat Yusop Jastina , Mohamed-Hussein Zeti-Azura , Ho Kok Lian , Teh Aik-Hong , Waterman Jitka , Ng Chyan Leong
Published: February 2016

C1ORF123 is a human hypothetical protein found in open reading frame 123 of chromosome 1. The protein belongs to the DUF866 protein family comprising eukaryote-conserved proteins with unknown function. Recent proteomic and bioinformatic analyses identified the presence of C1ORF123 in brain, frontal cortex and synapses, as well as its involvement in endocrine function and polycystic ovary syndrome (PCOS), indicating the importance of its biological role. In order to provide a better understanding of the biological function of the human C1ORF123 protein, the characterization and analysis of recombinant C1ORF123 (rC1ORF123), including overexpression and purification, verification by mass spectrometry and a Western blot using anti-C1ORF123 antibodies, crystallization and X-ray diffraction analysis of the protein crystals, are reported here. The rC1ORF123 protein was crystallized by the hanging-drop vapor-diffusion method with a reservoir solution comprised of 20% PEG 3350, 0.2 Mmagnesium chloride hexahydrate, 0.1 Msodium citrate pH 6.5. The crystals diffracted to 1.9 Å resolution and belonged to an orthorhombic space group with unit-cell parametersa= 59.32,b= 65.35,c= 95.05 Å. The calculated Matthews coefficient (VM) value of 2.27 Å3 Da−1suggests that there are two molecules per asymmetric unit, with an estimated solvent content of 45.7%.
N,N,N′,N′,N′′-Pentamethyl-N′′-[2-(trimethylazaniumyl)ethyl]guanidinium bis(tetraphenylborate) acetone monosolvate
Authors: Tiritiris Ioannis , Kantlehner Willi
Published: February 2016

The asymmetric unit of the title solvated salt, C11H28N42+·2C24H20B−·C3H6O, comprises two cations, four tetraphenylborate anions and two acetone molecules. One cation shows an orientational disorder at the CN3moiety and two sets of N-atom positions were found related by a 60° rotation, with a refined occupancy ratio of 0.935 (1):0.065 (1). The respective nitrogen-bonded –CH2and –CH3groups are included in the disorder model. The C—N bond lengths in the central CN3units of both guanidinium ions range between 1.3329 (17) and 1.364 (16) Å, indicating a degree of double-bond character. The central C atom is bonded to the three N atoms in a nearly ideal trigonal–planar geometry and one positive charge is delocalized in the CN3plane. The C—N bond lengths in the terminal trimethylammonium groups have values close to a typical single bond, and the second positive charge is localized there. In the crystal, the guanidinium ions are connected by C—H...O hydrogen bonds with the acetone molecules. C—H...π interactions are present between the guanidinium and acetone hydrogen atoms and the phenyl rings of the tetraphenylborate ions, leading to the formation of a two-dimensional supramolecular pattern along thebcplane.
Adding value to education for sustainability in Africa with inquiry-based approaches in open and distance learning
Authors: Pretorius Rudi , Lombard Andrea , Khotoo Anisa
Published: February 2016

Purpose

– Inquiry-based approaches can potentially enrich sustainability learning in any educational context, more so in open and distance learning (ODL – perceived as theoretically inclined) and in regions of educational need (such as the Global South, of which Africa forms part). The purpose of this paper is to map the benefits and challenges of using inquiry-based learning (IBL), with reference to ODL and the value added by IBL in terms of education for sustainability (EfS) in Africa.

Design/methodology/approach

– Evidence-based reflection is used to provide a narrative assessment of the experience gained with IBL in two undergraduate sustainability-focussed modules in the Department of Geography at the University of South Africa (Unisa), an ODL provider in Africa and the Global South.

Findings

– Consideration of enabling and limiting factors indicates that although constraints are experienced, adoption of IBL approaches holds potential as pedagogic for EfS in Africa, due to grounding of learning in theory and applied to local places/contexts. This indicates a role for IBL to change perceptions regarding the lack of practical utility of ODL.

Originality/value

– Implementing place-based and contextual IBL is innovative in ODL. It adds value to learning experiences and supports transformative learning, both important components of EfS and addressing a need in the African context. Practitioners will find the experience gained with implementation of IBL, coupled with possibilities associated with information and communication technologies, of value.
On display in East and West
Authors: Gatejel Luminita
Published: February 2016

Purpose

– The purpose of this paper is to show how state socialist countries used soft power to improve their image in the West and advocate “the socialist way of life” in the context of the Cold War.

Design/methodology/approach

– The author argues from a cultural history perspective that underlines transfers and entanglements among the two camps during the Cold War. The study is based on primary and secondary sources such as automotive periodicals and archival material from the German Bundesarchiv.

Findings

– International fairs turned in the late 1950s into a new “battlefield” of the Cold War. The Soviet Union and its allies were celebrating at these meetings, important medial victories, laying the grounds for a state socialist consumer society. For the first time, Western audiences were realizing that irrespective of certain stylistic differences, consumer goods and particularly cars were not that different on the other side of the Iron Curtain. However, ideological bias and manufacturing flaws prevented them from being fully acknowledged by the Western side.

Originality/value

– Cold War research mainly focused on bipolar confrontation and the high-level decision-making process. This study is part of a recent trend in historiography to reassess the history of the Cold War, focusing on the multi-layered interactions between the two camps. It also shows that consumption and material well-being were important topics for understanding the dynamics and the flow of ideas through the Iron Curtain.
Cold War consumption and the marketing of childhood in the Soviet Union and the United States, 1950-1960
Authors: Peacock Margaret
Published: February 2016

Purpose

– This paper aims to explore the relationship between childhood, consumption and the Cold War in 1950s America and the Soviet Union. The author argues that Soviet and American leaders, businessmen, and politicians worked hard to convince parents that buying things for their children offered the easiest way to raise good American and Soviet kids and to do their part in waging the economic battles of the Cold War. The author explores how consumption became a Cold War battleground in the late 1950s and suggests that the history of childhood and Cold War consumption alters the way we understand the conflict itself.

Design/Methodology/Approach

– Archival research in the USA and the Russian Federation along with close readings of Soviet and American advertisements offer sources for understanding the global discourse of consumption in the 1950s and 1960s.

Findings

– Leaders, advertisers, and propagandists in the Soviet Union and the USA used the same images in the same ways to sell the ethos of consumption to their populations. They did this to sell the Cold War, to bolster the status quo, and to make profits.

Originality/Value

– This paper offers a previously unexplored, transnational perspective on the role that consumption and the image of the child played in shaping the Cold War both domestically and abroad.
Cold War binaries and the culture of consumption in the late Soviet home
Authors: Reid Susan E.
Published: February 2016

Purpose

– The purpose of this paper is to challenge Cold War binaries, seeking a more nuanced understanding of popular experience of change in the Soviet Union’s last decades. This was a period of intensive modernization and rapid transformation in Soviet citizens’ everyday material environment, marked by the mass move to newly constructed housing and by changing relations with goods.

Design/methodology/approach

– To probe popular experience and changing meanings, the paper turns to qualitative, subjective sources, drawing on oral history interviews (Everyday Aesthetics in the Modern Soviet Flat, 2004-2007).

Findings

– The paper finds that qualitative changes took place in Soviet popular consumer culture during the 1960s-1970s, as millions of people made home in new housing amid the widespread media circulation of authoritative images representing a desirable modern lifestyle and modernist aesthetic. Soviet people began to make aesthetic or semiotic distinctions between functionally identical goods and were concerned to find the right furniture to fit a desired lifestyle, aesthetic ideal and sense of self.

Research limitations/implications

– The problem is how to conceptualize the trajectory of change in ways that do justice to historical subjects’ experience and narratives, while avoiding uncritically reproducing Cold War binaries or perpetuating the normative status claimed by the postwar West in defining modernity and consumer culture.

Originality/value

– The paper challenges dominant Cold War narratives, according to which Soviet popular relations with goods were encompassed by shortage and necessity. It advances understanding of the specific form of modern consumer culture, which, it argues, took shape in the USSR after Stalin.
Oral tofacitinib efficacy, safety and tolerability in Japanese patients with moderate to severe plaque psoriasis and psoriatic arthritis: A randomized, double‐blind, phase 3 study
Authors: Asahina Akihiko , Etoh Takafumi , Igarashi Atsuyuki , Imafuku Shinichi , Saeki Hidehisa , Shibasaki Yoshiyuki , Tomochika Yukiko , Toyoizumi Shigeyuki , Nagaoka Makoto , Ohtsuki Mamitaro ,   the study investigators
Published: February 2016

Tofacitinib is an oral Janus kinase inhibitor that is being investigated for psoriasis and psoriatic arthritis. Japanese patients aged 20 years or more with moderate to severe plaque psoriasis and/or psoriatic arthritis were double‐blindly randomized 1:1 to tofacitinib 5 or 10 mg b.i.d. for 16 weeks, open‐label 10 mg b.i.d. for 4 weeks, then variable 5 or 10 mg b.i.d. to Week 52. Primary end‐points at Week 16 were the proportion of patients achieving at least a 75% reduction in Psoriasis Area and Severity Index (PASI75) and Physician's Global Assessment of “clear” or “almost clear” (PGA response) for psoriasis, and 20% or more improvement in American College of Rheumatology criteria (ACR20) for patients with psoriatic arthritis. Safety was assessed throughout. Eighty‐seven patients met eligibility criteria for moderate to severe plaque psoriasis (5 mg b.i.d., n = 43; 10 mg b.i.d., n = 44), 12 met eligibility criteria for psoriatic arthritis (5 mg b.i.d., n = 4; 10 mg b.i.d., n = 8) including five who met both criteria (10 mg b.i.d.). At Week 16, 62.8% and 72.7% of patients achieved PASI75 with tofacitinib 5 and 10 mg b.i.d., respectively; 67.4% and 68.2% achieved PGA responses; all patients with psoriatic arthritis achieved ACR20. Responses were maintained through Week 52. Adverse events occurred in 83% of patients through Week 52, including four (4.3%) serious adverse events and three (3.2%) serious infections (all herpes zoster). No malignancies, cardiovascular events or deaths occurred. Tofacitinib (both doses) demonstrated efficacy in patients with moderate to severe plaque psoriasis and/or psoriatic arthritis through 52 weeks; safety findings were generally consistent with prior studies.
Primary hyperhidrosis: Implications on symptoms, daily life, health and alcohol consumption when treated with botulinum toxin
Authors: Shayesteh Alexander , Boman Jens , Janlert Urban , Brulin Christine , Nylander Elisabet
Published: February 2016

Primary hyperhidrosis affects approximately 3% of the population and reduces quality of life in affected persons. Few studies have investigated the symptoms of anxiety, depression and hazardous alcohol consumption among those with hyperhidrosis and the effect of treatment with botulinum toxin. The first aim of this study was to investigate the effect of primary hyperhidrosis on mental and physical health, and alcohol consumption. Our second aim was to study whether and how treatment with botulinum toxin changed these effects. One hundred and fourteen patients answered questionnaires regarding hyperhidrosis and symptoms, including hyperhidrosis disease severity scale (HDSS), visual analog scale (VAS) 10‐point scale for hyperhidrosis symptoms, hospital anxiety and depression scale (HADS), alcohol use disorder identification test (AUDIT) and short‐form health survey (SF‐36) before treatment with botulinum toxin and 2 weeks after. The age of onset of hyperhidrosis was on average 13.4 years and 48% described heredity for hyperhidrosis. Significant improvements were noted in patients with axillary and palmar hyperhidrosis regarding mean HDSS, VAS 10‐point scale, HADS, SF‐36 and sweat‐related health problems 2 weeks after treatment with botulinum toxin. Changes in mean AUDIT for all participants were not significant. Primary hyperhidrosis mainly impairs mental rather than physical aspects of life and also interferes with specific daily activities of the affected individuals. Despite this, our patients did not show signs of anxiety, depression or hazardous alcohol consumption. Treatment with botulinum toxin reduced sweat‐related problems and led to significant improvements in HDSS, VAS, HADS and SF‐36 in our patients.
Neutrophil extracellular Taps play an important role in clearance of Streptococcus suis in vivo
Authors: Zhao Jianqing , Lin Lan , Fu Lei , Han Li , Zhang Anding
Published: February 2016

Streptococcus suis infection induces formation of neutrophil extracellular traps (NETs) in vitro; however, the contribution of NETs‐mediated killing to the pathogenesis of S. suis in vivo is yet to be elicited. The findings of the present study indicated that extracellular DNA fiber can be induced in a murine model in response to S. suis infection. A nuclease that destroys their structure was used to evaluate the role of NETs on S. suis infection. Treatment with nuclease resulted in a greater bacteria load and higher serum TNF‐α concentrations in response to S. suis infection, indicating that NETs structure played an essential role in S. suis clearance and inflammation. Furthermore, nuclease treatment resulted in more severe clinical signs during and higher mortality from S. suis infection. These findings indicated that NETs structure contributes to protection against S. suis infection.
The Economics of Disclosure and Financial Reporting Regulation: Evidence and Suggestions for Future Research
Authors: LEUZ CHRISTIAN , WYSOCKI PETER D.
Published: February 2016

This paper discusses the empirical literature on the economic consequences of disclosure and financial reporting regulation, drawing on U.S. and international evidence. Given the policy relevance of research on regulation, we highlight the challenges with (1) quantifying regulatory costs and benefits, (2) measuring disclosure and reporting outcomes, and (3) drawing causal inferences from regulatory studies. Next, we discuss empirical studies that link disclosure and reporting activities to firm‐specific and market‐wide economic outcomes. Understanding these links is important when evaluating regulation. We then synthesize the empirical evidence on the economic effects of disclosure regulation and reporting standards, including the evidence on International Financial Reporting Standards (IFRS) adoption. Several important conclusions emerge. We generally lack evidence on market‐wide effects and externalities from regulation, yet such evidence is central to the economic justification of regulation. Moreover, evidence on causal effects of disclosure and reporting regulation is still relatively rare. We also lack evidence on the real effects of such regulation. These limitations provide many research opportunities. We conclude with several specific suggestions for future research.
What Works?
Authors: Schell‐Busey Natalie , Simpson Sally S. , Rorie Melissa , Alper Mariel
Published: February 2016

Research Summary

We conducted a meta‐analysis of corporate crime deterrence strategies by using 80 effect sizes calculated from 58 studies in four treatment areas—Law, Punitive Sanctions, Regulatory Policy, and Multiple Treatments. Of the single‐treatment strategies, only Regulatory Policy produced a significant deterrent impact at the company level, but the results were not consistent across all study and effect size types. Studies examining multiple treatments, though, produced a consistent, significant deterrent effect on offending at both the individual and company levels.

Policy Implications

Our results suggest that regulatory policies that involve consistent inspections and include a cooperative or educational component aimed at the industry may have a substantial impact on corporate offending. However, a mixture of agency interventions will likely have the biggest impact on broadly defined corporate crime. The variety of offenders and behaviors included in corporate crime and its relative complexity likely necessitate multiple intervention strategies, which is similar to the “pulling levers” approach developed to deter gang violence and the responsive regulation strategy advocated by Braithwaite (2011). However, given some of the shortcomings in the literature, we also recommend that scholars and practitioners more clearly and consistently define the phenomenon of “corporate crime” and target evaluation research toward specific programs and interventions.
Inactivation of Salmonella in Shell Eggs by Hot Water Immersion and Its Effect on Quality
Authors: Geveke David J. , Gurtler Joshua B. , Jones Deana R. , Bigley Andrew B. W.
Published: February 2016

Thermal inactivation kinetics of heat resistant strains of Salmonella Enteritidis in shell eggs processed by hot water immersion were determined and the effects of the processing on egg quality were evaluated. Shell eggs were inoculated with a composite of heat resistant Salmonella Enteritidis (SE) strains PT8 C405, 2 (FSIS #OB030832), and 6 (FSIS #OB040159). Eggs were immersed in a circulating hot water bath for various times and temperatures. Come‐up time of the coldest location within the egg was 21 min. SE was reduced by 4.5 log at both hot water immersion treatments of 56.7 C for 60 min and 55.6 °C for 100 min. Decimal reduction times (D‐values) at 54.4, 55.6, and 56.7 °C were 51.8, 14.6, and 9.33 min, respectively. The z‐value was 3.07 °C. Following treatments that resulted in a 4.5 log reduction (56.7 °C/60 min and 55.6 °C/100 min), the surviving population of SE remained static during 4 wk of refrigerated storage. After processing under conditions resulting in 4.5 log reductions, the Haugh unit and albumen height significantly increased (P < 0.01) and yolk index significantly decreased (P < 0.05). The shell dynamic stiffness significantly increased (P < 0.05), while static compression shell strength showed no significant difference (P < 0.05). Vitelline membrane strength significantly increased (P < 0.05); although, no significant difference (P < 0.05) was observed in vitelline membrane elasticity. In summary, the hot water immersion process inactivated heat resistant SE in shell eggs by 4.5 log, but also significantly affected several egg quality characteristics.
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines
Authors: Torondel Belen , Ensink Jeroen H.J. , Gundogdu Ozan , Ijaz Umer Zeeshan , Parkhill Julian , Abdelahi Faraji , Nguyen Viet‐Anh , Sudgen Steven , Gibson Walter , Walker Alan W. , Quince Christopher
Published: February 2016

Improving the rate and extent of faecal decomposition in basic forms of sanitation such as pit latrines would benefit around 1.7 billion users worldwide, but to do so requires a major advance in our understanding of the biology of these systems. As a critical first step, bacterial diversity and composition was studied in 30 latrines in Tanzania and Vietnam using pyrosequencing of 16S rRNA genes, and correlated with a number of intrinsic environmental factors such as pH, temperature, organic matter content/composition and geographical factors. Clear differences were observed at the operational taxonomic unit, family and phylum level in terms of richness and community composition between latrines in Tanzania and Vietnam. The results also clearly show that environmental variables, particularly substrate type and availability, can exert a strong structuring influence on bacterial communities in latrines from both countries. The origins and significance of these environmental differences are discussed. This work describes the bacterial ecology of pit latrines in combination with inherent latrine characteristics at an unprecedented level of detail. As such, it provides useful baseline information for future studies that aim to understand the factors that affect decomposition rates in pit latrines.
RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in r.
Authors: Bailleul Diane , Stoeckel Solenn , Arnaud‐Haond Sophie
Published: February 2016

Partially, clonal species are common in the Tree of Life. And yet, population genetic models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here, we present an R package built upon genclone software including new functions and several improvements.

The RClone package includes functions to handle clonal data sets, allowing (i) checking for data set reliability to discriminate multilocus genotypes (MLGs), (ii) ascertainment of MLG and semi‐automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs and (iv) describing several spatial components of clonality. RClone allows the one‐shot analysis of multipopulation data sets without size limitation, suitable for data sets now increasingly produced through next‐generation sequencing.

A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin.

RClone is provided with two vignettes to handle analysis on one (RClone_quickmanual) or several populations (RClone_qmsevpops).
Nationwide incidence of serious complications of epidural analgesia in the United States
Authors: Rosero E. B. , Joshi G. P.
Published: February 2016

Background

This study aimed to describe the incidence and risk factors of in‐hospital spinal hematoma and abscess associated with epidural analgesia in adult obstetric and non‐obstetric populations in the United States.

Methods

The Nationwide Inpatient Sample was analyzed to identify patients receiving epidural analgesia from 1998 to 2010. Primary outcomes were incidence of spinal hematoma and epidural abscess. Use of decompressive laminectomy was also investigated. Regression analyses were conducted to assess predictors of epidural analgesia complications. Differences in mortality and disposition of patients at discharge were compared in patients with and without neuraxial complications. Obstetric and non‐obstetric patients were studied separately.

Results

A total of 3,703,755 epidural analgesia procedures (2,320,950 obstetric and 1,382,805 non‐obstetric) were identified. In obstetric patients, the incidence of spinal hematoma was 0.6 per 100,000 epidural catheterizations (95% CI, 0.3 to 1.0 × 10−5). The incidence of epidural abscess was zero. In non‐obstetric patients, the incidence of spinal hematoma and epidural abscess were, respectively, 18.5 per 100,000 (95% CI, 16.3 to 20.9 × 10−5) and 7.2 per 100,000 (95% CI, 5.8 to 8.7 × 10−5) catheterizations. Predictors of spinal hematoma included type of surgical procedure (higher in vascular surgery), teaching status of hospital, and comorbidity score. Patients with spinal complications had higher in‐hospital mortality (12.2% vs. 1.1%, P < 0.0001) and were significantly less likely to be discharged to home.

Conclusions

This large nationwide data analysis reveals that the incidence of epidural analgesia‐related complications is very low in obstetric population epidural analgesia and much higher in patients having vascular surgery.
Trading in broken things: Gendered performances and spatial practices in a northern Vietnamese rural‐urban waste economy
Authors: NGUYEN MINH T. N.
Published: February 2016

Through their deeply gendered performative and place‐making practices, migrant waste traders take part in regenerating and revaluing urban space in Hanoi, Vietnam. Ethnographic research in the city and in their native rural district suggests that these practices are simultaneously strategic and contingent on the waste traders’ gender and class positions. This positioning is defined by their marginalization as rural migrants and the social ambiguity of waste, which they creatively use for their own purposes. Alongside creating value for the waste they deal in, the traders turn marginality and ambiguity into social and economic spaces essential for communal life and economy, albeit with uncertain outcomes. These spaces are not locally bounded but part of shifting trajectories of power in the global market and the urban order of Vietnam. [waste, rural migrants, performance, urban space, Vietnam]
Petitioning a giant: Debt, reciprocity, and mortgage modification in the Sacramento Valley
Authors: STOUT NOELLE
Published: February 2016

Following the 2007 mortgage crash, the US government established programs to assist homeowners by modifying their mortgages. But the oversight of these programs was granted to the same mortgage industry giants that provoked the crisis, and these lenders rejected over 70 percent of applicants’ requests for modifications. In the process, there emerged new mortgage‐modification bureaucracies, fusing corporate and state forms of administrative power. Yet as mortgagors demanded assistance from private lenders, they and lending company employees were drawn into reciprocal relationships that anthropologists have previously associated with “gift economies.” This convergence of government and corporate bureaucracies has inspired among homeowners and modification specialists in California's Sacramento Valley forms of reciprocity often considered antithetical to late‐capitalist finance. This surprising contemporary juxtaposition of reciprocity and indebtedness suggests a need to revise long‐standing anthropological theories about the social obligations born of debt ties within late liberal capitalist markets. [bureaucracy, corporations, debt, foreclosure, mortgaging, reciprocity, United States]
Ethical reasoning in business‐to‐business negotiations: evidence from relationships in the chemical industry in Germany
Authors: Moosmayer Dirk C. , Niemand Thomas , Siems Florian U.
Published: February 2016

This article explores managers’ ethical reasoning for behaviors in price negotiations using evidence from 15 in‐depth interviews conducted with sales and purchasing representatives in the chemical industry in Germany. Applying transaction cost economics, we find that negotiators in commoditized market‐like exchanges either refer to deontological norms such as not to lie, or they neglect a role for ethics, arguing that distributive negotiation is per se opportunistic. In contrast, exchanges of products with higher asset specificity lead to stronger informational integration which is supported with teleological justifications. Some negotiators use teleological justification to build business on trust rather than on economic safeguards as their firm norms would require. For negotiators, our results suggest considering institutional context and adjusting ethical reasoning to the negotiation situation. Firms need to recognize and find ways to address the potential conflicts of their internal norms with their frontline managers’ attempts to act in the firms’ best economic and ethical interests.
Stability and Marginal Bone Level Changes of SLActive Titanium‐Zirconium Implants Placed with Flapless Surgery: A Prospective Pilot Study
Authors: Altinci Pinar , Can Gulsen , Gunes Onur , Ozturk Caner , Eren Hakan
Published: February 2016

Background

Immediately‐loaded, narrow‐diameter implants can be a less invasive alternative for the implant‐supported fixed rehabilitation of narrow, posterior crests.

Purpose

To determine the stability and marginal bone level (MBL) changes of narrow‐diameter, titanium‐zirconium (TiZr) implants placed with flapless surgery and loaded immediately in the posterior region.

Materials and Methods

Thirty‐eight TiZr implants (3.3 mm diameter, 10 mm length, Roxolid, Straumann AG) were placed in the posterior crests of 14 patients with computer‐guided flapless surgery as a support of 3‐unit posterior bridges. Eighteen implants were loaded immediately, and 20 implants were loaded conventionally. The implant stability quotients were determined at the 1, 2, 4, and 8. weeks of healing before conventional loading, and at the 3, 6, and 12. months after loading by resonance frequency analysis. The MBL changes were measured by digital radiography.

Results

The surgical protocols were accomplished without any biological complications. There was no significant difference in the stability changes of TiZr implants between the loading groups (p > .05). The MBL changes were −0.18 ± 0.27 mm and −0.24 ± 0.27 mm at the 12. month of immediate and conventional loading, respectively, which was not statistically significant (p > .05).

Conclusion

The stability and MBL changes of TiZr implants supporting posterior 3‐unit bridges were clinically acceptable at the first year of loading.
Ethylhexylglycerin: a low‐risk, but highly relevant, sensitizer in ‘hypo‐allergenic’ cosmetics
Authors: Aerts Olivier , Verhulst Lien , Goossens An
Published: February 2016

Background

Ethylhexylglycerin is a relatively new cosmetic ingredient that is used for its surfactant, emollient, skin‐conditioning and antimicrobial properties. Since 2002, it has been occasionally reported as a contact allergen.

Objectives

To report on 13 patients who presented with allergic contact dermatitis caused by ethylhexylglycerin, evaluated at two Belgian university patch test clinics during the period 1990–2015.

Patients and methods

The patients were patch tested with the European baseline series, a cosmetic series, and – if indicated – additional series. Both the cosmetic products used and their single ingredients were patch tested.

Results

All but one of the ethylhexylglycerin‐allergic patients were female, with a median age of 43 years (range: 29–81 years), most often suffering from dermatitis on the face, and sometimes on the hands and/or axillae. As the culprit products, leave‐on cosmetics were identified, including a high number of proclaimed ‘hypo‐allergenic’ and ‘preservative‐free’ facial creams, sun protection creams, and deodorants.

Conclusions

Ethylhexylglycerin is a rare, but highly relevant, cosmetic sensitizer, even in those products advertised to be safe for consumers. Targeted patch testing with ethylhexylglycerin 5% pet. is very useful, and routine patch testing in a cosmetic series may be considered. Higher test concentrations might be indicated in selected cases.
Accidental aspiration of denture cleanser tablets caused severe mucosal edema in upper airway
Authors: Ochi Nobuaki , Yamane Hiromichi , Honda Yoshihiro , Takigawa Nagio
Published: February 2016

A 78‐year‐old man accidentally swallowed denture cleanser tablets (Polident®). Although he immediately spat them out, he felt difficulty in breathing. Observation using a fiber optic bronchoscope revealed a constricted glottis with edema and redness. The instillation of 1% xylocaine with epinephrine to the epiglottis and larynx reduced the edema and enabled the bronchoscope to pass the glottis. Red and edematous mucosa of the trachea and major bronchus were also observed. We should be aware that accidental aspiration of denture cleansers may cause laryngeal edema.
Interactions between levels of attention ability and levels of bilingualism in children's executive functioning
Authors: Sorge Geoff B. , Toplak Maggie E. , Bialystok Ellen
Published: February 2016

Attention difficulty is associated with poor performance on executive functioning (EF) tasks, yet EF is enhanced in bilingual children. However, no research to date has investigated the possible interaction between bilingualism and attention ability in children to determine the consequences for EF when both are present. We assessed a sample of typically developing children who were 8 to 11 years old for their ability in attention control and level of bilingualism on the basis of questionnaires completed by parents and teachers. Children performed three tasks requiring aspects of EF: stop signal task (inhibition), flanker task (interference control), and frogs matrices task (spatial working memory). Results from hierarchical regressions confirmed that both attention ability and bilingualism contributed to performance on the EF tasks. Where interaction effects were significant, they showed that attention ability was a stronger predictor for an inhibition task, namely stop signal, and bilingualism a stronger predictor for an interference task, namely flanker. Furthermore, these results allow us to discuss the relation between EF and attention ability.
Prevention of antibiotic‐associated metabolic syndrome in mice by intestinal alkaline phosphatase
Authors: Economopoulos K. P. , Ward N. L. , Phillips C. D. , Teshager A. , Patel P. , Mohamed M. M. , Hakimian S. , Cox S. B. , Ahmed R. , Moaven O. , Kaliannan K. , Alam S. N. , Haller J. F. , Goldstein A. M. , Bhan A. K. , Malo M. S. , Hodin R. A.
Published: February 2016

Aims

To examine whether co‐administration of intestinal alkaline phosphatase (IAP) with antibiotics early in life may have a preventive role against metabolic syndrome (MetS) in mice.

Methods

A total of 50 mice were allocated to four treatment groups after weaning. Mice were treated with azithromycin (AZT) ± IAP, or with no AZT ± IAP, for three intermittent 7‐day cycles. After the last treatment course, the mice were administered a regular chow diet for 5 weeks and subsequently a high‐fat diet for 5 weeks. Body weight, food intake, water intake, serum lipids, glucose levels and liver lipids were compared. 16S rRNA gene pyrosequencing was used to determine the differences in microbiome composition.

Results

Exposure to AZT early in life rendered mice susceptible to MetS in adulthood. Co‐administration of IAP with AZT completely prevented this susceptibility by decreasing total body weight, serum lipids, glucose levels and liver lipids to the levels of control mice. These effects of IAP probably occur as a result of changes in the composition of specific bacterial taxa at the genus and species levels (e.g. members of Anaeroplasma and Parabacteroides).

Conclusions

Co‐administration of IAP with AZT early in life prevents mice from susceptibility to the later development of MetS. This effect is associated with alterations in the composition of the gut microbiota. IAP may represent a novel treatment against MetS in humans.