bluuebunny/crossref_metadata_2025 huggingface dataset:
A Case of Unresolving Pneumonia
Authors: Hosokawa Sawako Kaku , Yamamoto Shuhei , Kataoka Yuki , Shimizu Taro
Published: June 2016

A 33‐year‐old woman was transferred to our hospital for an unresolving pneumonia, who initially presented with dyspnea. Initially antibiotic therapy was started under the suspicion of community‐acquired pneumonia, however, her respiratory status worsened at the previous hospital. Computed tomography (CT) on presentation showed peripheral ground glass opacities in both sides of the upper lobe. Also despite additional prednisolone therapy, her respiratory status worsened. On admission to our hospital, physical examination showed Gottoron's sign in her right elbow. From the nature of the rash, the absence of myositis symptoms and rapid respiratory worsening, we suspected clinically amyopathic dermatomyositis (CADM). After the triple drug therapy, her respiratory status improved.
A Case of Pyogenic Vertebral Osteomyelitis: Importance of Physical Examination for Correct Diagnosis
Authors: Ozaka Akihiro , Onishi Tsubasa , Ueda Yuki , Kenzaka Tsuneaki , Matsumura Masami
Published: June 2016

A 76‐year‐old‐man was admitted to hospital because of fever and back pain. Blood cultures yielded extended‐spectrum beta‐lactamase‐producing Escherichia coli (ESBLEC). We suspected pyogenic vertebral osteomyelitis (PVO) secondary to urosepsis. However, magnetic resonance imaging (MRI) of the lumbar spine did not reveal findings of PVO. The extent of tenderness in the back converged on the lumbar spine on repeated physical examinations. We decided to perform a second MRI, and it showed hypointensity on T1‐weighted images and contrast enhancement in L3/L4. Culture of computed tomography guided L3/L4 disc biopsy yielded ESBLEC. Daily repeated physical examinations contributed to the correct diagnosis.
Desregulación y personalización en escuelas de elite: El trabajo de los profesores para la consagración escolar de los sectores privilegiados
Authors: Ziegler Sandra
Published: June 2016

El presente artículo se basa en un estudio cualitativo desarrollado en tres escuelas secundarias de la Ciudad y la Provincia de Buenos Aires que se proclaman como formadoras de elite. La intención del mismo es analizar la labor pedagógica que desarrollan estas instituciones en base a las formas de promoción y acompañamiento que plantean a sus estudiantes. El trabajo identifica en las escuelas formas desreguladas en donde los alumnos quedan librados a sus propios recursos para transitar la escolaridad y estrategias de personalización previstas desde la instituciones que presuponen un mayor acompañamiento a los estudiantes. Estas diferencias están vinculadas con los sistemas de selección académica y promoción que sustentan los establecimientos. Por promoción de los estudiantes se hace referencia a los mecanismos institucionales que concretan la función selectiva que desempeñan las instituciones educativas. En este caso en particular se analizan los medios que estas escuelas instrumentan para seleccionar, diferenciar y legitimar a los estudiantes en escuelas orientadas a la preparación de los grupos selectos. Indagar estas dinámicas nos permite una aproximación al funcionamiento de estas instituciones y su contribución en los procesos de socialización y reproducción para la preparación de determinados sectores para la ocupación de posiciones de elite. En este trabajo se aborda además el papel que desarrollan los profesores en tanto operadores simbólicos que, mediante su trabajo, efectúan la labor de producir la consagración escolar de estos grupos en cuestión.
From Periphery to Center
Authors: Heinze Thomas , Hallonsten Olof , Heinecke Steffi
Published: June 2016

In its fifty-year history, the German national research laboratory DESY (Deutsches Elektronen-Synchrotron, German Electron Synchrotron) has undergone a gradual transformation from a single-mission particle physics laboratory to a multi-mission research center for accelerator physics, particle physics, and photon science. The last is an umbrella term for research using synchrotron radiation and, in later years, free-electron laser. Synchrotron radiation emerged initially as a peripheral part of the laboratory activities but grew to become a central experimental activity at DESY via a series of changes in the organizational, scientific, and infrastructural setup of the lab, and in its contextual scientific, political, and societal environment. Together with an earlier publication on the issue in this journal,1 this article chronicles the first thirty years in the history of synchrotron radiation at DESY. The focus is on the gradual transformation of DESY’s research program in synchrotron radiation from peripheral and parasitic into mainstream and mission. We provide insights about the crucial renewal of Big Science laboratories toward the end of the twentieth century. This renewal culminated in the close-down of several particle physics machines in the early 2000s and their replacement by facilities dedicated to the study of the structure, properties, and dynamics of matter by the interaction with vacuum ultraviolet and X-ray photons. Therefore, we contribute to better understanding the growth of synchrotron radiation as a laboratory resource, and processes of renewal in Big Science as part of the general history of late-twentieth-century science.
Bred for the Race
Authors: Tyrrell Brian
Published: June 2016

In the first four decades of the twentieth century, horse racing was one of America’s most popular spectator sports. Members of America’s elite took to breeding and racing horses as one of their preferred pastimes. Coinciding with an increase in immigration and the rediscovery of Mendelian genetics, the idea that careful breeding of thoroughbreds would result in improved horses resonated with Americans worried about racial degeneration. Scientists committed to racial ideologies looked to thoroughbreds—whose owners and breeders maintained extensive pedigree records—to understand the science of genetic inheritance. Harry H. Laughlin, superintendent of research at the Eugenics Record Office at Cold Spring Harbor, Long Island, pored over breeding charts and race results to develop a mathematical model of inheritance that he called the “inheritance coefficient.” He believed his careful study of horses would yield findings that he and his fellow eugenicists could apply to humans. Thoroughbred breeders followed trends in genetics while contributing to the production of scientific knowledge. Pedigree charts available to bettors at race tracks helped normalize concepts of biological inheritance for race track attendees of all classes. Horse racing’s popularity in the United States contributed to the diffusion of the concept of biological race that originated as an ideological project of the ruling class. This paper analyzes the role of thoroughbred breeding and racing in the formation and popularization of racial ideology by situating breeding farms as sites of knowledge production and racecourses as places that exhibited performances of racial science for large audiences.
A Climate for Science Policy
Authors: Wallace Matthew L.
Published: June 2016

Led by the Meteorological Service of Canada, atmospheric research in Canada underwent a period of rapid growth after the end of the Second World War. Within this federal organization, and in response to operational challenges and staff shortages, there were significant investments in basic research and in research oriented toward external users within Canada. Specifically, new policies and programs were put in place to enable the organization to gain legitimacy within the scientific community and within the federal government. New links with stakeholders and, more importantly, the development of explicit policies to guide research were a prime focus. These formalized strategies for pursuing two parallel types of research generated some internal conflict, but also helped form a common scientific identity among personnel. There were concerted efforts to disseminate research products and reinforce links both with the scientific community and with external users of meteorological and climatological research. Borne out by quantitative data, this science policy–centered history sheds light on the development of research and research specializations in the field in Canada. Most importantly, it provides insight into the global postwar expansion of the atmospheric sciences, which is strongly tied to national contexts. Indeed, the quest for legitimacy and the close connection to government priorities is central to the history of the atmospheric sciences in the twentieth century. More broadly, this case study points to a possible new conception of government science driven by political, bureaucratic, and scientific imperatives, as a means to shed light on scientific networks and practices.
Seeing Jaws
Authors: Martin Jennifer A.
Published: June 2016

Few scientists played a greater role in constructing how Americans envisioned sharks than marine biologist Perry W. Gilbert. From the 1940s to the 1980s, he and a handful of other scientists linked earlier investigations of morphology with newer studies on populations and ecosystem dynamics to understand predation in marine environments. Investigators often abstracted sharks by privileging body parts, such as the jaws or eyes, in ways that made it difficult to see this group of animals within larger ecological or historical contexts. Starting in the 1960s, shark tagging studies helped convince a growing number of researchers that these creatures were vulnerable to overexploitation.
Retouching the Past with Living Things
Authors: Jiang Lijing
Published: June 2016

Chinese scientists working during the early twentieth century are often understood as radical modernizers. A close examination of research practices in biology at the time, however, complicates such a view. Influential biologists in Nanjing examined in this paper appropriated traditional styles, concerns, and knowledge as crucial constituents in conducting and communicating biological subjects, such as plant taxonomy, comparative anatomy, and goldfish evolution. This paper shows that the prioritized study of those species collected within China was crucial in sustaining traditional styles and knowledge essential to modern biology. As biologists reinterpreted classics, poems, Confucian morality, and historical texts, incorporating them into a scientific life, they changed what it meant to be traditional and scientifically modern at the same time. Particularly, these trends shaped a predominant focus on indigenous species and taxonomic science over experimentation in Nanjing, forging a direction that ran counter to an experimental turn in biology in the wider world. Emphasis on the importance of indigenous species for science, however, added to a full-blown scientific nationalism during the Nanjing Decade (1928–1937), when territorial and economic sovereignty became major concerns for the Guomindang government. With expanding research programs and communities, biologists increasingly presented species within China as potent symbols for national sovereignty in classrooms, at customs, and for museum display. By showing ways of appropriating indigenous species in these scientific and cultural activities, this paper exposes intricate associations between biological things and scientific nationalism in Republican China.
Patronage and Practice in British Oceanography
Authors: Carlsson-Hyslop Anna
Published: June 2016

The history of twentieth-century American physical oceanography concentrates on naval patronage, but its significance for British oceanography is largely unknown. This case study analyzes a varied patronage structure, including naval, industrial, academic, and local and central governmental support, for one site of British physical oceanography, the Liverpool Observatory and Tidal Institute and, in particular, its work on storm surges between 1919 and 1959. Storm surges, caused by wind and changes in barometric pressure, can produce dramatic changes in sea levels. The local shipping industry initially funded the Institute’s research on surge forecasting to improve the accuracy of tidal predictions. After a flood in 1928, however, the focus shifted to flood forecasting. Local government then backed their work, during the Second World War support came from the Royal Navy, and since a flood in 1953, from central government. This case study reveals the range of negotiations carried out between patrons and researchers, and demonstrates how researchers managed competing demands from academic interests and those of industry, the navy, and the government. Studying institutions that did not see a dramatic increase in state patronage during the early Cold War enables us to see the impact of patronage more clearly, highlighting how research interests and methods differed (or not) between institutions with different patronage structures.
Transmitting Knowledge across Divides
Authors: Taltavull Marta Jordi
Published: June 2016

One model, the resonance model, shaped scientific understanding of optical dispersion from the early 1870s to the 1920s, persisting across dramatic changes in physical conceptions of light and matter. I explore the ways in which the model was transmitted across these conceptual divides by analyzing the use of the model both in the development of theories of optical dispersion and in the interpretation of experimental data. Crucial to this analysis is the integration of the model into quantum theory because of the conceptual incompatibility between the model and quantum theory. What is more, a quantum understanding of optical dispersion set the grounds for the emergence of the first theories of quantum mechanics in 1925. A long-term history of the model’s transmission from the 1870s to the 1920s illuminates the ways in which the continuity of knowledge is possible across these discontinuities.
Writing the Discipline
Authors: Simon Josep
Published: June 2016

The historiography of physics has reached a great degree of maturity and sophistication, providing many avenues to consider the making of science from a historical perspective. However, the big picture of the making of physics is characterized by a predominant narrative focused on a conception of disciplinary formation through leadership transfers in research among France, Germany, and Britain. This focus has provided the history of physics with a periodization, a geography, and a fundamental goal commonly considered to be conceptual and theoretical unification. In this paper, I suggest the interest of reassessing this picture by analyzing the temporal, national, and epistemological viewpoint from which it is written. I use for this purpose an exemplary case study: Adolphe Ganot’s physics textbooks in France and their translation by Edmund Atkinson in England. In this context, I suggest future avenues for the study of the making of physics as a discipline, which consider the canonical role of textbooks in disciplinary formation beyond the Kuhnian paradigm.
AKT isoforms modulate Th1‐like Treg generation and function in human autoimmune disease
Authors: Kitz Alexandra , de Marcken Marine , Gautron Anne‐Sophie , Mitrovic Mitja , Hafler David A , Dominguez‐Villar Margarita
Published: June 2016

Foxp3+ regulatory T cells (Tregs) exhibit plasticity, which dictates their function. Secretion of the inflammatory cytokine IFNγ, together with the acquisition of a T helper 1 (Th1)‐like effector phenotype as observed in cancer, infection, and autoimmune diseases, is associated with loss of Treg suppressor function through an unknown mechanism. Here, we describe the signaling events driving the generation of human Th1‐Tregs. Using a genome‐wide gene expression approach and pathway analysis, we identify the PI3K/AKT/Foxo1/3 signaling cascade as the major pathway involved in IFNγ secretion by human Tregs. Furthermore, we describe the opposing roles of AKT isoforms in Th1‐Treg generation ex vivo. Finally, we employ multiple sclerosis as an in vivo model with increased but functionally defective Th1‐Tregs. We show that the PI3K/AKT/Foxo1/3 pathway is activated in ex vivo‐isolated Tregs from untreated relapsing–remitting MS patients and that blockade of the pathway inhibits IFNγ secretion and restores the immune suppressive function of Tregs. These data define a fundamental pathway regulating the function of human Tregs and suggest a novel treatment paradigm for autoimmune diseases.
Genomic Signatures of Experimental Adaptation to Antimicrobial Peptides in Staphylococcus aureus
Authors: Johnston Paul R , Dobson Adam J , Rolff Jens
Published: June 2016

The evolution of resistance against antimicrobial peptides has long been considered unlikely due to their mechanism of action, yet experimental selection with antimicrobial peptides (AMPs) results in rapid evolution of resistance in several species of bacteria. Although numerous studies have utilized mutant screens to identify loci that determine AMP susceptibility, there is a dearth of data concerning the genomic changes that accompany experimental evolution of AMP resistance. Using genome resequencing, we analyzed the mutations that arose during experimental evolution of resistance to the cationic AMPs iseganan, melittin, and pexiganan, as well as to a combination of melittin and pexiganan, or to the aminoglycoside antibiotic streptomycin. Analysis of 17 independently replicated Staphylococcus aureus selection lines, including unselected controls, showed that each AMP selected for mutations at distinct loci. We identify mutations in genes involved in the synthesis and maintenance of the cell envelope. These include genes previously identified from mutant screens for AMP resistance, and genes involved in the response to AMPs and cell-wall-active antibiotics. Furthermore, transposon insertion mutants were used to verify that a number of the identified genes are directly involved in determining AMP susceptibility. Strains selected for AMP resistance under controlled experimental evolution displayed consistent AMP-specific mutations in genes that determine AMP susceptibility. This suggests that different routes to evolve resistance are favored within a controlled genetic background.
The Sorghum Gene for Leaf Color Changes upon Wounding (P) Encodes a Flavanone 4-Reductase in the 3-Deoxyanthocyanidin Biosynthesis Pathway
Authors: Kawahigashi Hiroyuki , Kasuga Shigemitsu , Sawada Yuji , Yonemaru Jun-ichi , Ando Tsuyu , Kanamori Hiroyuki , Wu Jianzhong , Mizuno Hiroshi , Momma Mitsuru , Fujimoto Zui , Hirai Masami Yokota , Matsumoto Takashi
Published: June 2016

Upon wounding or pathogen invasion, leaves of sorghum [Sorghum bicolor (L.) Moench] plants with the P gene turn purple, whereas leaves with the recessive allele turn brown or tan. This purple phenotype is determined by the production of two 3-deoxyanthocyanidins, apigeninidin and luteolinidin, which are not produced by the tan-phenotype plants. Using map-based cloning in progeny from a cross between purple Nakei-MS3B (PP) and tan Greenleaf (pp) cultivars, we isolated this gene, which was located in a 27-kb genomic region around the 58.1 Mb position on chromosome 6. Four candidate genes identified in this region were similar to the maize leucoanthocyanidin reductase gene. None of them was expressed before wounding, and only the Sb06g029550 gene was induced in both cultivars after wounding. The Sb06g029550 protein was detected in Nakei-MS3B, but only slightly in Greenleaf, in which it may be unstable because of a Cys252Tyr substitution. A recombinant Sb06g029550 protein had a specific flavanone 4-reductase activity, and converted flavanones (naringenin or eriodictyol) to flavan-4-ols (apiforol or luteoforol) in vitro. Our data indicate that the Sb06g029550 gene is involved in the 3-deoxyanthocyanidin synthesis pathway.
The HIST1 Locus Escapes Reprogramming in Cloned Bovine Embryos
Authors: Min Byungkuk , Cho Sunwha , Park Jung Sun , Jeon Kyuheum , Kang Yong-Kook
Published: June 2016

Epigenetic reprogramming is necessary in somatic cell nuclear transfer (SCNT) embryos in order to erase the differentiation-associated epigenetic marks of donor cells. However, such epigenetic memories often persist throughout the course of clonal development, thus decreasing cloning efficiency. Here, we explored reprogramming-refractory regions in bovine SCNT blastocyst transcriptomes. We observed that histone genes residing in the 1.5 Mb spanning the cow HIST1 cluster were coordinately downregulated in SCNT blastocysts. In contrast, both the nonhistone genes of this cluster, and histone genes elsewhere remained unaffected. This indicated that the downregulation was specific to HIST1 histone genes. We found that, after trichostatin A treatment, HIST1 histone genes were derepressed, and DNA methylation at their promoters was decreased to the level of in vitro fertilization embryos. Therefore, our results indicate that the reduced expression of HIST1 histone genes is a consequence of poor epigenetic reprogramming in SCNT blastocysts.
Several Critical Cell Types, Tissues, and Pathways Are Implicated in Genome-Wide Association Studies for Systemic Lupus Erythematosus
Authors: Liu Lu , Yin Xianyong , Wen Leilei , Yang Chao , Sheng Yujun , Lin Yan , Zhu Zhengwei , Shen Changbing , Shi Yinjuan , Zheng Yajie , Yang Sen , Zhang Xuejun , Cui Yong
Published: June 2016

We aimed to elucidate the cell types, tissues, and pathways influenced by common variants in systemic lupus erythematosus (SLE). We applied a nonparameter enrichment statistical approach, termed SNPsea, in 181 single nucleotide polymorphisms (SNPs) that have been identified to be associated with the risk of SLE through genome-wide association studies (GWAS) in Eastern Asian and Caucasian populations, to manipulate the critical cell types, tissues, and pathways. In the two most significant cells’ findings (B lymphocytes and CD14+ monocytes), we subjected the GWAS association evidence in the Han Chinese population to an enrichment test of expression quantitative trait locus (QTL) sites and DNase I hypersensitivity, respectively. In both Eastern Asian and Caucasian populations, we observed that the expression level of SLE GWAS implicated genes was significantly elevated in xeroderma pigentosum B cells (P ≤ 1.00 × 10−6), CD14+ monocytes (P ≤ 2.74 × 10−4) and CD19+ B cells (P ≤ 2.00 × 10−6), and plasmacytoid dendritic cells (pDCs) (P ≤ 9.00 × 10−6). We revealed that the SLE GWAS-associated variants were more likely to reside in expression QTL in B lymphocytes (q1/q0 = 2.15, P = 1.23 × 10−44) and DNase I hypersensitivity sites (DHSs) in CD14+ monocytes (q1/q0 = 1.41, P = 0.08). We observed the common variants affected the risk of SLE mostly through by regulating multiple immune system processes and immune response signaling. This study sheds light on several immune cells and responses, as well as the regulatory effect of common variants in the pathogenesis of SLE.
Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast
Authors: Larson Amy , Fair Benjamin Jung , Pleiss Jeffrey A
Published: June 2016

Pre-mRNA splicing is an essential component of eukaryotic gene expression and is highly conserved from unicellular yeasts to humans. Here, we present the development and implementation of a sequencing-based reverse genetic screen designed to identify nonessential genes that impact pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, an organism that shares many of the complex features of splicing in higher eukaryotes. Using a custom-designed barcoding scheme, we simultaneously queried ∼3000 mutant strains for their impact on the splicing efficiency of two endogenous pre-mRNAs. A total of 61 nonessential genes were identified whose deletions resulted in defects in pre-mRNA splicing; enriched among these were factors encoding known or predicted components of the spliceosome. Included among the candidates identified here are genes with well-characterized roles in other RNA-processing pathways, including heterochromatic silencing and 3ʹ end processing. Splicing-sensitive microarrays confirm broad splicing defects for many of these factors, revealing novel functional connections between these pathways.
Multiple Targets on the Gln3 Transcription Activator Are Cumulatively Required for Control of Its Cytoplasmic Sequestration
Authors: Rai Rajendra , Tate Jennifer J , Cooper Terrance G
Published: June 2016

A remarkable characteristic of nutritional homeostatic mechanisms is the breadth of metabolite concentrations to which they respond, and the resolution of those responses; adequate but rarely excessive. Two general ways of achieving such exquisite control are known: stoichiometric mechanisms where increasing metabolite concentrations elicit proportionally increasing responses, and the actions of multiple independent metabolic signals that cumulatively generate appropriately measured responses. Intracellular localization of the nitrogen-responsive transcription activator, Gln3, responds to four distinct nitrogen environments: nitrogen limitation or short-term starvation, i.e., nitrogen catabolite repression (NCR), long-term starvation, glutamine starvation, and rapamycin inhibition of mTorC1. We have previously identified unique sites in Gln3 required for rapamycin-responsiveness, and Gln3-mTor1 interaction. Alteration of the latter results in loss of about 50% of cytoplasmic Gln3 sequestration. However, except for the Ure2-binding domain, no evidence exists for a Gln3 site responsible for the remaining cytoplasmic Gln3-Myc13 sequestration in nitrogen excess. Here, we identify a serine/threonine-rich (Gln3477–493) region required for effective cytoplasmic Gln3-Myc13 sequestration in excess nitrogen. Substitutions of alanine but not aspartate for serines in this peptide partially abolish cytoplasmic Gln3 sequestration. Importantly, these alterations have no effect on the responses of Gln3-Myc13 to rapamycin, methionine sulfoximine, or limiting nitrogen. However, cytoplasmic Gln3-Myc13 sequestration is additively, and almost completely, abolished when mutations in the Gln3-Tor1 interaction site are combined with those in Gln3477–493 cytoplasmic sequestration site. These findings clearly demonstrate that multiple individual regulatory pathways cumulatively control cytoplasmic Gln3 sequestration.
Genetic Background, Maternal Age, and Interaction Effects Mediate Rates of Crossing Over inDrosophila melanogasterFemales
Authors: Hunter Chad M , Robinson Matthew C , Aylor David L , Singh Nadia D
Published: June 2016

Meiotic recombination is a genetic process that is critical for proper chromosome segregation in many organisms. Despite being fundamental for organismal fitness, rates of crossing over vary greatly between taxa. Both genetic and environmental factors contribute to phenotypic variation in crossover frequency, as do genotype–environment interactions. Here, we test the hypothesis that maternal age influences rates of crossing over in a genotypic-specific manner. Using classical genetic techniques, we estimated rates of crossing over for individual Drosophila melanogaster females from five strains over their lifetime from a single mating event. We find that both age and genetic background significantly contribute to observed variation in recombination frequency, as do genotype–age interactions. We further find differences in the effect of age on recombination frequency in the two genomic regions surveyed. Our results highlight the complexity of recombination rate variation and reveal a new role of genotype by maternal age interactions in mediating recombination rate.
Sdt97: A Point Mutation in the 5′ Untranslated Region Confers Semidwarfism in Rice
Authors: Tong Jiping , Han Zhengshu , Han Aonan , Liu Xuejun , Zhang Shiyong , Fu Binying , Hu Jun , Su Jingping , Li Shaoqing , Wang Shengjun , Zhu Yingguo
Published: June 2016

Semidwarfism is an important agronomic trait in rice breeding programs. The semidwarf mutant gene Sdt97 was previously described. However, the molecular mechanism underlying the mutant is yet to be elucidated. In this study, we identified the mutant gene by a map-based cloning method. Using a residual heterozygous line (RHL) population, Sdt97 was mapped to the long arm of chromosome 6 in the interval of nearly 60 kb between STS marker N6 and SNP marker N16 within the PAC clone P0453H04. Sequencing of the candidate genes in the target region revealed that a base transversion from G to C occurred in the 5′ untranslated region of Sdt97. qRT-PCR results confirmed that the transversion induced an obvious change in the expression pattern of Sdt97 at different growth and developmental stages. Plants transgenic for Sdt97 resulted in the restoration of semidwarfism of the mutant phenotype, or displayed a greater dwarf phenotype than the mutant. Our results indicate that a point mutation in the 5′ untranslated region of Sdt97 confers semidwarfism in rice. Functional analysis of Sdt97 will open a new field of study for rice semidwarfism, and also expand our knowledge of the molecular mechanism of semidwarfism in rice.
Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain ofSaccharomyces cerevisiaeUsed in Biofuels Research
Authors: McIlwain Sean J , Peris David , Sardi Maria , Moskvin Oleg V , Zhan Fujie , Myers Kevin S , Riley Nicholas M , Buzzell Alyssa , Parreiras Lucas S , Ong Irene M , Landick Robert , Coon Joshua J , Gasch Audrey P , Sato Trey K , Hittinger Chris Todd
Published: June 2016

The genome sequences of more than 100 strains of the yeast Saccharomyces cerevisiae have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of S. cerevisiae derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assembly approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any S. cerevisiae strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. The Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.
Race and 30-Day Morbidity in Pediatric Urologic Surgery
Authors: Chu David I. , Canning Douglas A. , Tasian Gregory E.
Published: June 2016

BACKGROUND AND OBJECTIVE:

Quality improvement in surgery involves identifying patients at high risk for postoperative complications. We sought to assess the impact of race and procedure type on 30-day surgical morbidity in pediatric urology.

METHODS:

The National Surgical Quality Improvement Program–Pediatrics (NSQIP-P) is a prospective registry of surgical cases from 50 and 56 pediatric hospitals in 2012 and 2013, respectively. We performed a cohort study of children followed in NSQIP-P who underwent urologic surgery. Forty unique operations were stratified into 6 clinically related procedure groups: ureteral, testicular, renal, urinary diversion, penile and urethral, or bladder procedures. Outcomes were 3 different composite measures of 30-day morbidity. Primary predictors were patient race and procedural group. Multivariate logistic regression was used to identify associations between race, procedure type, and postoperative morbidity.

RESULTS:

Of 114 395 patients in the NSQIP-P cohort, 11 791 underwent pediatric urologic procedures. Overall 30-day complication rate was 5.9% and was higher in bladder and urinary diversion procedures. On multivariate analyses, non-Hispanic black compared with non-Hispanic white children had higher odds of 30-day overall complications (odds ratio 1.34; 95% confidence interval, 1.03–1.74) and 30-day hospital-acquired infection (odds ratio 1.54; 95% confidence interval, 1.08–2.20). Bladder and urinary diversion procedures relative to testicular procedures had significantly higher odds of surgical morbidity across all composite outcome measures.

CONCLUSIONS:

Black race and bladder and urinary diversion operations were significantly associated with 30-day surgical morbidity. Future efforts should identify processes of care that decrease postoperative morbidity among children.
Spiritual Care and Logotherapy
Authors: Heyen Heye , Jonker Evert , Walton Martin
Published: June 2016

Chaplaincy and logotherapy seem related in several ways (conversational accompaniment, client centredness, confrontation of suffering, attention to meaning), but their practitioners seem little aware of each other. The authors clarify the different roles of chaplain and therapist by referring to Frankl’s distinction between salvation and healing of the soul. “Salvation” is reinterpreted as relationship to God. Concern is expressed on the instrumentalization of religion in coping. Ironically, logotherapy challenges chaplaincy to reconsider the question of truth and differentiation of values and chaplaincy challenges logotherapists to focus on acceptance of clients in a manner that can question some logotherapeutic dogmas.
Socio-Cultural Aspects of the Development of Contemporary Clinical Pastoral Care in Estonia
Authors: Meel Liidia
Published: June 2016

The current paper addresses the societal context of clinical pastoral care in Estonia, aiming to provide proposals for organizing the practice and education of clinical pastoral caregivers. The purpose is to identify the societal factors and to analyse the corresponding aspects of the development of contemporary clinical pastoral care in Estonia. Data originates from the Statistics Estonia database (2010–2015), related studies of the Estonian population and public information about Estonian health care institutions. Societal factors are identified as follows: (a) issues connected to patients’ psychosocial and material coping, (b) ethnic groups, spoken languages, (c) secularism and religious diversity. The proposed development of clinical pastoral care in Estonia would concentrate on: (a) interdisciplinarity in education and practice, (b) knowledge in cultural traditions, language skills, (c) finding the common ground for supporting the patients in secularism and religious diversity. Suggestions may also apply and contribute to the discussion in other countries with similar societal characteristics.
New Zealand Defence Forces and Spirituality
Authors: Hill Emily , Egan Richard , Llewellyn Rebecca , McBride David
Published: June 2016

In the context of military chaplaincy changing alongside a fluid global and New Zealand spiritual environment, this study aimed to elucidate the nature of New Zealand Defence Force (NZDF) chaplains’ (Padres’) role as providers of spiritual care to military personnel. Twelve NZDF Padres were interviewed and the transcripts thematically analysed. Three overarching themes emerged. Firstly, definitions and understandings of spirituality were informed by a Christian framework, however this often remained unspoken in their approach. Secondly Padres’ pastoral approach was holistic and relational as they actively lived and trained with other personnel. Thirdly, Padres acknowledged various role tensions, for example between their Christian values and the defence force mandate to use lethal force. Padres clearly professionally navigate the multi-cultural, multi-faith and non-faith needs that arise in the contemporary NZDF.
How Could Co-production Principles Improve Mental Health Spiritual and Pastoral Care (Chaplaincy) Services?
Authors: Wood Emily , Raffay Julian , Todd Andrew
Published: June 2016

This report reflects on our experiences of using co-production in mental health chaplaincy research and how the lessons learned can be applied both to research and to service design and delivery in the NHS. A panel of experts by experience was recruited to assist in planning and implementing a research project to explore service users’ views of NHS mental health chaplaincy (spiritual and pastoral care services). Both the panel and the interviewees provided clear insights into how services could be run in a more patient-centred manner, participants were thoughtful, usually realistic and considered in their suggestions. Recruitment was not difficult suggesting that those who use mental health services are keen to share their opinions on the spiritual care they receive. Eliciting views from service users in different Trusts will show if our findings can be considered representative of the UK.
Feeding the Dead: Ancestor Worship in Ancient India, by Matthew R. Sayers
Authors: Brodbeck Simon
Published: June 2016

Feeding the Dead: Ancestor Worship in Ancient India, by Matthew R. Sayers. New York: Oxford University Press, 2013. xvi + 188 pp., £64.00 (hb), £19.99 (pb). ISBN 978-0-19-991747-1 (hb), 978-0-19-989643-1 (pb).
Seva
Authors: Beckerlegge Gwilym
Published: June 2016

The study of seva in the Hindu tradition has increasingly come to focus on its relatively recent meaning of organized 'humanitarian service'. Acknowledging that this is but one understanding that has been attached to this concept, this article traces the emergence of a more clearly defined body of scholarly studies centred on the promotion of the practice of humanitarian service as a sadhana by Hindu movements and their teachers since the early nineteenth century. Noting links between the study of seva, social reform in India, voluntary action, and national and international humanitarianism, the article argues for the importance of this branch of study in the early twenty-first century.
Loss of Cystic Fibrosis Transmembrane Regulator Impairs Intestinal Oxalate Secretion
Authors: Knauf Felix , Thomson Robert B. , Heneghan John F. , Jiang Zhirong , Adebamiro Adedotun , Thomson Claire L. , Barone Christina , Asplin John R. , Egan Marie E. , Alper Seth L. , Aronson Peter S.
Published: June 2016

Patients with cystic fibrosis have an increased incidence of hyperoxaluria and calcium oxalate nephrolithiasis. Net intestinal absorption of dietary oxalate results from passive paracellular oxalate absorption as modified by oxalate back secretion mediated by the SLC26A6 oxalate transporter. We used mice deficient in the cystic fibrosis transmembrane conductance regulator gene (Cftr) to test the hypothesis that SLC26A6–mediated oxalate secretion is defective in cystic fibrosis. We mounted isolated intestinal tissue from C57BL/6 (wild-type) and Cftr−/−
mice in Ussing chambers and measured transcellular secretion of [14C]oxalate. Intestinal tissue isolated from Cftr−/−
mice exhibited significantly less transcellular oxalate secretion than intestinal tissue of wild-type mice. However, glucose absorption, another representative intestinal transport process, did not differ in Cftr−/−
tissue. Compared with wild-type mice, Cftr−/−
mice showed reduced expression of SLC26A6 in duodenum by immunofluorescence and Western blot analysis. Furthermore, coexpression of CFTR stimulated SLC26A6–mediated Cl−–oxalate exchange in Xenopus oocytes. In association with the profound defect in intestinal oxalate secretion, Cftr−/−
mice had serum and urine oxalate levels 2.5-fold greater than those of wild-type mice. We conclude that defective intestinal oxalate secretion mediated by SLC26A6 may contribute to the hyperoxaluria observed in this mouse model of cystic fibrosis. Future studies are needed to address whether similar mechanisms contribute to the increased risk for calcium oxalate stone formation observed in patients with cystic fibrosis.
Monetary Policy, Real Activity, and Credit Spreads: Evidence from Bayesian Proxy SVARs
Authors: Caldara Dario , Herbst Edward
Published: June 2016

This paper studies the interaction between monetary policy, financial markets, and the real economy. We develop a Bayesian framework to estimate proxy structural vector autoregressions (SVARs) in which monetary policy shocks are identified by exploiting the information contained in high frequency data. For the Great Moderation period, we find that monetary policy shocks are key drivers of fluctuations in industrial output and corporate credit spreads, explaining about 20 percent of the volatility of these variables. Central to this result is a systematic component of monetary policy characterized by a direct and economically significant reaction to changes in credit spreads. We show that the failure to account for this endogenous reaction induces an attenuation bias in the response of all variables to monetary shocks.
Bullying y Género. Prevención desde la Organización Escolar
Authors: Duque Sanchez Elena , Teixido Joan
Published: June 2016

Homophobia, biphobia, transphobia and gender violence in sexual-affective relationships appear frequently in the bases of bullying. The educational centres are more conscious about this reality and look for actions to prevent and eradicate this kind of violence. At the same time, international research states that bullying prevention needs a re-organization of the educational centre incorporating the work of all the educational community (students, family, teachers, etc.). In this article we gather data on bullying and its connection to gender, part of the Spanish legislation related to this problem is analysed and we conducted an international literature review. The main contribution of this article is to present orientations and actions that prevent and contribute to eradicate gender violence and violence for homophobia, biphobia and transphobia through the school organization and school management. Some of these actions are inclusive education, democratization of the centres, making visible and not trivializing violence, and mainly the community participation and active positioning of all the community against bullying and in favour of the victims.
Social Media in the Sexual Lives of African American and Latino Youth: Challenges and Opportunities in the Digital Neighborhood
Authors: Stevens Robin , Dunaev Jamie , Malven Ellen , Bleakley Amy , Hull Shawnika
Published: June 2016

There has been significant interest in the role of social media in the lives of adolescents, particularly as it relates to sexual risk. Researchers have focused on understanding usage behaviors, quantifying effects of social media exposure and activity, and using social media to intervene. Much of this work has focused on college students and non-minority youth. In this paper, we examine the growing body of literature around social media use among US minority youth and its intersection with sexual risk behavior. We introduce the concept of the “digital neighborhood” and examine the intersection of social media and sexual health in two domains: 1) sexual content in social media and 2) evidence of social media effects on sexual behavior. Finally, we discuss the opportunities and challenges for researchers and practitioners engaging youth of color.
Cyberbullying, Race/Ethnicity and Mental Health Outcomes: A Review of the Literature
Authors: Edwards Lynne , Kontostathis April Edwards , Fisher Christina
Published: June 2016

Cyberbullying is a relatively new phenomenon associated with the widespread adoption of various digital communication technologies, including the internet and mobile phones. As of 2013, nearly 20% of youths in grades 9–12 in the US reported being traditionally bullied in face-to-face encounters while almost 15% reported being cyberbullied (Kann et al., 2014). Bullying victimization is associated with a variety of behavioral and psychological effects, from becoming bullies themselves (i.e., bully-victims), to poor academic performance, depression and suicidal ideation (Nansel et al., 2001; Wang, Nansel, & Iannotti, 2011; Willard, 2007). Research on these phenomena has focused primarily on white youth, leaving a void in our understanding of how cyberbullying has affected youth of color. This narrative literature review addresses this oversight by providing an overview of recent cyberbullying research that focuses on Hispanic, Asian and black adolescents (k=15). We found that youth of color appear to be less likely to experience cyberbullying than white youth but they experience suicidal ideation and attempts at about the same rates when they do experience cyberbullying.
Afterword to the Issue “Adolescents in the Digital Age: Effects on Health and Development”
Authors: Romer Daniel , Rich Michael
Published: June 2016

The articles in this thematic issue suggest both opportunities and hazards for the health and development of adolescents in the digital age. We place these concerns in the context of improving health for young people in the US and elsewhere, and suggest that based on evidence uncovered to date, increasing digital connection may be having no less favorable than adverse effect on adolescents.
Estilo de Vida Influencia Variáveis Antropométricas e Pressão Arterial em Adultos Jovens
Authors: Numata Filho Eduardo Seiji , Teixeira-Araujo Alfredo Anderson , Cruz Loumaíra Carvalho da , Araujo Flavio de Souza , Moreira Sérgio Rodrigues
Published: June 2016

A composição corporal e a pressão arterial (PA) podem sofrer influências de padrões do estilo de vida (EV). Desse modo, o objetivo deste trabalho foi investigar a influência do EV em variáveis antropométricas e PA em adultos jovens frequentadores de parque de lazer. Cento e quatro indivíduos de ambos os sexos (31±8 anos) responderam o Questionário “Estilo de Vida Fantástico” e foram submetidos a mensurações de PA, circunferência da cintura (CC), massa corporal e estatura para cálculo do índice de massa corporal (IMC). A amostra foi dividida por sexo e estratificada em “Baixo EV” (BEV; 0-69 pontos) e “Alto EV” (AEV; 70-100 pontos). Diferenças foram encontradas quando comparados os estratos BEV vs. AEV para massa corporal (Geral: 74±16 vs. 67±13 kg; Masc: 84±17 vs. 74±13 kg; Fem: 66±10 vs. 61±8 kg; p
Marcadores Moleculares como Ferramenta Auxiliar no Diagnóstico Citológico de Anormalidades Cervicais
Authors: Crisóstomo Catharine de Araújo , Melo-Júnior Mario Ribeiro de , Medeiros Adrya Lúcia Peres Bezerra de
Published: June 2016

O câncer cervical é a quarta neoplasia mais diagnosticada em mulheres no mundo e a terceira no Brasil. A principal abordagem para conter seu avanço é o rastreamento pelo exame citológico. Para melhorar o desempenho desse teste, estudos vêm demonstrando o potencial de biomarcadores moleculares, principalmente aqueles envolvidos na regulação do ciclo celular. A detecção dessas moléculas por técnicas como a imunocitoquímica apresenta boa correlação com o grau de lesão intraepitelial e diminui a variabilidade interobservador. Desse modo, o objetivo desse trabalho foi avaliar evidências científicas da eficiência dos marcadores p16INK4A, Ki-67, TopIIα e MCM2 em pacientes com anormalidades cervicais e/ou positivas para o DNA do HPV. Para a realização desta revisão sistemática da literatura, no período de maio e junho de 2015, buscaram-se artigos nas principais bases de dados com os descritores “biomarkers”, “molecular marker” e “cervical dysplasias”. Incluíram-se artigos originais publicados na última década (2004-2015). Foram selecionados 15 artigos que contemplaram os critérios. Observou-se que o índice de positividade dos quatro marcadores se correlaciona com a gravidade da lesão. Eles demonstram potencial para a identificação de lesões intraepiteliais de alto grau implícitas. A coloração imunocitoquímica para detecção dessas moléculas ajuda na localização de células potencialmente anormais e contribui para a identificação de mulheres com maior probabilidade de desenvolver o câncer cervical, melhorando a sensibilidade do exame citológico.