bluuebunny/crossref_metadata_2025 huggingface dataset:
Treatment and prevention dilemmas
Authors: Whiteside Alan
Published: April 2017

AIDS is still a major threat. ‘Treatment and prevention dilemmas’ shows that prevention and public health programmes are the most cost-effective way to health. HIV infection is preventable through biomedical strategies, such as ensuring safe blood and blood products by screening donors and testing donations; social interventions advising behaviour change, such as using condoms, having fewer partners, and practicing monogamy or abstinence; and—crucial to behaviour change—community mobilization and leadership. AIDS treatment developments are described along with the current state of antiretroviral therapy. Looking ahead, prevention remains the priority—while HIV infected people can live normal, productive lives, it is challenging and expensive.
3. Extrasolar tests of gravity
Authors: Clifton Timothy
Published: April 2017

By studying objects outside our Solar System, we can observe star systems with far greater gravitational fields. ‘Extrasolar tests of gravity’ considers stars of different sizes that have undergone gravitational collapse, including white dwarfs, neutron stars, and black holes. A black hole consists of a region of space-time enclosed by a surface called an event horizon. The gravitational field of a black hole is so strong that anything that finds its way inside the event horizon can never escape. Other star systems considered are binary pulsars and triple star systems. With the invention of even more powerful telescopes, there will be more tantalizing possibilities for testing gravity in the future.
1. The many faces of home
Authors: Fox Michael Allen
Published: April 2017

Homes are central to human life, but defining what home is can be problematic. Home is a fundamental and universal concept, yet it has multiple associated and layered meanings for different people in a great range of circumstances. ‘The many faces of home’ considers the somewhat elusive notion of home. It looks at the many origins of the word ‘home’, how home is understood in other languages, positive and negative attitudes to home, and the concepts of parochialism and cosmopolitanism. It concludes that home, for all of its immediate and more traditional associations, is actually a multi-faceted, problematic notion, and for many, an almost undefinable thing.
4. Remembering, imagining, and other mindwork
Authors: Fox Michael Allen
Published: April 2017

What we put into our concept of home through acts of memory and imagination is an enormous part of what home means to us. ‘Remembering, imagining, and other mindwork’ looks at reviving the past through remembering the home; nostalgia; and what returning home means to us. It also considers homes as symbolic expressions. Homes communicate from within, by virtue of their patterns of placement, construction, and use; and they are interpreted from without, according to certain presuppositions and perspectives. Homes model, mirror, elaborate, symbolize, appropriate, and incorporate meanings from the world at large. In these ways, home is connected with larger spheres of existence and narrative, establishing cultural identity.
5. Knowledge
Authors: Balserak Jon
Published: April 2017

According to Calvinism, what is known about the character of God is limited due to the inscrutable nature of God’s being and because God does not always choose to reveal his mind. ‘Knowledge’ explains that a further limitation is located in the human heart. Due to sin’s effect on human thinking, people do not want to know the true God. Instead, people try to invent their own God and to reduce God to something manageable and fully comprehensible. The different sources of theological knowledge, according to Calvinism, are described along with the belief that the Bible is historically accurate and a reliable source for knowledge about Jesus, God, and salvation.
3. Social lives
Authors: Baddeley Michelle
Published: April 2017

‘Social lives’ explores some of the main ways in which social influences drive behaviour, including aversion to unequal outcomes, trust and reciprocity, social learning, and peer pressure. The interplay between trust and reciprocity is a key element in many of the cooperative and collaborative activities that we undertake daily. There are two main types of inequity aversion: disadvantageous and advantageous. Social norms are another set of social influences that drive our behaviour, and these are often reinforced through peer pressure. They help to explain how and why we have evolved as a cooperative species, but how do we ensure that no-one free rides on others’ generosity?
6. Physical infinity
Authors: Stewart Ian
Published: April 2017

‘Physical infinity’ moves from mathematics to the real world and tackles questions such as ‘is space infinite?’ In many areas of physics, the presence of an infinite quantity (often called a singularity) is construed as a warning that the theory is losing touch with reality. For instance, according to classical ray optics, the intensity of light at the focus of a lens is infinite. The physical resolution of this difficulty involves replacing light rays by waves. Singularities are discussed in three physical contexts: optics, Newtonian gravity, and Albert Einstein’s relativity. However, there’s one area of physics in which an actual infinity—physical, not conceptual—is presented as a possible truth: cosmology.
4. The chemistry of life
Authors: Patrick Graham
Published: April 2017

From very simple molecular building blocks, life has created an astonishing diversity of molecules, some of which are extremely complex structures that prove very difficult to synthesize in a laboratory. ‘The chemistry of life’ describes how proteins, which serve a myriad of purposes, and nucleic acids, another form of biopolymer, are constructed from molecular building blocks called amino acids and nucleotides respectively. It goes on to explain the polymerization processes involved in the biosynthesis of many other natural products; the functions of proteins, DNA, and RNA; and the different theories proposed to explain chemical evolution, or prebiotic chemistry. Enzymes and nucleic acids are increasingly being used in commercial applications.
The Dead Sea Scrolls as cultural icon
Authors: Lim Timothy H.
Published: April 2017

‘The Dead Sea Scrolls as cultural icon’ asks: how did the Dead Sea Scrolls become so popular? Discovered in 1947 and published fully in 1991, the term ‘Dead Sea Scrolls’ has become a catch-all term for ancient manuscripts. The media played an important part in the popularization of the scrolls, but advances in computer and digital technology have improved access to the scrolls. Dead Sea Scroll tourism is popular even during unrest in the Middle East. The discovery of the scrolls coincided with the founding of Israel, giving the documents a profound political importance. Vatican conspiracy theories and copyright lawsuits have also captured the public’s imagination.
The archaeological site and caves
Authors: Lim Timothy H.
Published: April 2017

‘The archaeological site and caves’ examines the archaeological evidence found at the Khirbet Qumran site. Palestinian archaeology was previously dominated by the biblical agenda, but Khirbet Qumran is not mentioned in the Bible, and was only excavated because of the Dead Sea Scrolls. The occupation of the site is generally divided into three phases: the Israelite phase, the communal phase (occupation by the Essenes), and the Second Revolt phase. A cemetery also exists at the site. This was the burial ground of the Qumran people (mixed with some later Bedouin burials), and arguments have raged over the importance of the different sections of the cemetery.
On scrolls and fragments
Authors: Lim Timothy H.
Published: April 2017

‘On scrolls and fragments’ explores the physical difficulties in working with the Dead Sea Scrolls. Firstly: how does one define a scroll? There is not a single, complete scroll in the entire collection, and questions exist about how many scrolls there were originally. Counting the scrolls is also difficult—are two fragments of the same scroll distinct? The scroll fragments are grouped together according to language, content, and handwriting, with obvious joins between fragments providing definitive proof that they are related. Handwriting was taught through scribal traditions, and as such palaeography is difficult but not impossible. Radiocarbon dating using accelerometer mass spectrometry has accurately dated the scrolls.
New light on the Hebrew Bible
Authors: Lim Timothy H.
Published: April 2017

‘New light on the Hebrew Bible’ investigates what the Dead Sea Scrolls can tell us about the textual diversity and canonicity of the Hebrew Bible. Before the scrolls were discovered, Hebrew manuscripts generally dated back to the medieval period. The Qumran texts, dating to between 250 bce and 100 ce, tell us what the Bible was like before its standardization. Errors from copying gave rise to different text-types, and the Dead Sea Scrolls showed that there were far more text-types than previously thought. Variations in readings of the Hebrew Bible and other ancient sources show there was greater diversity in biblical texts than previously realized.
Who owned the scrolls?
Authors: Lim Timothy H.
Published: April 2017

‘Who owned the scrolls?’ attempts to determine the ancient ownership of the Dead Sea Scrolls. The prevailing theory, with some modifications, is the Qumran–Essene theory, which posits that the Essene people lived in the site and were responsible for the creation of the Dead Sea Scrolls. Various evidence from the scrolls themselves, the archaeological Khirbet Qumran site, and primary historical sources support this. For instance, Pliny the Elder located a tribe living at Qumran during his travels in his Historia Naturalis that matched historical descriptions. Handwriting matches between the scrolls and inscriptions at Khirbet Qumran have also been found. Alternative but refuted theories suggest different uses for the site.
The religious beliefs of the sectarian communities
Authors: Lim Timothy H.
Published: April 2017

‘The religious beliefs of the sectarian communities’ explores Jewish beliefs in the Second Temple period. Judaism is a way of life rather than a common faith, but common beliefs are held. The Doctrine of the Two Spirits says that God divided men into those with good and those with evil spirits. Sectarians believed that a man’s spirit could be judged physically. The Jews believe that they are God’s chosen people, and as such they have a series of covenants with Yahweh. The sectarians believe that they are a remnant of true believers that have not strayed from God. Thus, the ‘New Covenant’ is actually a renewal of their existing agreement.
Prologue
Authors: Gingerich Owen
Published: April 2017

In or around 1510 Nicolaus Copernicus, one of the sixteen directors of the northernmost Catholic diocese in Poland, invented the solar system.

Wait a minute! you say. Wasn’t the sun always in the middle of the planets?

But that wasn’t the way everyone else thought about it. Farmers, professors, priests, and school children all assumed the earth was solidly fixed in the middle of the cosmos. Every day the sun and stars revolved around the earth. The sun also moved, more slowly, in a path against the more distant stars so that it was higher in the sky in the summer and much lower in winter....
6. Rheticus
Authors: Gingerich Owen
Published: April 2017

As Copernicus entered his sixties, he was still a busy canon, particularly with respect to his medical expertise. Martin Luther’s Reformation was gaining power at this time, and a young mathematician-astronomer from Wittenberg (home of Luther and his thriving university) became aware of Copernicus’s work. Georg Joachim Rheticus left Wittenberg early in May 1539 to travel to Varmia. Rheticus brought with him a gift: three technical books printed by Johannes Petreius in Nuremberg. He went on to assist Copernicus with observations of the planet Mercury and completion of De revolutionibus. In the autumn of 1541, Rheticus returned to Wittenberg armed with the manuscript of Copernicus’s magnum opus.
The inequalities of eugenics
Authors: Levine Philippa
Published: April 2017

The goal of eugenic fitness was intended, at its most utopian, to improve lives, to help eradicate disease and disability, and to foster productivity. In practice, however, eugenics mostly reinforced rather than dissolved existing class prejudices. ‘The inequalities of eugenics’ shows that it was frequently the poor, ill-educated, and minorities whose reproductive capacity and lifestyle came under attack, and it was women’s sexuality rather than men’s that was closely policed. The disparity between falling birthrates in the developed world and rising rates elsewhere also created racial inequalities in eugenic policies. Reproductive fitness was being undermined as those considered unfit outbred their superiors. Class, gender, and race differences were thus all central eugenic concerns.
2. The modern era: Diagnosis and classification of depression
Authors: Tacchi Mary Jane , Scott Jan
Published: April 2017

Although theories about the underlying causes of depression changed over the centuries, there was a remarkable level of consistency in the descriptions of the core symptoms with sadness and despondency accompanied by sleep problems and physical complaints. ‘The modern era: diagnosis and classification of depression’ reviews the contributions of Emil Kraepelin and Sigmund Freud to the current thinking on depression. Love them or loathe them, both men influenced thinking on the definition and boundaries of depression and how depression is diagnosed and classified. In more recent times, there have been international efforts to standardize approaches to diagnosis through the introduction of criterion-based classifications of mental disorders.
3. Who is at risk of depression?
Authors: Tacchi Mary Jane , Scott Jan
Published: April 2017

One advantage of the more consistent application of diagnostic criteria for identifying individuals with a depressive disorder is that it allows national and international comparisons to be undertaken. Large-scale studies make it possible to estimate the overall prevalence and distribution of depression cases by country, culture, economic and social status, and other demographic features such as age, gender, and marital status. ‘Who is at risk of depression?’ explores the epidemiology of depression (the distribution and determinants of depression-related states), gives examples of the presentation of depression across the lifespan, and discusses the association between physical disorders and depression. Lastly, it highlights some of the current thinking on prevention of suicide.
1. A history of blood
Authors: Cooper Chris
Published: April 2017

‘A history of blood’ considers why the colour red and blood hold such pre-eminence in human language and culture. Views about what function blood actually performed in the body have varied widely through history. The studies of 2nd-century physician Galen are described along with procedures such as bloodletting, used in medicine for a long time. The structure of the vessels that contain blood in the body—arteries and veins—has always intrigued scholars. The 13th-century Islamic physician Ibn al-Nafis was the first to propose a circulatory system, but it was in 1628, when William Harvey, physician to King James I, published his findings, that the true circulatory system was explained.
3. Securitized banking
Authors: Goddard John , Wilson John O. S.
Published: April 2017

Preceding the global financial crisis of 2007–09, an alternative business model of banking evolved. An important element in the development of the securitized banking model was a growing tendency for banks to rely less heavily on deposits as a source of short-term finance, and more heavily on other sources such as the repo market, commercial paper, and derivatives. ‘Securitized banking’ explains that having raised short-term funding through these means, the bank can deploy the funds to support loans to borrowers such as house purchasers. Often a bank will bundle a large number of loans together and sell the package to a Structured Investment Vehicle set up by the bank to administer the loans.
The Jews: Religion or Nation?
Authors: Stanislawski Michael
Published: April 2017

Zionism—the nationalist movement calling for the establishment and support of an independent Jewish state in its ancient homeland—is one of the world’s most controversial ideologies. Its supporters see it as the national liberation movement of the Jewish people that came to fruition in the creation of the State of Israel in 1948. Its opponents regard it as one of the last forms of colonial oppression in the world, defined by Israel’s occupation of the West Bank in the name of a racist ideology increasingly turning Israel into an apartheid state. “The Jews: Religion or Nation?” outlines the aims of this VSI, which does not promote any particular position on Zionism.
Swing to the right, 1977–1995
Authors: Stanislawski Michael
Published: April 2017

Menachem Begin became prime minister of Israel on June 20, 1977, with a clear goal: to implement as quickly and as extensively as possible the policies of Revisionist Zionism as articulated by his mentor and hero, Vladimir Jabotinsky. “Swing to the right: 1977–1995” outlines the key events in Israeli politics that led to a decisive swing to the right in Zionist ideology, including the 1978 peace treaty with Egypt that returned the Sinai Peninsula, the Declaration of Principles on Interim Self-Government Arrangements with the Palestinian Liberation Organization in 1993, and the assassination of Prime Minister Yitzhak Rabin in November 1995 by a member of the ultra-right-wing religious Zionist movement.
Epitope Preservation Methods for Tissue Microarrays
Authors: Andeen Nicole K , Bowman Regina , Baullinger Toni , Brooks J Mathew , Tretiakova Maria S
Published: April 2017

Objectives

We sought to test recent guidelines for preserving immunoreactivity of precut slides, to quantify loss of immunoreactivity, and to determine potential for preservation by altering storage conditions.

Methods

Precut slides from tissue microarrays were stored under one of several conditions: exposed to ambient air at room temperature, 4°C, or –20°C or in a vacuum-sealed container at room temperature, –20°C, –80°C, or with paraffin coating. At multiple intervals over 1 year, slides were stained with antibodies against p53, isocitrate dehydrogenase 1, Ki-67, synaptophysin, and androgen receptor and evaluated.

Results

Compared with time 0, the overall median percentage immunoreactivity was 66% at 6 months and 51% at 1 year. During the experiment, this was as low as 55% for precut slides stored in paraffin coating and up to 87% for those stored at –20°C. Vacuum sealing was an effective preservative for some antibody targets and detrimental for others. Storage at –80°C did not have added value.

Conclusions

For precut slides, there is a time, storage condition, and antibody-dependent loss of immunoreactivity that could compromise analysis of prognostic, predictive, and diagnostic markers. Our findings support previous recommendations and suggest that the best storage conditions are at –20°C, without paraffin coating or vacuum sealing.
Modelling haplotypes with respect to reference cohort variation graphs
Authors: Rosen Yohei , Eizenga Jordan , Paten Benedict
Published: April 2017

Motivation

Current statistical models of haplotypes are limited to panels of haplotypes whose genetic variation can be represented by arrays of values at linearly ordered bi- or multiallelic loci. These methods cannot model structural variants or variants that nest or overlap.

Results

A variation graph is a mathematical structure that can encode arbitrarily complex genetic variation. We present the first haplotype model that operates on a variation graph-embedded population reference cohort. We describe an algorithm to calculate the likelihood that a haplotype arose from this cohort through recombinations and demonstrate time complexity linear in haplotype length and sublinear in population size. We furthermore demonstrate a method of rapidly calculating likelihoods for related haplotypes. We describe mathematical extensions to allow modelling of mutations. This work is an important incremental step for clinical genomics and genetic epidemiology since it is the first haplotype model which can represent all sorts of variation in the population.

Availability and Implementation

Available on GitHub at https://github.com/yoheirosen/vg.

Supplementary information

Supplementary data are available at Bioinformatics online.
Association testing of bisulfite-sequencing methylation data via a Laplace approximation
Authors: Weissbrod Omer , Rahmani Elior , Schweiger Regev , Rosset Saharon , Halperin Eran
Published: April 2017

Motivation

Epigenome-wide association studies can provide novel insights into the regulation of genes involved in traits and diseases. The rapid emergence of bisulfite-sequencing technologies enables performing such genome-wide studies at the resolution of single nucleotides. However, analysis of data produced by bisulfite-sequencing poses statistical challenges owing to low and uneven sequencing depth, as well as the presence of confounding factors. The recently introduced Mixed model Association for Count data via data AUgmentation (MACAU) can address these challenges via a generalized linear mixed model when confounding can be encoded via a single variance component. However, MACAU cannot be used in the presence of multiple variance components. Additionally, MACAU uses a computationally expensive Markov Chain Monte Carlo (MCMC) procedure, which cannot directly approximate the model likelihood.

Results

We present a new method, Mixed model Association via a Laplace ApproXimation (MALAX), that is more computationally efficient than MACAU and allows to model multiple variance components. MALAX uses a Laplace approximation rather than MCMC based approximations, which enables to directly approximate the model likelihood. Through an extensive analysis of simulated and real data, we demonstrate that MALAX successfully addresses statistical challenges introduced by bisulfite-sequencing while controlling for complex sources of confounding, and can be over 50% faster than the state of the art.

Availability and Implementation

The full source code of MALAX is available at https://github.com/omerwe/MALAX.

Supplementary information

Supplementary data are available at Bioinformatics online.
HLA class I binding prediction via convolutional neural networks
Authors: Vang Yeeleng S , Xie Xiaohui
Published: April 2017

Motivation

Many biological processes are governed by protein–ligand interactions. One such example is the recognition of self and non-self cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases.

Results

We apply machine learning techniques from the natural language processing (NLP) domain to address the task of MHC-peptide binding prediction. More specifically, we introduce a new distributed representation of amino acids, name HLA-Vec, that can be used for a variety of downstream proteomic machine learning tasks. We then propose a deep convolutional neural network architecture, name HLA-CNN, for the task of HLA class I-peptide binding prediction. Experimental results show combining the new distributed representation with our HLA-CNN architecture achieves state-of-the-art results in the majority of the latest two Immune Epitope Database (IEDB) weekly automated benchmark datasets. We further apply our model to predict binding on the human genome and identify 15 genes with potential for self binding.

Availability and Implementation

Codes to generate the HLA-Vec and HLA-CNN are publicly available at: https://github.com/uci-cbcl/HLA-bind.

Supplementary information

Supplementary data are available at Bioinformatics online.
Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression
Authors: Ammad-ud-din Muhammad , Khan Suleiman A , Wennerberg Krister , Aittokallio Tero
Published: April 2017

Motivation

A prime challenge in precision cancer medicine is to identify genomic and molecular features that are predictive of drug treatment responses in cancer cells. Although there are several computational models for accurate drug response prediction, these often lack the ability to infer which feature combinations are the most predictive, particularly for high-dimensional molecular datasets. As increasing amounts of diverse genome-wide data sources are becoming available, there is a need to build new computational models that can effectively combine these data sources and identify maximally predictive feature combinations.

Results

We present a novel approach that leverages on systematic integration of data sources to identify response predictive features of multiple drugs. To solve the modeling task we implement a Bayesian linear regression method. To further improve the usefulness of the proposed model, we exploit the known human cancer kinome for identifying biologically relevant feature combinations. In case studies with a synthetic dataset and two publicly available cancer cell line datasets, we demonstrate the improved accuracy of our method compared to the widely used approaches in drug response analysis. As key examples, our model identifies meaningful combinations of features for the well known EGFR, ALK, PLK and PDGFR inhibitors.

Availability and Implementation

The source code of the method is available at https://github.com/suleimank/mvlr.

Supplementary information

Supplementary data are available at Bioinformatics online.
Sharing and helping: predictors of adolescents’ willingness to share diabetes personal health information with peers
Authors: Vaala Sarah E , Lee Joyce M , Hood Korey K , Mulvaney Shelagh A
Published: April 2017

Objective

Sharing personal information about type 1 diabetes (T1D) can help adolescents obtain social support, enhance social learning, and improve self-care. Diabetes technologies, online communities, and health interventions increasingly feature data-sharing components. This study examines factors underlying adolescents’ willingness to share personal T1D information with peers.

Materials and Methods

Participants were 134 adolescents (12–17 years of age; 56% female) who completed an online survey regarding experiences helping others with T1D, perceived social resources, beliefs about the value of sharing information and helping others, and willingness to share T1D information. Hemoglobin A1c values were obtained from medical records.

Results

Adolescents were more willing to share how they accomplished T1D tasks than how often they completed them, and least willing to share glucose control status. In multivariate analyses, sharing/helping beliefs (β = 0.26, P < .01) and glucose control (HbA1c value; β = −0.26, P < .01) were related to greater willingness to share personal health information. Glucose control moderated relationships such that adolescents with worse A1c values had stronger relationships between sharing/helping beliefs and willingness to share (β = 0.18, P < .05) but weaker relationships between helping experience and willingness to share (β = −0.22, P = .07).

Discussion

Many adolescents with T1D are willing to share personal health information, particularly if they have better diabetes health status and a stronger belief in the benefits of sharing.

Conclusion

Social learning and social media components may improve intervention participation, engagement, and outcomes by boosting adolescents’ beliefs about the benefits of sharing information and helping others.
Immediate dense circumstellar environment of supernova progenitors caused by wind acceleration: its effect on supernova light curves
Authors: Moriya Takashi J. , Yoon Sung-Chul , Gräfener Götz , Blinnikov Sergei I.
Published: April 2017

Type IIP supernova progenitors are often surrounded by dense circumstellar media that may result from mass-loss enhancement of the progenitors shortly before their explosions. Previous light-curve studies suggest that the mass-loss rates are enhanced up to ∼0.1 M⊙ yr−1, assuming a constant wind velocity. However, the density of circumstellar media at the immediate stellar vicinity can be much higher than previously inferred for a given mass-loss rate if wind acceleration is taken into account. We show that the wind acceleration has a huge impact when we estimate mass-loss rates from early light curves of Type IIP supernovae by taking SN 2013fs as an example. We perform numerical calculations of the interaction between supernova ejecta and circumstellar media with a constant mass-loss rate but with a β-law wind velocity profile. We find that the mass-loss rate of the progenitor of SN 2013fs shortly before the explosion, which was inferred to be ∼0.1 M⊙ yr−1 with a constant wind velocity of 10 km s−1 by a previous light-curve modelling, can be as low as ∼10−3 M⊙ yr−1 with the same terminal wind velocity of 10 km s−1 but with a wind velocity profile with β ≃ 5. In both cases, the mass of the circumstellar medium is similar (≃0.5 M⊙). Therefore, the beginning of the progenitor’s mass-loss enhancement in our interpretation is ∼100 yr before the explosion, not several years. Our result indicates that the immediate dense environment of Type II supernova progenitors may be significantly influenced by wind acceleration.
Mitochondrial Recombination and Introgression during Speciation by Hybridization
Authors: Leducq Jean-Baptiste , Henault Mathieu , Charron Guillaume , Nielly-Thibault Lou , Terrat Yves , Fiumera Heather L. , Shapiro B. Jesse , Landry Christian R.
Published: April 2017

Genome recombination is a major source of genotypic diversity and contributes to adaptation and speciation following interspecies hybridization. The contribution of recombination in these processes has been thought to be largely limited to the nuclear genome because organelles are mostly uniparentally inherited in animals and plants, which prevents recombination. Unicellular eukaryotes such as budding yeasts do, however, transmit mitochondria biparentally, suggesting that during hybridization, both parents could provide alleles that contribute to mitochondrial functions such as respiration and metabolism in hybrid populations or hybrid species. We examined the dynamics of mitochondrial genome transmission and evolution during speciation by hybridization in the natural budding yeast Saccharomyces paradoxus. Using population-scale mitochondrial genome sequencing in two endemic North American incipient species SpB and SpC and their hybrid species SpC*, we found that both parental species contributed to the hybrid mitochondrial genome through recombination. We support our findings by showing that mitochondrial recombination between parental types is frequent in experimental crosses that recreate the early step of this speciation event. In these artificial hybrids, we observed that mitochondrial genome recombination enhances phenotypic variation among diploid hybrids, suggesting that it could play a role in the phenotypic differentiation of hybrid species. Like the nuclear genome, the mitochondrial genome can, therefore, also play a role in hybrid speciation.
The Role of Extent of Resection in IDH1 Wild-Type or Mutant Low-Grade Gliomas
Authors: Patel Toral , Bander Evan D , Venn Rachael A , Powell Tiffany , Cederquist Gustav Young-Min , Schaefer Peter M , Puchi Luis A , Akhmerov Akbarshakh , Ogilvie Shahiba , Reiner Anne S , Moussazadeh Nelson , Tabar Viviane
Published: April 2017

BACKGROUND

Maximizing extent of resection (EOR) improves outcomes in adults with World Health Organization (WHO) grade II low-grade gliomas (LGG). However, recent studies demonstrate that LGGs bearing a mutation in the isocitrate dehydrogenase 1 (IDH1) gene are a distinct molecular and clinical entity. It remains unclear whether maximizing EOR confers an equivalent clinical benefit in IDH mutated (mtIDH) and IDH wild-type (wtIDH) LGGs.

OBJECTIVE

To assess the impact of EOR on malignant progression-free survival (MPFS) and overall survival (OS) in mtIDH and wtIDH LGGs.

METHODS

We performed a retrospective review of 74 patients with WHO grade II gliomas and known IDH mutational status undergoing resection at a single institution. EOR was assessed with quantitative 3-dimensional volumetric analysis. The effect of predictor variables on MPFS and OS was analyzed with Cox regression models and the Kaplan–Meier method.

RESULTS

Fifty-two (70%) mtIDH patients and 22 (30%) wtIDH patients were included. Median preoperative tumor volume was 37.4 cm3; median EOR of 57.6% was achieved. Univariate Cox regression analysis confirmed EOR as a prognostic factor for the entire cohort. However, stratifying by IDH status demonstrates that greater EOR independently prolonged MPFS and OS for wtIDH patients (hazard ratio [HR] = 0.002 [95% confidence interval {CI} 0.000-0.074] and HR = 0.001 [95% CI 0.00-0.108], respectively), but not for mtIDH patients (HR = 0.84 [95% CI 0.17-4.13] and HR = 2.99 [95% CI 0.15-61.66], respectively).

CONCLUSION

Increasing EOR confers oncologic and survival benefits in IDH1 wtLGGs, but the impact on IDH1 mtLGGs requires further study.
Indoor Exposure to Natural Bright Light Prevents Afternoon Sleepiness
Authors: Kaida Kosuke , Takahashi Masaya , Haratani Takashi , Otsuka Yasumasa , Fukasawa Kenji , Nakata Akinori
Published: April 2017

Study Objectives:

The present study examined the effects of indoor exposure to natural bright light on afternoon sleepiness.

Design:

Participants took part in 3 experimental conditions: (1) a natural bright light condition in which they carried out performance and arousal tests sitting near a window (3260.0 ± 1812.43 lux) from 12:40 PM to 1:10 PM, (2) a nap condition in which they were provided a nap opportunity for 20 minutes from 12:45 PM, and (3) a control condition in which they performed the tests in less than 100 lux surroundings from 12:40 PM to 1:10 PM. Before and after each treatment, the same series of tests were administered.

Setting:

A temperature- and light-controlled sleep laboratory.

Participants:

Sixteen healthy female paid volunteers aged 33 to 43 (38.1 ± 2.68) years.

Interventions:

Indoor natural bright light and a short nap.

Measurements and Results:

Arousal levels were measured by the Psychomotor Vigilance Task, Alpha Attenuation Test, Karolinska Drowsiness Test, and Karolinska Sleepiness Scale. The tests were repeated every 30 minutes from 11:00 AM to 4:10 PM. Ambient light intensity was maintained at less than 100 lux, except during natural bright light exposure. Short-term exposure to natural bright light significantly improved afternoon arousal levels, as measured by the Karolinska Drowsiness Test and Alpha Attenuation Test, the effects of which continued for at least 60 minutes (1:10–2:10 PM). However, no significant differences were observed between conditions for Psychomotor Vigilance Test performance.

Conclusions:

Brief indoor exposure to natural bright light may decrease afternoon sleepiness. This technique of light could be used in work settings in which napping is not permitted.

Citation:

Kaida K; Takahashi M; Haratani T et al. Indoor exposure to natural bright light prevents afternoon sleepiness.
OCULAR HYPERTENSION AND GLAUCOMA FOLLOWING VITRECTOMY
Authors: Miele Alba , Govetto Andrea , Fumagalli Carlo , Donati Simone , Biagini Ilaria , Azzolini Claudio , Rizzo Stanislao , Virgili Gianni
Published: April 2017

Purpose:

Pars plana vitrectomy has been reported to increase the risk of ocular hypertension and open-angle glaucoma. The authors conducted a systematic review of randomized and nonrandomized studies to compare the incidence of open-angle glaucoma and ocular hypertension in vitrectomized versus nonvitrectomized eyes.

Methods:

A literature search was performed using MEDLINE and EMBASE until August 2016. Data on ocular hypertension and open-angle glaucoma incidence and mean intraocular pressure after at least 1 year were pooled using random-effects metaanalysis models. Because only nonrandomized studies were retrieved, ROBINS-I tool was used to assess risk of bias in the review.

Results:

Seven included studies had a paired design to compare the outcomes of vitrectomized versus fellow eyes, with mean follow-up of least 12 months. Four studies (851 patients) provided data on open-angle glaucoma: incidence in vitrectomized versus non-vitrectomized eyes was 7.8% and 4.8%, respectively, yielding a metaanalytic odds ratio of 1.67 (95% CI: 1.08–2.57). Six studies (1,060 patients) reported on the occurrence of ocular hypertension, which was 5.8% in vitrectomized eyes versus 3.1% in fellow eyes (odds ratio: 2.03, 95% CI: 0.97–4.22), without significant differences in the mean postoperative intraocular pressure (mean difference 0.31 mmHg, 95% CI: −0.26 to 0.89).

Conclusion:

Although the review found increased risk of open-angle glaucoma with pars plana vitrectomy, the studies were heterogenous or inconsistent regarding ocular hypertension and intraocular pressure increase. Larger studies should be conducted in homogenous cohorts of patients undergoing macular surgery, excluding complex conditions such as retinal detachment or diabetic retinopathy.
The Effect of Cancer Patients’ and Their Family Caregivers’ Physical and Emotional Symptoms on Caregiver Burden
Authors: Johansen Safora , Cvancarova Milada , Ruland Cornelia
Published: April 2017

Background:

Although there is significant evidence that the family caregivers (FCs) of cancer patients can experience significant caregiver burden and symptoms, less is known about the relationships between FCs and patient characteristics that influence caregiver burden.

Objective:

The purpose of this study was to examine the effect of cancer patients’ and FCs’ symptoms and demographic characteristics on caregiver burden at initiation of the patients’ radiation treatment.

Methods:

Two hundred eighty-one dyads of FCs and cancer patients who received a diagnosis of breast, prostate, melanoma, lymphoma, and head and neck cancers were recruited at the beginning of the patients’ radiation treatment. Measures of depression, sleep disturbance, fatigue, social support, and self-efficacy were obtained from both FCs and cancer patients. The family caregivers were also assessed for caregiver burden. Associations between patients’ and caregivers’ symptoms and demographic characteristics and caregiver burden were investigated using multivariate analyses.

Results:

There were significant associations between caregiver burden and the patient-related variables such as self-efficacy (P = .02), sleep disturbance (P = .03), and social support (P = .04). Among FC-related variables, higher scores of depression (P < .01), fatigue (P < .01), and symptoms (P < .01) were significantly associated with higher caregiver burden. Being a female, either as a patient or FC, increased the likelihood of experiencing fatigue and sleep disturbance.

Conclusion:

Caregiver burden in FCs is influenced by interplay of patients’ and their own symptoms and problems. These interdependencies exist from the beginning of treatment.

Implications for Practice:

Nurses should systematically assess the problems and symptoms of the patients and FCs and support them from the time of diagnosis to help prevent symptom development and deterioration.
The Impact of Couple HIV Testing and Counseling on Consistent Condom Use Among Pregnant Women and Their Male Partners: An Observational Study
Authors: Rosenberg Nora E. , Graybill Lauren A. , Wesevich Austin , McGrath Nuala , Golin Carol E. , Maman Suzanne , Bhushan Nivedita , Tsidya Mercy , Chimndozi Limbikani , Hoffman Irving F. , Hosseinipour Mina C. , Miller William C.
Published: April 2017

Background:

In sub-Saharan Africa couple HIV testing and counseling (CHTC) has been associated with substantial increases in safe sex, especially when at least one partner is HIV infected. However, this relationship has not been characterized in an Option B+ context.

Setting:

The study was conducted at the antenatal clinic at Bwaila District Hospital in Lilongwe, Malawi in 2016 under an Option B+ program.

Methods:

Ninety heterosexual couples with an HIV-infected pregnant woman (female-positive couples) and 47 couples with an HIV-uninfected pregnant woman (female-negative couples) were enrolled in an observational study. Each couple member was assessed immediately before and 1 month after CHTC for safe sex (abstinence or consistent condom use in the last month). Generalized estimating equations were used to model change in safe sex before and after CHTC and to compare safe sex between female-positive and female-negative couples.

Results:

Mean age was 26 years among women and 32 years among men. Before CHTC, safe sex was comparable among female-positive couples (8%) and female-negative couples (2%) [risk ratio (RR): 3.7, 95% confidence interval (CI): 0.5 to 29.8]. One month after CHTC, safe sex was higher among female-positive couples (75%) than among female-negative couples (3%) (RR: 30.0, 95% CI: 4.3 to 207.7). Safe sex increased substantially after CTHC for female-positive couples (RR 9.6, 95% CI: 4.6 to 20.0), but not for female-negative couples (RR: 1.2, 95% CI: 0.1 to 18.7).

Conclusions:

Engaging pregnant couples in CHTC can have prevention benefits for couples with an HIV-infected pregnant woman, but additional prevention approaches may be needed for couples with an HIV-uninfected pregnant woman.
Motor-Like Properties of Non-Motor Enzymes
Authors: Slochower David R. , Gilson Michael K.
Published: April 2017

Molecular motors are thought to generate force and directional motion via nonequilibrium switching between energy surfaces. Because all enzymes can undergo such switching, we hypothesized that the ability to generate rotary motion and torque is not unique to highly adapted biological motor proteins, but is instead a common feature of enzymes. We used molecular dynamics simulations to compute energy surfaces for hundreds of torsions in three enzymes, adenosine kinase, protein kinase A, and HIV-1 protease, and used these energy surfaces within a kinetic model that accounts for intersurface switching and intrasurface probability flows. When substrate is out of equilibrium with product, we find computed torsion rotation rates up ~140 cycle s-1, with stall torques up to ~2 kcal mol-1cycle-1, and power outputs up to ~50 kcal mol-1s-1. We argue that these enzymes are instances of a general phenomenon of directional probability flows on asymmetric energy surfaces for systems out of equilibrium. Thus, we conjecture that cyclic probability fluxes, corresponding to rotations of torsions and higher-order collective variables, exist in any chiral molecule driven between states in a non-equilibrium manner; we call this the Asymmetry-Directionality conjecture. This is expected to apply as well to synthetic chiral molecules switched in a nonequilibrium manner between energy surfaces by light, redox chemistry, or catalysis.
Non-monotonic spatial structure of inter-neuronal correlations in prefrontal microcircuits
Authors: Safavi Shervin , Dwarakanath Abhilash , Kapoor Vishal , Werner Joachim , Hatsopoulos Nicholas G. , Logothetis Nikos K. , Panagiotaropoulos Theofanis I.
Published: April 2017

Correlated fluctuations of single neuron discharges, on a mesoscopic scale, decrease as a function of lateral distance in early sensory cortices, reflecting a rapid spatial decay of lateral connection probability and excitation. However, spatial periodicities in horizontal connectivity and associational input as well as an enhanced probability of lateral excitatory connections in the association cortex could theoretically result in non-monotonic correlation structures. Here we show such a spatially non-monotonic correlation structure, characterized by significantly positive long-range correlations, in the inferior convexity of the macaque prefrontal cortex. This functional connectivity kernel was more pronounced during wakefulness than anesthesia and could be largely attributed to the spatial pattern of correlated variability between functionally similar neurons during structured visual stimulation. These results suggest that the spatial decay of lateral functional connectivity is not a common organizational principle of neocortical microcircuits. A non-monotonic correlation structure could reflect a critical topological feature of prefrontal microcircuits, facilitating their role in integrative processes.

Significance statement

The spatial structure of correlated activity of neurons in lower-order visual areas has been shown to linearly decrease as a measure of distance. The shape of correlated variability is a defining feature of cortical microcircuits as it constrains the computational power and diversity of a region. We show here for the first time a non-monotonic spatial structure of functional connectivity in the pre-frontal cortex where distal interactions are just as strong as proximal interactions during visual engagement of functionally similar PFC neurons. Such a nonmonotonic structure of functional connectivity could have far-reaching consequences in rethinking the nature and the role of prefrontal microcircuits in various cognitive states.
NOTES ON THE BIOMETRY, ORIENTATION AND SPATIAL LOCALIZATION OF THE NESTS OF THE GLOBALLY NEAR-THREATENED STRAIGHT-BILLED REEDHAUNTER (LIMNOCTITES RECTIROSTRIS)
Authors: Gonçalves Maycon S. S. , Pons Priscila dos S. , Andretti Christian B. , Bonow Felipe C.
Published: April 2017

We report the records of three nests of Straight-billed Reedhaunter,Limnoctites rectirostris, in southernmost Brazil. For each nest, we collected information about the biometry, spatial localization within the patch (border or inland) and cardinal orientation of the incubation chamber. Information on number of eggs and reproductive success is also presented. All nests were found early in September. The three nests were situated on the edge of patches and guided incubation chamber opening between north and east. All results are discussed. The information presented herein extends the scarce knowledge about the breeding biology of the Straight-billed Reedhaunter.
Dissociating frontoparietal brain networks with neuroadaptive Bayesian optimization
Authors: Lorenz Romy , Violante Ines R. , Monti Ricardo Pio , Montana Giovanni , Hampshire Adam , Leech Robert
Published: April 2017

Understanding the unique contributions of frontoparietal networks (FPN) in cognition is challenging because different FPNs spatially overlap and are co-activated for diverse tasks. In order to characterize these networks involves studying how they activate across many different cognitive tasks, which previously has only been possible with meta-analyses. Here, building upon meta-analyses as a starting point, we use neuroadaptive Bayesian optimization, an approach combining real-time analysis of functional neuroimaging data with machine-learning, to discover cognitive tasks that dissociate ventral and dorsal FPN activity from a large pool of tasks. We identify and subsequently refine two cognitive tasks (Deductive Reasoning and Tower of London) that are optimal for dissociating the FPNs. The identified cognitive tasks are not those predicted by meta-analysis, highlighting a different mapping between cognitive tasks and FPNs than expected. The optimization approach converged on a similar neural dissociation independently for the two different tasks, suggesting a possible common underlying functional mechanism and the need for neurally-derived cognitive taxonomies.
Convex polyhedra with minimum and maximum names
Authors: Voytekhovsky Yury L.
Published: April 2017

The paper reports the combinatorial types of convexn-acra (i.e.n-vertex polyhedra) for which the minimum (min.) and maximum (max.) names are attained. Hence, min. and max. names can be independently found without generating the whole combinatorial variety of convexn-acra (e.g.by the routine recurrence Fedorov algorithm) and calculating names for eachn-acron.