bluuebunny/crossref_metadata_2025 huggingface dataset:
Fitness heterogeneity in adult Snow and Ross’s geese: Survival is higher in females with brood patches
Authors: Calvert Anna M , Alisauskas Ray T , Kellett Dana K
Published: August 2019

Life-history theory broadly predicts a fitness tradeoff between costs of raising offspring and parental survival. Waterfowl with precocial young face particularly high costs of egg production, incubation, and brood-rearing, but not all evidence supports a corresponding decline in survival. We used multi-state mark–recapture–recovery models to estimate annual probabilities of survival, reported mortality, and transition between 2 states for female Ross’s Geese (Anser rossii) and Lesser Snow Geese (A. caerulescens caerulescens) that attempted nesting near Karrak Lake, Nunavut, Canada. States were possession of a brood patch (high likelihood of successful nesting, “B”) vs. no brood patch (attempted nesting but failed, “N”). Based on over 43,000 birds marked from 2000 to 2015, we found that females of each species with a brood patch had consistently higher probabilities of survival than those without, subsequent to capture in early August. Virtually all of the state differences in survival were due to nonhunting mortality. These patterns are consistent with the concept of variable individual quality impacting vital rates across multiple seasons. Higher survival of females with brood patches may be linked to greater breeding success but also to a hypothesized dominance advantage afforded to family groups of geese during winter. Moreover, although hunting pressure can play a key role in regulating Arctic goose populations, it does not appear to affect this relationship between inferred breeding state and survival. Instead, coincident with recent declines in harvest rate in these populations, higher individual quality of breeding females appears to outweigh the higher hunting vulnerability of presumed parents with young. The potential influence of social dominance in reducing natural winter mortality among families may thus contribute to the survival advantage seen in successful, relative to failed, breeders.
A reinforcement-learning-based approach to enhance exhaustive protein loop sampling
Authors: Barozet Amélie , Molloy Kevin , Vaisset Marc , Siméon Thierry , Cortés Juan
Published: August 2019

Motivation

Loop portions in proteins are involved in many molecular interaction processes. They often exhibit a high degree of flexibility, which can be essential for their function. However, molecular modeling approaches usually represent loops using a single conformation. Although this conformation may correspond to a (meta-)stable state, it does not always provide a realistic representation.

Results

In this paper, we propose a method to exhaustively sample the conformational space of protein loops. It exploits structural information encoded in a large library of three-residue fragments, and enforces loop-closure using a closed-form inverse kinematics solver. A novel reinforcement-learning-based approach is applied to accelerate sampling while preserving diversity. The performance of our method is showcased on benchmark datasets involving 9-, 12- and 15-residue loops. In addition, more detailed results presented for streptavidin illustrate the ability of the method to exhaustively sample the conformational space of loops presenting several meta-stable conformations.

Availability and implementation

We are developing a software package called MoMA (for Molecular Motion Algorithms), which includes modeling tools and algorithms to sample conformations and transition paths of biomolecules, including the application described in this work. The binaries can be provided upon request and a web application will also be implemented in the short future.

Supplementary information

Supplementary data are available at Bioinformatics online.
Immunodetection and quantification of enzymatic markers in theca cells: the early process of ovarian steroidogenesis†
Authors: Asiabi P , Leonel E C R , Marbaix E , Dolmans M M , Amorim C A
Published: August 2019

The association between theca cells (TCs) and granulosa cells is pivotal to steroid biosynthesis in the ovary. During the late secondary follicle stage, TCs form a layer around granulosa cells, after which their steroidogenic function falls under the control of luteinizing hormone (LH) that activates the cAMP signaling pathway via a G protein-coupled receptor. In addition to perilipin-2, a marker for lipid droplets containing esters as substrates for TCs to produce steroidogenic hormones, other essential proteins, like steroidogenic acute regulatory protein (StAR), cytochrome P450 11A1, cytochrome P450c17, 3 beta-hydroxysteroid dehydrogenase/delta 5 —> 4-isomerase type 1, and 3 beta-hydroxysteroid dehydrogenase/delta 5 —> 4-isomerase type 2, play a role in the cascade after luteinizing hormone–choriogonadotropic hormone receptor (LH/CG-R) occupation by LH. The aim of the present study was to assess expression levels and corresponding amounts of LH/CG-R, perilipin-2, and enzymes involved in the steroidogenic pathway of TCs based on follicle stage. Immunohistochemical analysis of each of these proteins was therefore performed on ovarian samples from nine adult women, most (n = 8) with BRCA1 and/or BRCA2 mutations undergoing prophylactic bilateral oophorectomy. Pictures were taken of the theca layer of secondary, small (<3000 μm), and large (>3000 μm) antral follicles and corpora lutea at 100× magnification. ImageJ software was used to analyze the surface area and expression intensity of each protein at each stage, known as the staining index. Overall, our data showed that LH/CG-R, perilipin-2, and StAR expression increased in the course of folliculogenesis and luteinization. Similarly, cytochrome P450 11A1, cytochrome P450c17, 3 beta-hydroxysteroid dehydrogenase/delta 5 —> 4-isomerase type 1, and 3 beta-hydroxysteroid dehydrogenase/delta 5 —> 4-isomerase type 2 expression were substantially elevated in TCs during folliculogenesis, evidenced by their coordinated action in terms of area covered and expression intensity. This study, conducted for the first time on human ovarian tissue, contributes to localizing and quantifying expression of key steroidogenic proteins at both intracellular and tissue levels. These findings may shed new light on pathological conditions involving the human ovary, such as androgen-secreting tumors of the ovary and other disorders associated with ovarian TCs in patients with polycystic ovary syndrome.
The long noncoding RNA PTENP1 regulates human endometrial epithelial adhesive capacity in vitro: implications in infertility
Authors: Takamura Masashi , Zhou Wei , Rombauts Luk , Dimitriadis Evdokia
Published: August 2019

There is general consensus that the synchronous development of the embryo and endometrium is absolutely essential for successful implantation. Recent studies have strongly suggested that embryo-secreted factors are able to deliver into the endometrial cavity/endometrium and alter its protein profile in preparation for implantation. However, there is limited research focusing on long noncoding RNA (lncRNA) changes in the endometrium that brought about by the embryonic derived factors. It has been suggested that lncRNA has intricate interplay with microRNA (miR), small (~19–22 nucleotides), non-protein-coding RNA, to regulate protein production in the endometrium, thus controlling adhesive capacity. Here through microarray assays, we compare the lncRNA profile of the primary human endometrial epithelial cells (HEECs) that have been precultured with blastocyst-conditioned media (BCM) from embryos that implanted versus nonimplanted. Our data indicate a substantial change of lncRNA expression in HEECs, including 9 up-regulated and 12 down-regulated lncRNAs after incubation with implanted BCM. Selective knockdown of PTENP1, the most increased lncRNA after implanted BCM treatment in the HEECs, compromised the spheroid adhesion (P < 0.001). Characterization of PTENP1 confirmed its expression in the luminal epithelium with staining appeared most intense in the midsecretory phase. Furthermore, we have recorded a substantial change of miR profile upon PTENP1 knockdown in HEECs. Overexpression of miR-590-3p, a novel predicted target of PTENP1, impaired spheroid adhesion (P < 0.001). Collectively, these data have supported a novel regulation system that lncRNAs were able to participate in the regulation of implantation through association with miRs.
The Effect of Helminth Infections and Their Treatment on Metabolic Outcomes: Results of a Cluster-Randomized Trial
Authors: Sanya Richard E , Webb Emily L , Zziwa Christopher , Kizindo Robert , Sewankambo Moses , Tumusiime Josephine , Nakazibwe Esther , Oduru Gloria , Niwagaba Emmanuel , Nakawungu Prossy Kabuubi , Kabagenyi Joyce , Nassuuna Jacent , Walusimbi Bridgious , Andia-Biraro Irene , Elliott Alison M
Published: August 2019

Background

Helminths may protect against cardiometabolic risk through effects on inflammation and metabolism; their treatment may be detrimental to metabolic outcomes.

Methods

In a cluster-randomized trial in 26 Ugandan fishing communities we investigated effects of community-wide intensive (quarterly single-dose praziquantel, triple-dose albendazole) vs standard (annual single-dose praziquantel, biannual single-dose albendazole) anthelminthic treatment on metabolic outcomes, and observational associations between helminths and metabolic outcomes. The primary outcome, homeostatic model assessment of insulin resistance (HOMA-IR), and secondary outcomes (including blood pressure, fasting blood glucose, lipids) were assessed after 4 years' intervention among individuals aged ≥10 years.

Results

We analyzed 1898 participants. Intensive treatment had no effect on HOMA-IR (adjusted geometric mean ratio, 0.96 [95% confidence interval {CI}, .86–1.07]; P = .42) but resulted in higher mean low-density lipoprotein cholesterol (LDL-c) (2.86 vs 2.60 mmol/L; adjusted mean difference, 0.26 [95% CI, −.03 to .56]; P = .08). Lower LDL-c levels were associated with Schistosoma mansoni (2.37 vs 2.80 mmol/L; −0.25 [95% CI, −.49 to −.02]; P = .04) or Strongyloides (2.34 vs 2.69 mmol/L; −0.32 [95% CI, −.53 to −.12]; P = .003) infection. Schistosoma mansoni was associated with lower total cholesterol (4.24 vs 4.64 mmol/L; −0.25 [95% CI, −.44 to −.07]; P = .01) and moderate to heavy S. mansoni infection with lower triglycerides, LDL-c, and diastolic blood pressure.

Conclusions

Helminth infections improve lipid profiles and may lower blood pressure. Studies to confirm causality and investigate mechanisms may contribute to understanding the epidemiological transition and suggest new approaches to prevent cardiometabolic disease.

Clinical Trials Registration

ISRCTN47196031.
An investigation into colour combination in paintings via graph theory
Authors: Vangah Samaneh Jolany , Jamali Yousef , Jamali Mozaffar
Published: August 2019

In visual arts, painting is deeply reliant on the colour combination for its impact, depth and emotion. Recently, many studies have focused on image processing, regarding identification and classification of images, using some colour features such as saturation, hue, luminance and so forth. This study aims to delve into some of the painting styles from the perspective of graph theory and network science. We compared a number of famous paintings to find out the likely pattern that an artist uses for colour combination and juxtaposition. To achieve this aim, the digital image of a painting is converted to a graph where each vertex represents one of the painting’s colours. In this graph, two vertices would be adjacent if and only if the two relative colours could be found in at least two adjacent pixels in the digital image. Among the several tools for network analysis, clustering, node centrality and degree distribution are used. Outcomes showed that artists unconsciously are following subtle mathematical rules to reach harmony and coordination in their work.
Surgical repair of aortic coarctation in adults: half a century of a single centre clinical experience
Authors: Abjigitova Djamila , Mokhles Mostafa M , Witsenburg Maarten , van de Woestijne Pieter C , Bekkers Jos A , Bogers Ad J J C
Published: August 2019

OBJECTIVES

Coarctation of the aorta (CoA) is rarely diagnosed and treated in adults and nowadays mostly treated with percutaneous techniques. The objective of this study is to report the long-term outcomes and health-related quality of life in a unique cohort of patients treated with an open surgical repair for their primary adult CoA.

METHODS

Ninety adult patients underwent primary surgical repair of CoA at our tertiary referral centre between 1961 and 2008 when the treatment strategy for adult CoA was exclusively surgical.

RESULTS

The median age at surgery was 24 years (interquartile range 20–36 years), and 39 patients (43%) were asymptomatic at presentation. CoA was located paraductally in most patients (64%), and bicuspid aortic valve was present in 39 (43%) patients. Surgical reconstruction of CoA with an end-to-end anastomosis was performed in majority of the patients (57%). Overall, in-hospital mortality occurred in 1 patient (1%). There was no in-hospital stroke, spinal cord ischaemia, renal replacement therapy or respiratory failure. The cumulative survival was 97.7%, 89.5%, 82.6%, 70.9% and 61.4% at 10, 20, 30, 40 and 50 years, respectively. Thirty-one patients (34%) required an additional cardiac surgery during follow-up. The majority of patients (77%) suffered from refractory hypertension even after decades of surgery. Compared with the matched Dutch population, patients reported a lower social functioning, mental health, vitality and general health with a higher body pain.

CONCLUSIONS

Patients with native adult CoA have low in-hospital morbidity and mortality when treated with an open surgical reconstruction. However, refractory hypertension and impaired quality of life remain important challenges during follow-up.
The European Union and the Law of Treaties: A Fruitful Relationship
Authors: Andrés Sáenz De Santa María Paz
Published: August 2019

This article examines the European Union’s (EU) treaty practice from the perspective of the international law of treaties, focusing on its most significant examples. The starting point is the EU’s attitude towards the codification of treaty law involving states and international organizations. The article discusses certain terminological specificities and a few remarkable aspects, such as the frequent use of provisional application mechanisms as opposed to much less use of reservations, the contributions regarding treaty interpretation, the wide variety of clauses and the difficulties in determining the legal nature of certain texts. The study underlines that treaty law is a useful instrument for the Union and is further enriched with creative contributions; the outcome is a fruitful relationship.
Zoonotic Tuberculosis in Humans: Control, Surveillance, and the One Health Approach
Authors: Macedo Couto Rodrigo , Ranzani Otavio T , Waldman Eliseu Alves
Published: August 2019

Zoonotic tuberculosis is a reemerging infectious disease in high-income countries and a neglected one in low- and middle-income countries. Despite major advances in its control as a result of milk pasteurization, its global burden is unknown, especially due the lack of surveillance data. Additionally, very little is known about control strategies. The purpose of this review was to contextualize the current knowledge about the epidemiology of zoonotic tuberculosis and to describe the available evidence regarding surveillance and control strategies in high-, middle-, and low-income countries. We conducted this review enriched by a One Health perspective, encompassing its inherent multifaceted characteristics. We found that the burden of zoonotic tuberculosis is likely to be underreported worldwide, with higher incidence in low-income countries, where the surveillance systems are even more fragile. Together with the lack of specific political commitment, surveillance data is affected by lack of a case definition and limitations of diagnostic methods. Control measures were dependent on risk factors and varied greatly between countries. This review supports the claim that a One Health approach is the most valuable concept to build capable surveillance systems, resulting in effective control measures. The disease characteristics and suggestions to implement surveillance and control programs are discussed.
Training community health nurses to measure parent–child interaction: a mixed-methods study
Authors: Levickis Penny , McKean Cristina , Walls Elaine , Law James
Published: August 2019

Background

This study aims to determine whether the Parental Responsiveness Rating Scale (PaRRiS) completed at child age 24–30 months can be used by community child health nurses (CCHNs) to reliably measure the quality of parent–child interactions in practice.

Methods

A mixed-methods design was used involving CCHNs working in public health settings. Five CCHNs recruited from the North-East of England were trained to use PaRRiS. Thirty parent–child dyads attending their routine 24–30-month check were observed. Nurses rated parent–child dyads during 5 min of free-play using PaRRiS. The free-play sessions were video recorded and rated blind by the first author to the nurse observation. Semi-structured phone interviews were conducted with the five CCHNs once observations of parent–child interactions were complete. Interviews were audio-recorded, transcribed, anonymized and thematically analyzed.

Results

Two-thirds of participating parents were mothers. Half the families (15/30) were from the 10% most deprived areas based on the English Index of Multiple Deprivation. The average PaRRiS score was 3.03 [standard deviation (SD) = 0.8; all ratings were <5.0]. Reliability between the first author (‘gold standard’) and CCHNs was excellent [Intra-class correlation coefficient (ICC): 0.85; 95% confidence interval (CI): 0.67–0.93]. CCHNs found PaRRiS aligned well with current practice and was acceptable to parents. There was no evidence of a relationship between social disadvantage and PaRRiS scores.

Conclusions

With further development and evaluation work, PaRRiS could potentially be incorporated into existing universal health services to provide child health nurses with an additional tool for identifying families most likely to be in need of parent–child interaction interventions.
Effect of cardiac arrest with aortic cross-clamping during left ventricular assist device implantation
Authors: Kawabori Masashi , Kurihara Chitaru , Critsinelis Andre , Chou Brendan Pen-Haw , Zhang Qianzi , Kaku Yuji , Civitello Andrew B , Morgan Jeffrey A
Published: August 2019

OBJECTIVES

Some patients who undergo continuous-flow left ventricular assist device (CF-LVAD) implantation require concomitant procedures that can be performed with or without cardiac arrest under aortic cross-clamping (AXC). Procedures normally performed with cardiac arrest are sometimes avoided or performed without cardiac arrest because it may be detrimental to right heart function. However, the effects of cardiac arrest on patients with advanced heart failure necessitating CF-LVAD support have not been thoroughly studied. We examined our single-centre experience to determine whether cardiac arrest during CF-LVAD implantation was associated with worse patient outcomes.

METHODS

From November 2003 to March 2016, a total of 526 patients with chronic end-stage heart failure underwent primary CF-LVAD implantation. Preoperative demographics, postoperative complications and mortality rates were compared between patients who required cardiac arrest with AXC (n = 50) and those who did not (n = 476).

RESULTS

The most frequently performed procedure requiring AXC was aortic valve closure (n = 23, 26.1%). Although the AXC group had longer cardiopulmonary bypass times (P < 0.01), long-term (5-year) survival was similar in AXC and non-AXC patients (P = 0.13). Also, postoperative right heart failure (P = 0.15) and neurological dysfunction (P = 0.89) rates were not significantly different between the 2 groups. Cox proportional hazards analysis showed that cardiac arrest with AXC was not an independent predictor of mortality (hazard ratio, 0.89; P = 0.73).

CONCLUSIONS

Cardiac arrest with AXC during CF-LVAD implantation did not negatively affect long-term survival or the incidence of right ventricular failure or stroke. These findings should be considered in deciding surgical strategies. Additional investigation may be warranted to further understand the effects of cardiac arrest during LVAD implantation.
Patterns of amino acid intake are strongly associated with cardiovascular mortality, independently of the sources of protein
Authors: Tharrey Marion , Mariotti Francois , Mashchak Andrew , Barbillon Pierre , Delattre Maud , Huneau Jean-François , Fraser Gary E
Published: August 2019

Background

The intake of specific amino acids (AA) has been associated with cardiovascular health, but amino acids are consumed together as dietary protein. Here we investigated the association between identified patterns of amino acid intake and cardiovascular mortality.

Methods

A total of 2216 cardiovascular deaths among 79 838 men and women from the Adventist Health Study-2 were included in our analysis. Baseline dietary patterns based on the participants' amino acids intakes were derived by factor analysis. Using Cox regression analyses, we estimated multivariate-adjusted hazard ratios (HRs) adjusted for sociodemographic and lifestyle factors and other dietary components.

Results

Three patterns of amino acids were identified. Factor 1 was positively associated with cardiovascular disease (CVD) mortality [hazard ratio (HR)Q5-Q1: 1.62, 98.75% confidence interval (CI): 1.15, 2.28; P-trend <0.001]; and Factors 2 and 3 were inversely associated with CVD mortality (HR Q5-Q1 Factor 2: 0.74, 98.75% CI: 0.53, 1.04; P-trend <0.01 and HR Q5-Q1 Factor 3: 0.65, 98.75% CI: 0.44, 0.95; P-trend <0.05]. The associations with Factor 1 (with high loadings on indispensable amino acids such as branched chain amino acids, lysine, methionine) and Factor 3 (with high loadings on non-indispensable amino acids, namely arginine, glycine, aspartate+asparagine) remained significant after further adjustment for nutrient intake and for the five protein source patterns identified previously (HR Q5-Q1: 1.56 (0.99, 2.45) and 0.55 (0.35, 0.85); P-trends < 0.01).

Conclusions

Indispensable AA have a positive and some non-indispensable AA have a negative, independent, strong association with the risk of cardiovascular mortality.
Rectified Sites of Violence from Westgate to Lampedusa: Exploring the Link between Public Amnesia and Conflict in Ongoing Confrontations
Authors: Purdeková Andrea
Published: August 2019

This article investigates whether and how public amnesia of violent incidents such as mass drownings or mass killings impacts ongoing conflict dynamics. Specifically, the article compares and contrasts two forms of public amnesia in the relatively little-studied space of the rectified site – a site of violence returned to prior use without monumentation or commemoration. Looking at the unmarked sites of violence in East Africa’s confrontation with Al-Shabaab, such as the Westgate Mall, and the Mediterranean crossings within the system of migration deterrence, the article asks: How do rectification practices and associated public production of silence feed into conflict dynamics and conflict transformation? The article shows that while public amnesia tends to entrench the confrontation, recognition through commemoration needs to be calibrated carefully in order to avoid further conflict escalation. Epistemic redress must precede physical and symbolic memory work in rectified sites of violence. By tackling the puzzle of (non)commemoration and active forgetting of violence in contexts of ongoing confrontation, the article decentres dominant transitional justice concerns over memory from the present to the absent, and from the space of the ‘post’ to the lingering ‘in-between’ of conflict that defines many contemporary violent confrontations.
Incorporating Laboratory Animal Science into Responsible Biomedical Research
Authors: Barbee R Wayne , Turner Patricia V
Published: August 2019

Biomedical research has made great strides in the past century leading to rapid advances in human life expectancy, all derived from improved understanding, prevention, and treatment of many diseases and conditions. Research involving laboratory animals has played a significant role in this medical progress. However, there continues to be controversy surrounding the use of animals in research, and animal models have been questioned regarding their relevance to human conditions. While research fraud and questionable research practices could potentially contribute to this problem, we argue that a relative ignorance of laboratory animal science has contributed to the “uncontrolled vivarium experiment” that runs parallel to the more controlled scientific experiment. Several variables are discussed, including husbandry, animal environment, social housing, and more, that can contribute to this uncontrolled experiment, and that can simultaneously decrease quality of life for rodent test subjects when ignored. An argument is put forward that laboratory animal veterinarians and scientists can and should play an important role in better controlling such variables. Similarly, the laboratory animal veterinarian and scientist should play an important role in responsible science by addressing complex interdisciplinary challenges.
Maximal 3D printing extrusion rates
Authors: Edwards D A , Mackay M E , Swain Z R , Banbury C R , Phan D D
Published: August 2019

Many applications of 3D printing are enhanced by increased printing speed. In the hot end of a 3D printer, the polymer feed stock flows in a heated cylinder at a set temperature. Since the polymer must be hot enough to reach a pliant state before extrusion, this establishes a maximum velocity beyond which the polymer is too rigid to be extruded. A mathematical model is presented for this system, and both amorphous and crystalline polymer systems are examined. The former is a heat transfer problem; the latter is a Stefan problem. Several different conditions for establishing the maximum velocity are considered; using the average polymer temperature in the hot end matches well with experimental data.
On the Andreadakis Problem for Subgroups of IA
n
Authors: Darné Jacques
Published: August 2019

Let $F_n$ be the free group on $n$ generators. Consider the group $IA_n$ of automorphisms of $F_n$ acting trivially on its abelianization. There are two canonical filtrations on $IA_n$: the 1st one is its lower central series $\Gamma _*$; the 2nd one is the Andreadakis filtration $\mathcal A_*$, defined from the action on $F_n$. The Andreadakis problem consists in understanding the difference between these filtrations. Here, we show that they coincide when restricted to the subgroup of triangular automorphisms and to the pure braid group.
Refocusing Research on Sexually Transmitted Infections
Authors: Eisinger Robert W , Erbelding Emily , Fauci Anthony S
Published: August 2019

This article highlights biomedical research goals for the development of critical tools, including innovative diagnostics, safe and effective vaccines, and new and improved therapeutics, necessary to achieve an end to the global epidemic of sexually transmitted infections. The incidence of sexually transmitted infections (STIs), including gonorrhea, syphilis, chlamydia, and trichomoniasis, is increasing by over 1 million new cases daily and represents a global public health crisis. There is an alarming increase of gonorrhea and syphilis among men who have sex with men and bisexual men, 2 key populations also at high risk for human immunodeficiency virus. A refocused, dedicated, and intensive biomedical research program is needed targeting development of innovative diagnostics, safe and effective vaccines, and new and improved therapeutics. This article highlights biomedical research goals providing critical tools necessary to achieve an end to the global STIs epidemic.
Search-based Endogenous Asset Liquidity and the Macroeconomy
Authors: Cui Wei , Radde Sören
Published: August 2019

We develop a search-theory of asset liquidity which gives rise to endogenous financing constraints on investment in an otherwise standard dynamic general equilibrium model. Asset liquidity describes the ease of issuance and resaleability of private financial claims, which is the outcome of a costly search-and-matching process for such claims implemented by financial intermediaries. Limited liquidity of private claims creates a role for liquid assets, such as government bonds, to ease financing constraints. We show that endogenising liquidity is essential to generate positive co-movement between asset liquidity and asset prices. When the cost of intermediating funds to entrepreneurs rises, investment and output fall whereas the hedging value of liquid assets increases, driving up liquidity premia. In the United States, such intermediation cost shocks can account for at least 37% of the variation in output, and more than 78% of the variation in liquidity premia.
Price Discovery in High Resolution
Authors: Hasbrouck Joel
Published: August 2019

U.S. equity market data are currently timestamped to nanosecond precision. This permits models of price dynamics at resolutions sufficient to capture the reactions of the fastest agents. Direct estimation of multivariate time series models at sub-millisecond frequencies nevertheless poses substantial challenges. To facilitate such analyses, this paper applies long distributed lag models, computations that take advantage of the inherent sparsity of price transitions, and bridged modeling. At resolutions ranging from 1 s down to 10 μs, I estimate representative models for two stocks (IBM and NVDA) bearing on three topics of current interest. The first analysis examines the extent to which the conventional source of market data (the consolidated tape) accurately reflects the prices observed by agents who subscribe (at additional cost) to direct exchange feeds. At a 1-s resolution, the information share of the direct feeds is indistinguishable from that of the consolidated tape. At resolutions of 100 and 10 μs, however, the direct feeds are totally dominant, and the consolidated share approaches zero. The second analysis examines the quotes from the primary listing exchange vs. the non-listing exchanges. Here, too, information shares that are essentially indeterminate at 1-s resolution become much more distinct at higher resolutions. Although listing exchanges execute about one-fifth of the trading volume, their information shares are slightly above one-half. The third analysis examines quotes, lit trades, and dark trades. At a 1-s resolution, dark trades appear to have a small, but discernible, information contribution. This vanishes at higher resolutions. Quotes and lit trades essentially account for all price discovery, with information shares of roughly 65% and 35%, respectively.
Asymptomatic congenital intrapericardial diaphragmatic hernia in a woman becoming symptomatic after childbirth
Authors: Kakaje Ameer , Mahfouz Mohammad , Chaban Hussain
Published: August 2019

This paper describes a rare case presentation of congenital asymptomatic intrapericardial diaphragmatic hernia. In this case, the female patient survived without symptoms for over 30 years until becoming symptomatic at childbirth. Diaphragmatic hernia occurs when abdominal viscera protrude into the thoracic cavity, with pericardial hernias being the rarest type. Diaphragmatic hernia can be caused by trauma that raises the intra-abdominal pressure, whereas congenital hernias are often symptomatic at birth. It is rare to have a congenital asymptomatic intrapericardial diaphragmatic hernia, where the patient survives until adulthood and subsequently becomes symptomatic after delivering a child; hence, that is the uniqueness of this case.
A case report of necrotizing fasciitis with growth of Actinomyces europaeus and Actinotignum schaalii
Authors: Kus Nicole Joanne , Kim Bryan Jordan , Ross Howard M
Published: August 2019

Actinomyces europeaeus and Actinotignum schaalii are two facultative anaerobes that are common contaminants of human flora; namely the urinary tract, the female genital tract and the gastrointestinal tract. A. europeaeus has been linked with abscesses, decubitus ulcers and purulent urethritis, while A. schaalii has been associated with urinary tract infections, bacteremia and Fournier’s gangrene. Here we present a case report of an 84-year-old female patient found to have a necrotizing soft tissue infection caused by A. europeaeus and A. schaalii. To our knowledge, this is the first case report that documents A. europeaeus as a causal agent of a necrotizing infection.
Legacy Data Confound Genomics Studies
Authors: Anderson-Trocmé Luke , Farouni Rick , Bourgey Mathieu , Kamatani Yoichiro , Higasa Koichiro , Seo Jeong-Sun , Kim Changhoon , Matsuda Fumihiko , Gravel Simon
Published: August 2019

Recent reports have identified differences in the mutational spectra across human populations. Although some of these reports have been replicated in other cohorts, most have been reported only in the 1000 Genomes Project (1kGP) data. While investigating an intriguing putative population stratification within the Japanese population, we identified a previously unreported batch effect leading to spurious mutation calls in the 1kGP data and to the apparent population stratification. Because the 1kGP data are used extensively, we find that the batch effects also lead to incorrect imputation by leading imputation servers and a small number of suspicious GWAS associations. Lower quality data from the early phases of the 1kGP thus continue to contaminate modern studies in hidden ways. It may be time to retire or upgrade such legacy sequencing data.
Philosophy of Cosmology
Authors: Fox Craig , Gueguen Marie , Koberinski Adam , Smeenk Chris
Published: August 2019

Physical cosmology, the study of the large-scale structure of the universe and its evolution, has become a central area of research in fundamental physics. Theoretical and observational developments have led to acceptance of a “standard model” describing the history of the universe in impressive detail. These developments raise a number of challenging foundational questions that have stimulated the emerging field of philosophy of cosmology. Many of these questions are closely tied to discussions in general philosophy of science and philosophy of physics, whereas others are distinctive to the field. This bibliography aims to provide an orientation for both kinds of questions. As philosophy of cosmology is an emerging field, the literature in this area is sparse. Hence this bibliography includes two kinds of references that do not explicitly address philosophy of cosmology. First, it identifies several philosophical papers regarding other scientific fields, with the thought that these will inform discussions of parallel issues in cosmology. Second, it includes several references to the scientific literature, to provide philosophers with a useful orientation to contemporary scientific debates.
Electronically Monitored Home Confinement
Authors: Staples William G. , Sullivan Darcy L.
Published: August 2019

As a tactic of control and punishment, “house arrest’’ has been used for millennia to sequester individuals such as deposed leaders, government officials, and political dissidents in a residence. Since the late 1980s, various forms of house arrest—typically involving some kind of electronic monitoring (EM) and therefore broadly referred to as electronically monitored home confinement (EMHC)—have come to play a role in both the criminal and juvenile justice systems of the United States and in other countries. Unfortunately, the US Department of Justice does not collect data on the numbers of persons under EM. According to a 2015 survey conducted by the Pew Charitable Trusts, more than 125,000 people were supervised by electronic means, up from 53,000 in 2005. The survey also found that all fifty states, the District of Columbia, and the federal government use electronic devices to monitor people at various stages of the justice system including pretrial defendants, immigrants awaiting deportation hearings, and convicted offenders. EMHC is considered an intermediate sanction that permits an individual to live at home except when authorized to attend school, treatment programs, and go to work, or meet with program officials. Participants must agree to an extensive list of conditions of their participation and they are often required to pay for their EMHC (typically $10–15 a day). Violators are commonly jailed for non-compliance. A variety of monitoring systems are used, the original and most common being some form of a continuous radio frequency (RF) signal between a receiver-dialer that is attached to a telephone line in the home and a transmitter that is worn by the offender on the ankle or wrist. With these “tagging” systems, individuals cannot stray further than 150 feet or so from the monitoring box without triggering a violation. More sophisticated designs are based on the Global Positioning System (GPS) that can track the whereabouts of individuals at all times, even if they have absconded from the home. Other systems have added biometric measurements such as transdermal alcohol testing to the anklet to determine a person’s blood alcohol content. Yet another version dispenses with the anklet monitor and a digital device is installed in the home and random phone calls from the program’s computer system must be answered by the offender when they are required to be in the home. To verify compliance, the system uses voice and facial recognition capabilities and collects a breath sample to test for alcohol.
Redistricting and Electoral Competition in American Politics
Authors: Williamson Ryan
Published: August 2019

Redistricting, or the process of redrawing congressional district boundaries, can be a highly contentious and political affair. Electoral competition within districts is dependent on both of the major American political parties being evenly balanced. Therefore, redistricting can enhance or diminish competition through how it distributes partisans across districts. Indeed, politicians have used this process to manipulate boundaries in their favor for centuries. In fact, the term most commonly used for exploiting the redistricting process for partisan gain—gerrymandering—was coined in 1812 as Massachusetts governor Elbridge Gerry signed legislation creating a map with heavily distorted districts, one of which resembled a salamander. Thus, the portmanteau “gerry-mander” was born. The misshapen districts produced the intended effect of facilitating greater electoral success for members of the governor’s party. Throughout history, Congress, the US Supreme Court, individual states, the American electorate, and an ever-evolving political environment have all impacted the construction of district maps. Additionally, each of these factors further influences the level of electoral competition within the district. Therefore, this work seeks to outline how redistricting can directly or indirectly influence electoral competition within congressional districts. Directly, different redistricting entities (legislatures, commissions, and courts) possess different motivations and constraints when drawing district lines, which can impact competition. Indirectly, redistricting can influence voting behavior and the incumbency advantage, which can also impact competition. This work also explores the tradeoff between representation and competition, the relationship between redistricting and polarization, what constitutes a gerrymander, and how durable redistricting plans are over time. Each can have a substantial impact on electoral competition, which in turn bears consequences for our understanding of the consequences of redistricting.
Puerto Rican Literature
Authors: Rivera Juan Pablo
Published: August 2019

What constitutes “Puerto Rican literature”? This question is as literary as it is political, to a greater degree than it would be when considering the canon of a sovereign nation. Two reasons may be given to account for this exceptionality: (1) Puerto Rico has been the colony of two successive empires, Spain and the United States, and (2) more than half its people live in the United States, as part of a diaspora shaped sometimes by choice and, more often, by colonial (political, economic) pressures. Scholars interested in the literature of this Puerto Rican majority, which is the diaspora in the United States, should consult Edna Acosta-Belén’s entry in Oxford Bibliographies, as the present entry limits itself to criticism about literature in Spanish that has predominantly circulated within the confines of the island(s) of Puerto Rico. In fact, this geographic and linguistic split (mainland is to island, as English is to Spanish) had conditioned scholarly approaches to Puerto Rican literature throughout most of the 20th century and only began to be questioned in the 1980s by daring scholars such as Acosta-Belén herself. Moreover, this linguistic, geographic, and political split between English and Spanish reflects one of Puerto Rican literature’s most persistent topics: the call for independence from the United States, a feature that sets Puerto Rican literature apart from other literatures in Spanish. More broadly, from the 19th century onward, Puerto Rican authors have been concerned with the question of national identity within a colonial context. Only after the 1970s does this question cease to be the guiding concern of Puerto Rican authors, a rupture (and a new beginning) driven by the voices of women, queer, and Afro-Puerto Rican authors, who continue to insist on the expansion of the literary canon. While the question of national identity still exists, many contemporary authors refuse to join in this totalizing search, and prefer to write about spaces, characters, and situations that have been traditionally marginalized by the heteropatriarchal, Hispanophile literary establishment.
Variationist Sociolinguistics
Authors: Bayley Robert , Cameron Richard
Published: August 2019

Researchers in language variation seek to understand how linguistic, social, and individual factors influence speakers’ choices within sets of related variable forms as in, for example, the alternation between working and workin’ in English. A central premise in this approach is that the variation observed at all linguistic levels is not random. Rather, provided that one has sufficient information about speakers’ backgrounds and the linguistic contexts in which a variable form occurs (e.g., whether a final /t/ or /d/ in English followed by a consonant or a vowel), one can predict, in a probabilistic sense, which speakers will be more likely to choose one variant or another. Further, variationists maintain that variation is an essential characteristic of language change. By applying rigorous multivariate statistical analysis to a wide range of variable forms at all linguistic levels, ranging from phonetic detail to language choice, variationists have demonstrated conclusively that most of the variation that is observed in language is highly systematic. The demonstration of systematic variability has been particularly important for minority languages and dialects, which, until the development of sociolinguistics, were often regarded as imperfect copies of the standard languages or dialects with which they co-existed. In recent decades, variationists have expanded the scope of their work and shown that systematic variation is characteristic of all human languages regardless of modality or stage of development. Research on variation in sign languages, for example, has shown that they are subject to many of the same linguistic and social influences as spoken languages. Moreover, language learners, whether first, second, or nth, have been shown to vary systematically in their use of forms that are usually considered obligatory in the target language as well as in their use of forms that vary in the target language. Finally, variationists have sought to use the findings from their research to improve conditions in the communities from which they draw their data, particularly in education for children who speak a minority language or dialect.
Species Distribution Modeling
Authors: Elith Jane
Published: August 2019

Models of species distributions aim to describe and often to predict the spatial distribution of individual species, using as a basis the species’ relationship with its environment. At a broad level this can be done in two main ways. The first is to model the processes that underpin where the species occur: demographic or physiological processes that fundamentally define the species distribution. The second and much more common approach is to fit a numerical model that defines the relationships between observations of the species occurrence and any covariates considered relevant. This article focuses on the second, aiming to introduce the reader to key texts and ideas in this large and popular field of modeling whose applications span ecology, biogeography, evolutionary biology, conservation, biosecurity, health, and computation. It focuses on the models and the mapped predictions often derived from them. Referred to as species distribution models (SDMs) here, these (or their variants) are also referred to as ecological niche models, habitat models, or bioclimatic envelope models. Several textbooks have now been published on SDMs, giving good insights into background, theory, applications, data, and models. Thousands of manuscripts are published including those developing new methods, those that apply SDMs to ecological theory and understanding, and those that apply the maps in conservation, planning, and management applications. This bibliography leads the reader through the literature, first covering the background and standard approaches to fitting, evaluating, and reporting SDMs. Then, aiming to extend beyond the information presented thoroughly in existing textbooks, it describes related models that are still correlative and applicable for modeling individual species but that provide important extensions. These allow modelers to deal with the common complexities in data (structured datasets, imperfect detection, spatio-temporal issues) and to broaden the models to include biological processes or issues of interest such as biotic interactions, movement, traits and phylogenetic data.