bluuebunny/crossref_metadata_2025 huggingface dataset:
Lineament analysis of digital elevation model to identification of geological structure in Northern Manna Sub-Basin, Bengkulu
Authors: Fajri SN , Surtiyono E , Nalendra S
Published: October 2019

Digital Elevation Model (DEM) is a representation of the actual landform based on elevation. DEM is part of the technological sophistication that is very helpful in planning, mapping, and surveying. This study applies DEM, which is constructed from DEMNAS, focusing on DEM optimization for geological structures identification.The applied method is ellipsoid stress model analysis approach to determine the type of structure. The scope of this study is located in North Manna Sub-Basin, tectonically is a basin that formed on Paleogen by an extensional force that forms half-graben along the Bengkulu Shelf. Interpretation of DEM in the study area showed the existence of 10 lineament patterns of NE-SW and five NNE-SSW patterns, controlled by normal fault, nine lineament patterns of NW-SE and six WNW-ESE patterns, controlled by a thrust fault and fold. Field observation using direct measurement method obtained by four faults with NE-SW and NNE-SSW pattern, one fault and four folds with NW-SE pattern,three faults and two folds with WNW-ESE trending pattern. This indicates that the accuracy level of DEM in the study area reaches 90%. The geological structure that is still active, certainly requires special attention in building construction.
Transformations of Urban Space in Community and Pedestrian Wellbeing
Authors: Villanueva CMS
Published: October 2019

Resiliency and well-being are pressing issues in communities worldwide as we cope with the challenges of economy, climate change, and the sustainable development goals. Resilience is the ability of ecological systems to absorb changes of state variables, driving variables, and parameters, and still persist (Holling, 1973). The measure of one nation’s ability to adapt to these evolving issues may vary greatly with another because of their culture and way of life. The ultimate goal of a resilient society is the wellbeing of its community.

Wellbeing is when individuals have the psychological, social, and physical resources they need to meet a particular psychological, social, and/or physical challenge. When individuals have more challenges than resources, the see-saw dips, along with their wellbeing, and vice-versa (Dodge, 2012).

With two-thirds of the world’s population is being expected to reside in cities by 2050, it is clear that urban areas will be the engines of economic growth and sustainable development (UNODC, 2019). Cities across the globe are undermined by chronic insecurity, violence, and corruption, which are often connected to crime challenges originating beyond urban boundaries (UNODC, 2019). Studies show that street crimes are affected by the physical characteristics within a community’s field of vision (Lee, et al, 2017).

This study attempts to model the collective experiences of stakeholders and pedestrians from 2015 - 2018. This study will feature the existing conditions on the urban spaces, such as the sidewalks, the road networks, and barangays (barangays are the smallest unit of government in the Philippines). Mapping the social impacts of lighting, noise, crime, and accidents will feature their geographical distribution along España Boulevard; a major access route in the country’s University Belt.

Findings show that the manifestations of transformations in urban space occur in fluid trajectories that can be in patterns of horizontal, vertical, and cyclical schemes in achieving community and pedestrian wellbeing.
Theoretical Performance of a Multi-Cyclone Fine Particulate Emission Control System
Authors: Hussein Norelyza , Rashid Mohd , Hasyimah Hashim Nor , Ruwaida Jamian Nor , Hafizan Che Hassan Che
Published: October 2019

The study involves the development of theoretical performance background of a newly developed multi-cyclones fine particulate emission control system named as MR-deDuster. The theoretical background of the unit was developed based on the modifications of established design equations available in literatures. The Leith & Licht model and modified Lapple model with different definitions of maximum radial distance travelled by a particulate (W) were used to predict the performance of the unit under various volumetric gas flow rate ranging from 0.13 to 0.21 m3/s. The result reveals significant differences among predictions, but yet all the predictions approve the capability of the unit to capture the particulate matter, especially the fine size fraction.
Layering of History in Malaysian Modern Architecture through Analytical Diagramming
Authors: Balkish Roslan Siti , Ariff Amir
Published: October 2019

The paper looks at the Malaysian Modern Architecture buildings of historical significance from the post-independence (post-Merdeka) period of 1950s by using analytical diagrams to examine their historical layers. The 1950s beheld an important transition of architecture history in Malaysia as the newly independent nation sought to formulate an identity through various enterprises, including architecture. The usage of these historical buildings has changed over time. Considering a building as a singular entity and ignoring its past influences diminishes its historical significance and neglects history as a continuous evolutionary pressure upon the building. As architectural history develops over time, it will have layer upon layer of its physical, functional, and contextual aspects affected by factors pertaining to socio-culture, politics, and economy. Visual representation is important to capture changes and to be open in anticipation of new layers that encapsulate the building’s reading at a certain point of time. The idea is to not only capture the momentous spirit of a building, but also multiple monumental and ambiguous changes that keep true to history. Such a visual representation allows an easy reading of the historical value and an open discussion through visual clues and analytical diagramming. In this study, we have selected the Modern building, Angkasapuri, as an archetype for interrogation via analytical diagrams.
The influence of surface inhomogeneity on the overcharge and lithium plating of graphite electrodes
Authors: Verbrugge Mark W , Baker Daniel R
Published: October 2019

We seek to clarify phenomena involved in the overcharge of a graphite electrode in a lithium ion battery, including lithium (Li) plating. In Baker and Verbrugge (2019 J. Electrochem. Soc.), we developed a set of equations that can be used to treat Li plating and subsequent electro-dissolution, and we analyzed how the equation system behaved for a particle of graphite, a fundamental unit of the negative (porous) electrode in lithium ion cells. In this work, we employ the same governing equations, but we render them in a two-dimensional setting to examine the graphite-electrolyte interface, allowing us to clarify phenomena involved in Li plating over graphitic electrode elements in the absence of complicating factors associated with the architecture of a porous electrode. For a variety of reasons described in the Introduction of this work, the surface of graphite is nonuniform in terms of reaction rates for Li insertion and plating, and we show that when the electrode is subjected to constant-current charging, as is commonly employed, such nonuniformities lead to early Li plating over the highly reactive surfaces. These observations underscore the importance of maintaining a uniform electrode surface, especially when the cell is to be subjected to high rates of charge.
Bidirectional Associations of Momentary Affect with Physical Activity and Sedentary Behaviors in Working Adults
Authors: Kim Jinhyuk , Conroy David E , Smyth Joshua M
Published: October 2019

Background

Affective experiences and movement-based behaviors form a system that has been shown to influence exercise adherence and mental health outcomes. Little is known about the naturalistic dynamics of the reciprocal associations in this system.

Purpose

We examined the time intervals at which momentary affect precedes and follows movement-based behaviors in everyday life.

Methods

A community sample of working adults (n = 111) completed ecological momentary assessments (EMA) asking about current affect states (sad, happy, tired, and interested) six times a day for three consecutive days. Ratings were used to generate scores for momentary affective arousal and valence. Participants also wore an activity monitor. Total activity counts and sedentary duration in the shorter to longer time intervals (5–120 min) before or after EMA were used as indicators of movement-based behaviors.

Results

Multilevel modeling showed that current affective arousal predicted higher subsequent activity counts in the longer time intervals (120 min) and less subsequent sedentary behavior in the shorter to longer time intervals (5, 60, and 120 min). For the reversed sequence, neither movement-based behavior predicted subsequent momentary arousal or valence. Affective valence was unrelated to movement-based behaviors in either temporal direction.

Conclusions

Some naturally occurring affective experiences (i.e., arousal) might precede, rather than follow, movement-based behaviors. Understanding affective arousal may contribute to improved management of subsequent movement-based behaviors in everyday life.
Death Caused by Vaginal Injection of Hyaluronic Acid and Collagen: A Case Report
Authors: Yang Yang , Sheng Hengwei , Gu Qinmei , Su Lei , Tong Huasheng , Chen Jianwu , Qi Xiangdong
Published: October 2019

With the expanding utilization of hyaluronic acid (HA) and collagen as cosmetic fillers in plastic and reconstructive surgery, complications due to their excessive use and/or irregular procedures warrant great caution. Recently, a fatal case occurred caused by a poorly regulated procedure of vaginal injection of HA and collagen. A 33-year-old female was admitted to the emergency department 3 hours after the operation with a chief complaint of dyspnea, which initiated 5 to 10 minutes after the operation. Her blood pressure remained low while dopamine pressor and fluid replacement were used. Computed tomography of the chest showed local exudation in the lower lobe of the left lung, enlargement of right atrium and ventricle, and uneven development of the bilateral inferior lobar artery with filling defects. Pulmonary computed tomography angiography and three-dimensional reconstruction showed continuous interruption of pulmonary artery branches of the posterior basal segment of the right lower lobe. Unfortunately, the clinical symptoms caused by vaginal injection aggravated rapidly and could not be effectively controlled. The patient died 9 hours after injection. Pulmonary complications after injection of cosmetic fillers are scarcely reported. Thus far, only 2 cases of HA-related pulmonary complications after vaginal injection have been described. The present case emphasizes that surgeons and other healthcare providers must be aware of the risk of serious pulmonary complications and even death associated with these 2 widely utilized injectable fillers.

Level of Evidence: 5
Tools for fundamental analysis functions of TCR repertoires: a systematic comparison
Authors: Zhang Yanfang , Yang Xiujia , Zhang Yanxia , Zhang Yan , Wang Minhui , Ou Jin Xia , Zhu Yan , Zeng Huikun , Wu Jiaqi , Lan Chunhong , Zhou Hong-Wei , Yang Wei , Zhang Zhenhai
Published: October 2019

The full set of T cell receptors (TCRs) in an individual is known as his or her TCR repertoire. Defining TCR repertoires under physiological conditions and in response to a disease or vaccine may lead to a better understanding of adaptive immunity and thus has great biological and clinical value. In the past decade, several high-throughput sequencing-based tools have been developed to assign TCRs to germline genes and to extract complementarity-determining region 3 (CDR3) sequences using different algorithms. Although these tools claim to be able to perform the full range of fundamental TCR repertoire analyses, there is no clear consensus of which tool is best suited to particular projects. Here, we present a systematic analysis of 12 available TCR repertoire analysis tools using simulated data, with an emphasis on fundamental analysis functions. Our results shed light on the detailed functions of TCR repertoire analysis tools and may therefore help researchers in the field to choose the right tools for their particular experimental design.
Matched Forest: supervised learning for high-dimensional matched case–control studies
Authors: Shomal Zadeh Nooshin , Lin Sangdi , Runger George C
Published: October 2019

Motivation

Matched case–control analysis is widely used in biomedical studies to identify exposure variables associated with health conditions. The matching is used to improve the efficiency. Existing variable selection methods for matched case–control studies are challenged in high-dimensional settings where interactions among variables are also important. We describe a quite different method for high-dimensional matched case–control data, based on the potential outcome model, which is not only flexible regarding the number of matching and exposure variables but also able to detect interaction effects.

Results

We present Matched Forest (MF), an algorithm for variable selection in matched case–control data. The method preserves the case and control values in each instance but transforms the matched case–control data with added counterfactuals. A modified variable importance score from a supervised learner is used to detect important variables. The method is conceptually simple and can be applied with widely available software tools. Simulation studies show the effectiveness of MF in identifying important variables. MF is also applied to data from the biomedical domain and its performance is compared with alternative approaches.

Availability and implementation

R code for implementing MF is available at https://github.com/NooshinSh/Matched_Forest.

Supplementary information

Supplementary data are available at Bioinformatics online.
Increased Mortality After Tuberculosis Treatment Completion in Persons Living With Human Immunodeficiency Virus in Latin America
Authors: Koenig Serena P , Kim Ahra , Shepherd Bryan E , Cesar Carina , Veloso Valdilea , Cortes Claudia P , Padgett Denis , Crabtree-Ramírez Brenda , Gotuzzo Eduardo , McGowan Catherine C , Sterling Timothy R , Pape Jean W
Published: October 2019

We assessed the association between cured tuberculosis (TB) and mortality among persons living with human immunodeficiency virus (HIV) in Latin America. We compared survival among persons with and without TB at enrollment in HIV care, starting 9 months after clinic enrollment. In multivariable analysis, TB was associated with higher long-term mortality (hazard ratio, 1.57; 95% confidence interval, 1.25–1.99).
The effect of natriuretic C-type peptide and its change over time on mortality in patients on haemodialysis or haemodiafiltration
Authors: de Roij van Zuijdewijn Camiel L M , van Gastel Lieke H A , ter Wee Piet M , Bots Michiel L , Blankestijn Peter J , van den Dorpel Marinus A , Fouque Denis , Nubé Menso J , Grooteman Muriel P C
Published: October 2019

Background

C-type natriuretic peptide (CNP) and its co-product N-terminal proCNP (NTproCNP) have been associated with beneficial effects on the cardiovascular system. In prevalent dialysis patients, however, a relation between NTproCNP and mortality has not yet been investigated. Furthermore, as a middle molecular weight substance, its concentration might be influenced by dialysis modality.

Methods

In a cohort of patients treated with haemodialysis (HD) or haemodiafiltration (HDF), levels of NTproCNP were measured at baseline and 6, 12, 24 and 36 months. The relation between serum NTproCNP and mortality and the relation between the 6-month rate of change of NTproCNP and mortality were analysed using Cox regression models. For the longitudinal analyses, linear mixed models were used.

Results

In total, 406 subjects were studied. The median baseline serum NTproCNP was 93 pmol/L and the median follow-up was 2.97 years. No relation between baseline NTproCNP or its rate of change over 6 months and mortality was found. NTproCNP levels remained stable in HD patients, whereas NTproCNP decreased significantly in HDF patients. The relative decline depended on the magnitude of the convection volume.

Conclusions

In our study, levels of NTproCNP appear strongly elevated in prevalent dialysis patients. Second, while NTproCNP remains unaltered in HD patients, its levels decline in individuals treated with HDF, with the decline dependent on the magnitude of the convection volume. Third, NTproCNP is not related to mortality in this population. Thus NTproCNP does not seem to be a useful marker for mortality risk in dialysis patients.
Impact of cardiology follow-up care on treatment and outcomes of patients with new atrial fibrillation discharged from the emergency department
Authors: Hawkins Nathaniel M , Scheuermeyer Frank X , Youngson Erik , Sandhu Roopinder K , Ezekowitz Justin A , Kaul Padma , McAlister Finlay A
Published: October 2019

Aims

The first presentation of atrial fibrillation (AF) is often to an emergency department (ED). We evaluated the association of subsequent specialist care with morbidity and mortality.

Methods and results

Retrospective cohort study of all adults in Alberta, Canada, with a new primary diagnosis of AF treated and released during an index ED visit between 2009 and 2015. Types of physician follow-up within 3 months of ED visit was analysed using Cox proportional hazards models with time-varying covariates. Outcomes were evaluated at 1 year. Of 7986 patients, 476 (6.0%) had no physician follow-up within 3 months, whereas 2730 (34.2%) attended a non-specialist only, 1277 (16.0%) an internal medicine specialist, and 3503 (43.9%) cardiology. An increasing gradient of cardiac investigations occurred across these groups. Cardiology compared with non-cardiologist care was associated with approximately two-fold greater electrophysiology interventions and revascularization, and increased use of beta-blockers (48.9% vs. 43.0%, P < 0.0001), statins (31.4% vs. 26.7%, P < 0.0001), and oral anticoagulation in patients with CHADS2 scores ≥1 (53.7% vs. 43.6%, P < 0.0001). In the subsequent year, cardiology care was associated with fewer deaths [adjusted hazard ratio (aHR) 0.72, 95% confidence interval (CI) 0.55–0.93], strokes (aHR 0.60, 95% CI 0.37–0.96), or major bleeds (aHR 0.69, 95% CI 0.53–0.89). No differences in the risk of hospitalization or ED visits were associated with cardiology care.

Conclusion

Cardiology care after an ED visit for symptomatic new-onset AF is associated with better prognosis. The benefit may be mediated through more intensive investigation, identification, and treatment of cardiovascular risk factors and disease.
Intrinsic role of bacterial secretion systems in phylogenetic niche conservation of Bradyrhizobium spp.
Authors: Banerjee Goutam , Basak Swarnendu , Roy Tathagato , Chattopadhyay Pritam
Published: October 2019

Bradyrhizobium is a biologically important bacterial genus. Different Bradyrhizobium strains exhibit distinct niche selection like free living, root nodular and stem nodular. The present in-silico study was undertaken to identify the role of bacterial secretome in the phylogenetic niche conservation (PNC) of Bradyrhizobium sp. Analysis was carried out with the publicly available 19 complete genome assembly and annotation reports. A protocol was developed to screen the secretome related genes using three different database, viz. genome, proteome and gene ortholog. This resulted into 139 orthologs that include type secretion systems (T1SS-T6SS) along with flagella (Flg), type IV pili (T4P) and tight adherence (Tad) systems. Multivariate analysis using bacterial secretome was undertaken to find out the role of these secretion systems in PNC. In free living strains, T3SS, T4SS and T6SS were completely absent. Whereas, in the stem nodulating strains, T3SS and T6SS were absent, but T4SS was found to be present. On the other hand, the T3SS was found to be present only in the root-nodulating strains. The present investigation clearly demonstrated a pattern of PNC based on the distribution of secretion system components. To the best of our knowledge, this is the first report on PNC of Bradyrhizobium using the multivariate analysis of secretome.
Unique Shine–Dalgarno Sequences in Cyanobacteria and Chloroplasts Reveal Evolutionary Differences in Their Translation Initiation
Authors: Wei Yulong , Xia Xuhua
Published: October 2019

Microorganisms require efficient translation to grow and replicate rapidly, and translation is often rate-limited by initiation. A prominent feature that facilitates translation initiation in bacteria is the Shine–Dalgarno (SD) sequence. However, there is much debate over its conservation in Cyanobacteria and in chloroplasts which presumably originated from endosymbiosis of ancient Cyanobacteria. Elucidating the utilization of SD sequences in Cyanobacteria and in chloroplasts is therefore important to understand whether 1) SD role in Cyanobacterial translation has been reduced prior to chloroplast endosymbiosis or 2) translation in Cyanobacteria and in plastid has been subjected to different evolutionary pressures. To test these alternatives, we employed genomic, proteomic, and transcriptomic data to trace differences in SD usage among Synechocystis species, Microcystis aeruginosa, cyanophages, Nicotiana tabacum chloroplast, and Arabidopsis thaliana chloroplast. We corrected their mis-annotated 16S rRNA 3′ terminus using an RNA-Seq-based approach to determine their SD/anti-SD locational constraints using an improved measurement DtoStart. We found that cyanophages well-mimic Cyanobacteria in SD usage because both have been under the same selection pressure for SD-mediated initiation. Whereas chloroplasts lost this similarity because the need for SD-facilitated initiation has been reduced in plastids having much reduced genome size and different ribosomal proteins as a result of host-symbiont coevolution. Consequently, SD sequence significantly increases protein expression in Cyanobacteria but not in chloroplasts, and only Cyanobacterial genes compensate for a lack of SD sequence by having weaker secondary structures at the 5′ UTR. Our results suggest different evolutionary pressures operate on translation initiation in Cyanobacteria and in chloroplast.
A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona
Authors: Satou Yutaka , Nakamura Ryohei , Yu Deli , Yoshida Reiko , Hamada Mayuko , Fujie Manabu , Hisata Kanako , Takeda Hiroyuki , Satoh Noriyuki
Published: October 2019

Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114–120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.
Financial Stress and Risk for Entry into Medicaid Among Older Adults
Authors: Willink Amber , Wolff Jennifer L , Mulcahy John , Davis Karen , Kasper Judith D
Published: October 2019

Background and Objectives

Spending in the Medicaid program is a significant concern to both state and federal policy makers. Medicaid spending is driven by program enrollment and services use. Older adults with high health care needs incur a disproportionate proportion of program spending. This analysis identifies factors that place older Medicare beneficiaries at increased risk for entering into Medicaid.

Research Design and Methods

We use multinomial logistic regression and the 2011–2017 National Health and Aging Trends Study (NHATS) to examine the risks among older Medicare beneficiaries for entering into Medicaid over a 6-year follow-up period. We examine both time-invariant and time-varying factors to measure the impact of social and health and functioning changes at older ages.

Results

The risk of entry into Medicaid was higher for older adults who relocated to a nursing home (relative risk ratio [RRR]: 7.75; 95% confidence interval [CI]: 5.33–11.26) or other residential care setting (RRR: 1.36; 95% CI: 0.96–1.92) compared to those who remained in traditional community settings. Older adults who reported skipping a meal in the last month because there was not enough money to buy food were 2.4 times (95% CI: 1.10–5.21) more likely to enter Medicaid than those who did not. Similarly, older adults who reported not having enough money to pay household utility bills in the last year were 1.89 times (95% CI: 1.08–3.30) more likely to enter Medicaid.

Discussion and Implications

Study findings suggest that trouble paying for basic needs increases the risk of entry into Medicaid. Further research is required to examine whether addressing these needs through improved access to social services that enable older adults to live safely in their home may delay or mitigate entry into Medicaid.
Multitasking and Dual Motivational Systems: A Dynamic Longitudinal Study
Authors: Xu Shan , Wang Zheng , Woods Kelsey
Published: October 2019

This study further explores the myth of media multitasking: that is, why people increasingly media multitask despite its known harmful effects on performance. Building on previous research on the emotional gratifications of media multitasking and guided by the dynamic motivational activation (DMA) approach, this study specifies emotional gratifications in terms of positive and negative emotions, as well as their underlying appetitive and aversive motivational changes. Using a dynamic panel analysis of longitudinal experience sampling data collected from 71 adolescents (ages 11–17; 61% girls) over 2 weeks, this study identifies several dynamic reciprocal impacts of media multitasking and the dual motivational systems. As predicted by DMA, media multitasking coactivates both the appetitive and aversive motivational systems, and increases both positive and negative emotions; interestingly, only the appetitive system goes on to determine subsequent media multitasking.
Genetic and genomic studies of pathogenic EXOSC2 mutations in the newly described disease SHRF implicate the autophagy pathway in disease pathogenesis
Authors: Yang Xue , Bayat Vafa , DiDonato Nataliya , Zhao Yang , Zarnegar Brian , Siprashvili Zurab , Lopez-Pajares Vanessa , Sun Tao , Tao Shiying , Li Chenjian , Rump Andreas , Khavari Paul , Lu Bingwei
Published: October 2019

Missense mutations in the RNA exosome component exosome component 2 (EXOSC2), also known as ribosomal RNA-processing protein 4 (RRP4), were recently identified in two unrelated families with a novel syndrome known as Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies (SHRF, #OMIM 617763). Little is known about the mechanism of the SHRF pathogenesis. Here we have studied the effect of mutations in EXOSC2/RRP4 in patient-derived lymphoblasts, clustered regularly interspaced short palindromic repeats (CRISPR)-generated mutant fetal keratinocytes and Drosophila. We determined that human EXOSC2 is an essential gene and that the pathogenic G198D mutation prevents binding to other RNA exosome components, resulting in protein and complex instability and altered expression and/or activities of critical genes, including those in the autophagy pathway. In parallel, we generated multiple CRISPR knockouts of the fly rrp4 gene. Using these flies, as well as rrp4 mutants with Piggy Bac (PBac) transposon insertion in the 3′UTR and RNAi flies, we determined that fly rrp4 was also essential, that fly rrp4 phenotypes could be rescued by wild-type human EXOSC2 but not the pathogenic form and that fly rrp4 is critical for eye development and maintenance, muscle ultrastructure and wing vein development. We found that overexpression of the transcription factor MITF was sufficient to rescue the small eye and adult lethal phenotypes caused by rrp4 inhibition. The autophagy genes ATG1 and ATG17, which are regulated by MITF, had similar effect. Pharmacological stimulation of autophagy with rapamycin also rescued the lethality caused by rrp4 inactivation. Our results implicate defective autophagy in SHRF pathogenesis and suggest therapeutic strategies.
Genetic and biophysical modelling evidence of generational connectivity in the intensively exploited, Western North Atlantic red grouper (Epinephelus morio)
Authors: Bernard Andrea M , Johnston Matthew W , Pérez-Portela Rocío , Oleksiak Marjorie F , Coleman Felicia C , Shivji Mahmood S
Published: October 2019

Understanding the connectivity of reef organisms is important to assist in the conservation of biological diversity and to facilitate sustainable fisheries in these ecosystems. Common methods to assess reef connectivity include both population genetics and biophysical modelling. Individually, these techniques can offer insight into population structure; however, the information acquired by any singular analysis is often subject to limitations, underscoring the need for a multi-faceted approach. To assess the connectivity dynamics of the red grouper (Epinephelus morio), an economically important reef fish species found throughout the Gulf of Mexico and USA western Atlantic, we utilized two sets of genetic markers (12 microsatellite loci and 632 single nucleotide polymorphisms) to resolve this species’ population genetic structure, along with biophysical modelling to deliver a spatial forecast of potential larval “sources” and “sinks” across these same regions and spatial scale. Our genetic survey indicates little, if any, evidence of population genetic structure and modelling efforts indicate the potential for ecological connectivity between sampled regions over multiple generations. We offer that using a dual empirical and theoretical approach lessens the error associated with the use of any single method and provides an important step towards the validation of either of these methodologies.
Safety, Tolerability, and Pharmacokinetics of the Broadly Neutralizing Human Immunodeficiency Virus (HIV)-1 Monoclonal Antibody VRC01 in HIV-Exposed Newborn Infants
Authors: Cunningham Coleen K , McFarland Elizabeth J , Morrison R Leavitt , Capparelli Edmund V , Safrit Jeffrey T , Mofenson Lynne M , Mathieson Bonnie , Valentine Megan E , Perlowski Charlotte , Smith Betsy , Hazra Rohan , Purdue Lynette , Muresan Petronella , Harding Paul A , Mbengeranwa Tapiwa , Robinson Lisa-Gaye , Wiznia Andrew , Theron Gerhard , Lin Bob , Bailer Robert T , Mascola John R , Graham Barney S ,   IMPAACT P1112 team, Aldrovandi Grace , Bone Frederic , Dayton Dale , Johnston Benjamin , Morgan Patricia , Myers Kathryn , Tobin Nicole , Zimmer Bonnie , Rossouw Magdel , Rossouw Lindie , Louw Jeanne , Dobroszycki Joanna , Burey Marlene , Auguste Raphaelle , Graham Kathleen K , Major-Wilson Hanna , Mhembere Tsungai , Maturure Sukunena , Bwakura-Dangarembizi Mutsa , Barr Emily , Dunn Jennifer , Glenny Carrie , Chambers Carrie , Mirza Baig Mahboobullah , Purswani Murli , Deville Jaime G , Nielsen-Saines Karin , Shin Christina , Carter Michele F , Chahroudi Ann , Ahonen Alexis , Badell Martina , Chakraborty Rana , Agwu Allison , Christopher Golden W , Anderson Thuy , Collinson-Streng Aleisha , Diaz-Velasco Rodrigo , Rosario Nicolas , Pérez Elvia , Marrero Wanda I , Febo Irma , Santos Ruth , Zorrilla Carmen D
Published: October 2019

Background

Although mother-to-child human immunodeficiency virus (HIV) transmission has dramatically decreased with maternal antiretroviral therapy, breast milk transmission accounts for most of the 180 000 new infant HIV infections annually. Broadly neutralizing antibodies (bNAb) may further reduce transmission.

Methods

A Phase 1 safety and pharmacokinetic study was conducted: a single subcutaneous (SC) dose of 20 or 40 mg/kg (Dose Groups 1 and 2, respectively) of the bNAb VRC01 was administered to HIV-exposed infants soon after birth. Breastfeeding infants (Dose Group 3) received 40 mg/kg SC VRC01 after birth and then 20 mg/kg/dose SC monthly. All infants received appropriate antiretroviral prophylaxis.

Results

Forty infants were enrolled (21 in the United States, 19 in Africa). Subcutaneous VRC01 was safe and well tolerated with only mild-to-moderate local reactions, primarily erythema, which rapidly resolved. For multiple-dose infants, local reactions decreased with subsequent injections. VRC01 was rapidly absorbed after administration, with peak concentrations 1–6 days postdose. The 40 mg/kg dose resulted in 13 of 14 infants achieving the serum 50 micrograms (mcg)/mL target at day 28. Dose Group 3 infants maintained concentrations greater than 50 mcg/mL throughout breastfeeding.

Conclusions

Subcutaneous VRC01 as single or multiple doses is safe and well tolerated in very young infants and is suitable for further study to prevent HIV transmission in infants.
Do You Feel Welcome? Gendered Experiences in International Security Studies
Authors: Rublee Maria Rost , Jackson Emily B , Parajon Eric , Peterson Susan , Duncombe Constance
Published: October 2019

Unlike in the broader field of international relations, relatively little research on gender representation and gendered experiences exists within the subfield of security studies. This article begins to fill that gap by sharing the results of a 2019 survey of members of the International Security Studies Section (ISSS) of the International Studies Association (ISA). The survey results show striking gender differences in members’ experiences, with women more likely than men to describe ISSS as “insular,” “clubby,” and an “Old Boys’ Network”; more likely to report experiences of hostility and exclusion; and more likely to believe that diversity initiatives are needed. Our analysis reveals that women in the ISSS report (1) harassment, (2) negative experiences participating in various section activities, (3) more significant barriers to attending and being selected for the section's ISA program, and (4) a sense of feeling unwelcome at ISSS meetings, all at higher rates than male respondents.
Red Blood Cells and Platelets Conventional and Research Parameters: Stability Remarks Before Their Interpretation
Authors: Pérez Irene , Redín Maria Elena
Published: October 2019

Objectives

To analyze the stability of red blood cells, platelets, and reticulocytes of the research parameters, in combination with the respective conventional parameters, for each analyte; and to quantify the morphological changes in these analytes, to propose a correction factor for each.

Methods

Ethylenediaminetetraacetic acid (EDTA) blood specimens from patients were reanalyzed in 2-hour intervals and then, the mean percentage (X¯t%) changes were calculated. To evaluate the stability of the analyzed material, we used different criteria according to within-run and between-batch analytical variation, as well as intraindividual biological variation. Next, the mean deviation percentage of the parameters that undergo time-dependent significant changes was calculated, to obtain a correction factor.

Results

Several conventional and research parameters showed significant alterations in the stability at an early time after arrival at the laboratory.

Conclusion

Cell variations over time can be quantified and corrected by applying a multiplying factor to the signal obtained in the analyzer.
Multiwavelength observations of the triple-peaked AGN Mrk 622
Authors: Benítez E , Cruz-González I , Rodríguez-Espinosa J M , González-Martín O , Negrete C A , Gutiérrez L , Jiménez-Bailón E , Ruschel-Dutra D , Rodríguez L F , Loinard L , Binette L
Published: October 2019

A detailed multiwavelength study of the properties of the triple-peaked active galactic nucleus (AGN) Mrk 622 showing different aspects of the nuclear emission region is presented. Radio, near- and mid-infrared, optical, and X-ray data have been considered for the analysis. In the optical, the WHAN diagnostic diagrams show that the three nuclear peaks are strong active galactic nuclei since the equivalent width of H α is > 6 Å  and log  [N ii] λ6584/H α  ratio is > −0.4. Optical variability of both the continuum flux and intensity of the narrow emission lines is detected in a time span of 13 yr. The size of the narrow-line region is found to be 2.7 pc, with a light-crossing time of 8.7 yr. Analysis done to an archival Hubble Space Telescope image at 1055.2 nm shows that the host galaxy has a 3.6 kpc inner bar with PA  =  74°, faint spiral arms, and a pseudobulge, evolving through secular processes. High-resolution mid-infrared images obtained with the Gran Telescopio Canarias (GTC) and the instrument CanariCam show that the nuclear emission at 11.6 $\rm{\mu m}$ is not spatially resolved. Very Large Array archival observations at 10 GHz reveal a core source with a total flux density of 1.47 ± 0.03 mJy. The spectral index of the core between 8 and 12 GHz is −0.5 ± 0.2, characteristic of AGN. The core deconvolves into a source with dimensions of 82 ± 13 mas $\, \times \,$ 41 ± 20 mas, and a PA = 70  ±  18 deg, which suggests that the core is elongated or that it is constituted by multiple components distributed along a ∼65° axis.
Recalibrating the cosmic star formation history
Authors: Wilkins Stephen M , Lovell Christopher C , Stanway Elizabeth R
Published: October 2019

The calibrations linking observed luminosities to the star formation rate (SFR) depend on the assumed stellar population synthesis model, initial mass function, star formation and metal enrichment history, and whether reprocessing by dust and gas is included. Consequently the shape and normalization of the inferred cosmic star formation history is sensitive to these assumptions. Using v2.2.1 of the Binary Population and Spectral Synthesis (bpass) model we determine a new set of calibration coefficients for the ultraviolet, thermal infrared, and hydrogen recombination lines. These ultraviolet and thermal infrared coefficients are 0.15–0.2 dex higher than those widely utilized in the literature while the H α coefficient is ∼0.35 dex larger. These differences arise in part due to the inclusion binary evolution pathways but predominantly reflect an extension in the IMF to 300 M⊙ and a change in the choice of reference metallicity. We use these new coefficients to recalibrate the cosmic star formation history, and find improved agreement between the integrated cosmic star formation history and the in situ measured stellar mass density as a function of redshift. However, these coefficients produce new tension between SFR densities inferred from the ultraviolet and thermal infrared and those from H α.
Exploring particle escape in supernova remnants through gamma rays
Authors: Celli S , Morlino G , Gabici S , Aharonian F A
Published: October 2019

The escape process of particles accelerated at supernova remnant (SNR) shocks is one of the poorly understood aspects of the shock acceleration theory. Here we adopt a phenomenological approach to study the particle escape and its impact on the gamma-ray spectrum resulting from hadronic collisions both inside and outside of a middle-aged SNR. Under the assumption that in the spatial region immediately outside of the remnant the diffusion coefficient is suppressed with respect to the average Galactic one, we show that a significant fraction of particles are still located inside the SNR long time after their nominal release from the acceleration region. This fact results into a gamma-ray spectrum that resembles a broken power law, similar to those observed in several middle-aged SNRs. Above the break, the spectral steepening is determined by the diffusion coefficient outside of the SNR and by the time dependence of maximum energy. Consequently, the comparison between the model prediction and actual data will contribute to determining these two quantities, the former being particularly relevant within the predictions of the gamma-ray emission from the halo of escaping particles around SNRs, which could be detected with future Cherenkov telescope facilities. We also calculate the spectrum of runaway particles injected into the Galaxy by an individual remnant. Assuming that the acceleration stops before the SNR enters the snowplow phase, we show that the released spectrum can be a featureless power law only if the accelerated spectrum is ∝ p−α with α > 4.
Modified Orbitozygomatic Craniotomy for Previously Coiled Giant Basilar Apex Aneurysm: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: October 2019

Basilar apex aneurysms are generally preferentially managed with endovascular intervention; however, these lesions can demonstrate refractory persistence despite this treatment and, in such cases, must be managed microsurgically. Successful navigation to and manipulation of the basilar apex through the orbitozygomatic approach requires an intricate understanding of the cerebrovascular microanatomy and arachnoid planes within interpeduncular fossa and comfort with use of the operating microscope for the long surgical trajectory to the basilar apex. This patient had a multiply recurrent basilar apex aneurysm; 3 previous coil embolization attempts had been made without successful aneurysm obliteration. This case presented multiple complicating factors, including the presence of a large coil mass and the significant size of the basilar apex lesion. An Allcock test was performed to determine the collateralization across the posterior communicating arteries, and no posterior communicating arteries were visualized, which suggested isolation of the posterior and anterior circulation. A fenestrated clip was utilized from the right side to occlude the base of the aneurysm. Single-clip application was not impeded by the coil mass. Postoperative angiography demonstrated complete occlusion of the aneurysm. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Microscopic optical potentials including breakup effects for elastic scattering
Authors: Ogawa Shoya , Horinouchi Ryo , Toyokawa Masakazu , Matsumoto Takuma
Published: October 2019

We construct a microscopic optical potential including breakup effects for the elastic scattering of weakly binding projectiles within the Glauber model, in which a nucleon–nucleus potential is derived using the $g$-matrix folding model. The derived microscopic optical potential is referred to as the eikonal potential. For $d$ scattering, calculation with the eikonal potential, i.e., the EP model, reasonably reproduces the result of the exact calculation with the continuum-discretized coupled-channels method at intermediate energies. From the properties of the EP model, the inaccuracy of the eikonal approximation used in the Glauber model is partially excluded. Also analyzed with the eikonal potential is the scattering of $^6$He from $^{12}$C, and its applicability to scattering with many-body projectiles is shown.
Time series analysis for multi-dimensional dynamical systems combining wavelet transformation and local principal component analysis
Authors: Fuji Kana , Toda Mikito
Published: October 2019

To analyze trajectories for systems of many degrees of freedom, we propose a new method called wavelet local principal component analysis (WlPCA) combining the wavelet transformation and local PCA in time. Our method enables us to reduce the dimensionality of time series both in degrees of freedom and frequency so that characteristic features of oscillatory behavior can be captured. To test the new method, we apply WlPCA to a non-autonomous model of multiple degrees of freedom, the Froeschlé maps of $N=2$ and $N=4$, which correspond to autonomous systems of three and five degrees of freedom, respectively. The eigenvalues and eigenvectors obtained by WlPCA reveal those times when frequency variation exhibits switching between relatively stationary features. Moreover, further analyses indicate which degrees of freedom and frequencies are involved in the switching. We confirm that the switching corresponds to the onset of transport in phase space. These findings imply that, even for systems of larger degrees of freedom, barriers can exist in phase space that block transport for a finite time, thereby dividing the phase space into multiple quasi-stationary regions. Thus, our method is promising for understanding dynamics in systems of many degrees of freedom, such as vibrational-energy redistribution in molecules.
Mine, Yours or Ours? The Efficiency of Household Investment Decisions: An Experimental Approach
Authors: Mani Anandi
Published: October 2019

This article sheds light on the impact on household investment efficiency of a social norm that a man should not earn less than his wife. The experiment distinguishes this impact from that of spouses’ desire for control over household resources. Both husbands and wives are found to sacrifice household income (efficiency) for greater control; but, consistent with this social norm, husbands alone behave inefficiently if assigned a smaller income share than their spouse. The evidence suggests spiteful behavior among such husbands: they are willing to undercut their own income to narrow the gap with their wives’ earnings. The magnitude of husbands’ inefficiency influenced by this social norm is comparable to that when husbands have the least control over household earnings. These results, taken together with evidence from developed countries, show that this social norm has a persistent effect on household efficiency, distinct from spouses’ economic concerns.
Illicit Financial Flows: Concepts, Measurement, and Evidence
Authors: Collin Matthew
Published: October 2019

There is a growing consensus that the presence of illegal and harmful cross-border financial flows is one of the factors impeding economic and human development. In recent years, a new conceptual framework for describing these “illicit” financial flows (IFFs) has emerged that combines issues ranging from cross-border money laundering to tax evasion. This article summarizes and clarifies recent empirical work in this area. Three types of studies are considered and critiqued: (i) methods of measuring IFFs, (ii) constructed risk indicators, and (iii) forensic studies that aim to uncover instances where illicit flows have occurred. The article discusses the limitations of all three approaches and proposes ways in which the research agenda on IFFs could be reasonably advanced, given the hidden nature of the subject.