bluuebunny/crossref_metadata_2025 huggingface dataset:
Equity Finance: Matching Liability to Power
Authors: Goodhart C A E , Lastra R M
Published: October 2019

In this article we question the wisdom of limited liability for all equity holders in the case of banks and systemically important financial institutions (SIFIs), though our proposals could be extended to all public limited companies. Limited liability can be a major source of moral hazard and excessive risk taking—a privilege that allows shareholders to enjoy the upside from their commercial activity while limiting their exposure in the event of failure. We propose that there should be two different classes of equity for banks and SIFIs. The division should be between outsiders, with no inside knowledge of the working of the firm and/or ability to control its decisions, and insiders, who have both the information and capacity to influence corporate decision-making. Outsiders would remain with limited liability, while multiple liability (double, triple, and potentially unlimited) would apply to insiders. The purpose of our proposal is to shift the costs of failure back to those who have responsibility for taking these decisions. The idea of financial liability ‘with teeth’—which is rooted in history—provides an innovative solution that improves the incentives for managers to take responsible decisions, and promotes a radical change in the structure of capitalism—addressing the unfairness of the current system which has enhanced inequality and encouraged populism.
A multicenter randomized phase III study for newly diagnosed maximally resected glioblastoma comparing carmustine wafer implantation followed by chemoradiotherapy with temozolomide with chemoradiotherapy alone; Japan Clinical Oncology Group Study JCOG1703 (MACS study)
Authors: Kadota Tomohiro , Saito Ryuta , Kumabe Toshihiro , Mizusawa Junki , Katayama Hiroshi , Sumi Minako , Igaki Hiroshi , Kinoshita Manabu , Komori Takashi , Ichimura Koichi , Narita Yoshitaka , Nishikawa Ryo
Published: October 2019

A randomized phase III trial in Japan commenced in June 2019. The present standard treatment for newly diagnosed glioblastoma is maximal resection followed by chemoradiotherapy with temozolomide. The purpose of this study is to confirm the superiority of maximal resection with carmustine wafer implantation followed by chemoradiotherapy with temozolomide over the standard maximal resection followed by chemoradiotherapy with temozolomide in terms of overall survival for newly diagnosed glioblastoma. A total of 250 patients will be accrued from 35 Japanese institutions in 5.5 years. Patients with >90% surgical resection will be registered and randomly assigned to each group with 1:1 allocation. The primary endpoint is overall survival and the secondary endpoints are progression-free survival, loco-regional progression-free survival and incidence of adverse events. This trial has been registered in the Japan Registry of Clinical Trial, as jRCT1031190035 [https://jrct.niph.go.jp/en-latest-detail/jRCT1031190035].
The Octopamine Receptor Is a Possible Target for Eugenol-Induced Hyperactivity in the Blood-Sucking Bug Triatoma infestans (Hemiptera: Reduviidae)
Authors: Reynoso Mercedes M N , Lucia Alejandro , Zerba Eduardo N , Alzogaray Raúl A
Published: October 2019

Eugenol is a major component of the essential oils in cloves and other aromatic plants. In insects, it produces toxic effects and repellency, and there is evidence that its site of action is the octopamine receptor. The objective of the present study was to explore whether the octopamine receptor is involved in the hyperactivity produced by eugenol in the blood-sucking bug Triatoma infestans (Klug). This insect is the main vector of Chagas disease in Latin America. Four treatments were topically applied on third instar nymphs: 1) octopamine, 2) eugenol, 3) phentolamine hydrochloride (an antagonist of the octopamine receptor) followed by octopamine, and 4) phentolamine hydrochloride followed by eugenol. Both octopamine and eugenol hyperactivated the nymphs. However, pretreatment with phentolamine hydrochloride inhibited the hyperactivating effect of both compounds. These results are in agreement with previous works on Drosophila melanogaster (Meigen) (Diptera: Drosophilidae) and the American cockroach. They suggest that the octopamine receptor is a possible site of action for eugenol.
Measurements of Endpoint Titers Based on the Fluorescence Intensity Trend in Anti-Nuclear Antibody Testing
Authors: Won Dong I L
Published: October 2019

Background

Automated systems for antinuclear antibody (ANA) testing provide endpoint titers that are predicted based on the fluorescence intensity (FI) value at a screening dilution (single-well titration [SWT]) showing frequent titration errors (more than plus or minus 1 dilution).

Methods

Line slope titration (LST) was based on the trend of FI values on dilutions. Three dilutions per specimen were prepared considering a patient’s previous titer or FI at the screening dilution. On the XY plot, with the reciprocal of dilution as the X-axis and FI value as the Y-axis, a fitted line was drawn to obtain the endpoint titers.

Results

The titration error rate (no. of errors/total no.) of LST using a regression line was lower than that of SWT (31/710 [4.4%] and 152/674 [22.6%], respectively; P < .000000001), with serial dilution as a reference. When comparing a regression line using 3 dilution points with a line using 2 dilution points, the error rate of the former was not significantly different from that of the latter (31/710 [4.4%] and 31/746 [4.2%], respectively; P = .842).

Conclusions

This LST method is useful as an accurate, cost-effective, and rapid approach to measure endpoint titers in routine ANA testing.
Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees
Authors: Hu Dalong , Liu Bin , Wang Lei , Reeves Peter R
Published: October 2019

An ideal bacterial phylogenetic tree accurately retraces evolutionary history and accurately incorporates mutational, recombination and other events on the appropriate branches. Current strain-level bacterial phylogenetic analysis based on large numbers of genomes lacks reliability and resolution, and is hard to be replicated, confirmed and reused, because of the highly divergent nature of microbial genomes. We present SNPs and Recombination Events Tree (SaRTree), a pipeline using six “living trees” modules that addresses problems arising from the high numbers and variable quality of bacterial genome sequences. It provides for reuse of the tree and offers a major step toward global standardization of phylogenetic analysis by generating deposit files including all steps involved in phylogenetic inference. The tree itself is a “living tree” that can be extended by addition of more sequences, or the deposit can be used to vary the programs or parameters used, to assess the effect of such changes. This approach will allow phylogeny papers to meet the traditional responsibility of providing data and analysis that can be repeated and critically evaluated by others. We used the Acinetobacter baumannii global clone I to illustrate use of SaRTree to optimize tree resolution. An Escherichia coli tree was built from 351 sequences selected from 11,162 genome sequences, with the others added back onto well-defined branches, to show how this facility can greatly improve the outcomes from genome sequencing. SaRTree is designed for prokaryote strain-level analysis but could be adapted for other usage.
Peroxiredoxin 6 regulates the phosphoinositide 3-kinase/AKT pathway to maintain human sperm viability
Authors: Fernandez Maria C , Yu Alex , Moawad Adel R , O’Flaherty Cristian
Published: October 2019

Peroxiredoxins (PRDXs) are antioxidant enzymes proven to control the levels of reactive oxygen species (ROS) and to avoid oxidative damage in the spermatozoon. Previously, we have shown that low amounts of PRDXs are associated with male infertility and that PRDX6 is the primary antioxidant defence in human spermatozoa, maintaining survival and DNA integrity (Gong et al., 2012, Fernandez and O’Flaherty, 2018). Oxidative stress can trigger different pathway cascades in the spermatozoa, including truncated apoptosis. It has been reported that the phosphorylation status of phosphoinositide 3-kinase (PI3K) and its target AKT (protein kinase B) prevent the spermatozoon from entering the truncated apoptotic cascade. Here, we aim to study the regulation of the PI3K/AKT pathway by PRDX6 and assess its role in maintaining sperm viability. Human semen samples were obtained over 1 year from 20 healthy non-smoking volunteers aged 22–30 years old. Sperm viability, lipid peroxidation and apoptosis-like changes were determined by flow cytometry while phosphorylation of PI3K and AKT substrates were assessed by immunoblotting using anti-phospho-PI3K and anti-phospho-AKT substrates antibodies. We found that the addition of arachidonic acid and lysophosphatidic acid, products of PRDX6 calcium independent phospholipase A2 (Ca2+-iPLA2), prevented loss of sperm viability and maintained the phosphorylation of PI3K. Antioxidant compounds such as D-penicillamine partially prevented the oxidative damage on spermatozoa that led to a reduction of their viability. Thus, other pathways can also participate in sperm survival and be regulated by PRDXs. In conclusion, PRDX6 contributes to the regulation of ROS production and the PI3K/AKT pathway for the maintenance of sperm survival.
Temporal trends in living kidney donation in France between 2007 and 2017
Authors: Gaillard François , Jacquemont Lola , Roberts Veena , Albano Laetitia , Allard Julien , Bouvier Nicolas , Buchler Mathias , Titeca-Beauport Dimitri , Couzi Lionel , Delahousse Michel , Ducloux Didier , Durrbach Antoine , Etienne Isabelle , Frimat Luc , Garrouste Cyril , Grimbert Philippe , Hazzan Marc , Hertig Alexandre , Kamar Nassim , Quintrec Moglie Le , Mariat Christophe , Moal Valérie , Moulin Bruno , Mousson Christiane , Pouteil-Noble Claire , Rieu Philippe , Rostaing Lionel , Thierry Antoine , Vigneau Cécile , Macher Marie Alice , Hourmant Maryvonne , Legendre Christophe
Published: October 2019

Background

Long-term studies have demonstrated a slight increased risk for end-stage renal disease (ESRD) for living kidney donors (LKD). In France, living kidney donation doubled within the past 10 years. We investigated the change in characteristics of LKD between 2007 and 2017 and the adequacy of follow-up.

Methods

Data were obtained from the national registry for LKD. We compared characteristics of LKD between two study periods: 2007–11 and 2012–17, and stratified donors by age and relation to recipient. We aggregated four characteristics associated with higher ESRD risk [young age, first-degree relation to recipient, obesity, low glomerular filtration rate (GFR) for age] in a single risk indicator ranging from 0 to 4.

Results

We included 3483 donors. The proportion of unrelated donors >56 years of age increased significantly. The proportion of related donors <56 years of age decreased significantly. The body mass index and proportion of obese donors did not change significantly. The proportion of donors with low estimated GFR for age decreased significantly from 5% to 2.2% (P < 0.001). The proportion of donors with adequate follow-up after donation increased from 19.6% to 42.5% (P < 0.001). No donor had a risk indicator equal to 4, and the proportion of donors with a risk indicator equal to 0 increased significantly from 19.2% to 24.9% (P < 0.001).

Conclusions

An increase in living kidney donation in France does not seem to be associated with the selection of donors at higher risk of ESRD and the proportion of donors with adequate annual follow-up significantly increased.
ZmDREB1A Regulates RAFFINOSE SYNTHASE Controlling Raffinose Accumulation and Plant Chilling Stress Tolerance in Maize
Authors: Han Qinghui , Qi Junlong , Hao Guanglong , Zhang Chunxia , Wang Chunmei , Dirk Lynnette M A , Downie A Bruce , Zhao Tianyong
Published: October 2019

Raffinose accumulation is positively correlated with plant chilling stress tolerance; however, the understanding of the function and regulation of raffinose metabolism under chilling stress remains in its infancy. RAFFINOSE SYNTHASE (RAFS) is the key enzyme for raffinose biosynthesis. In this study, we report that two independent maize (Zea mays) zmrafs mutant lines, in which raffinose was completely abolished, were more sensitive to chilling stress and their net photosynthetic product (total soluble sugars and starch) accumulation was significantly decreased compared with controls after chilling stress. A similar characterization of the maize dehydration responsive element (DRE)-binding protein 1A mutant (zmdreb1a) showed that ZmRAFS expression and raffinose content were significantly decreased compared with its control under chilling stress. Overexpression of maize ZmDREB1A in maize leaf protoplasts increased ZmDREB1A amounts, which consequently upregulated the expression of maize ZmRAFS and the Renilla LUCIFERASE (Rluc), which was controlled by the ZmRAFS promoter. Deletion of the single dehydration-responsive element (DRE) in the ZmRAFS promoter abolished ZmDREB1A’s influence on Rluc expression, while addition of three copies of the DRE in the ZmRAFS promoter dramatically increased Rluc expression when ZmDREB1A was simultaneously overexpressed. Electrophoretic mobility shift assays and chromatin immunoprecipitation-quantitative PCR demonstrated that ZmDREB1A directly binds to the DRE motif in the promoter of ZmRAFS both in vitro and in vivo. These data demonstrate that ZmRAFS, which was directly regulated by ZmDREB1A, enhances both raffinose biosynthesis and plant chilling stress tolerance.
Nudging healthy and sustainable food choices: three randomized controlled field experiments using a vegetarian lunch-default as a normative signal
Authors: Hansen Pelle G , Schilling Mathilde , Malthesen Mia S
Published: October 2019

Background

This study investigates a simple, generic and easily scalable nudge to promote healthy and sustainable food choices at conferences by using a vegetarian lunch-default as a normative signal.

Methods

At three conferences, participants registering electronically were randomized into two groups: Group 1 received a standard lunch registration presenting a non-vegetarian buffet as the default, but allowing the active choice of a vegetarian option; Group 2 received a registration presenting a vegetarian buffet as the default, allowing the active choice of a non-vegetarian option. The study also assessed gender differences for two of the conferences and the participants’ acceptance of the nudge at one of the conferences.

Results

In experiment A the vegetarian choice increased from 2% to 87% (N = 108, P < 0.001). In experiment B it increased from 6% to 86% (N = 112, P < 0.001). In experiment C it increased from 12.5% to 89% (N = 110, P < 0.001). A significant tendency for men, but not women, to opt out of the vegetarian default was found and a clear majority of participants reported positive attitudes toward the nudge.

Conclusions

Changing the lunch-default to a vegetarian option is an effective, generic, easy to scale and well-accepted nudge to promote healthy and sustainable food choices at conferences.
Measuring the prevalence of sleep disturbances in people with dementia living in care homes: a systematic review and meta-analysis
Authors: Webster Lucy , Costafreda Gonzalez Sergi , Stringer Aisling , Lineham Amy , Budgett Jessica , Kyle Simon , Barber Julie , Livingston Gill
Published: October 2019

Study Objectives

Sleep disturbances are a feature in people living with dementia, including getting up during the night, difficulty falling asleep, and excessive daytime sleepiness and may precipitate a person with dementia moving into residential care. There are varying estimates of the frequency of sleep disturbances, and it is unknown whether they are a problem for the individual. We conducted the first systematic review and meta-analysis on the prevalence and associated factors of sleep disturbances in the care home population with dementia.

Methods

We searched Embase, MEDLINE, and PsycINFO (29/04/2019) for studies of the prevalence or associated factors of sleep disturbances in people with dementia living in care homes. We computed meta-analytical estimates of the prevalence of sleep disturbances and used meta-regression to investigate the effects of measurement methods, demographics, and study characteristics.

Results

We included 55 studies of 22,780 participants. The pooled prevalence on validated questionnaires of clinically significant sleep disturbances was 20% (95% confidence interval, CI 16% to 24%) and of any symptom of sleep disturbance was 38% (95% CI 33% to 44%). On actigraphy using a cutoff sleep efficiency of <85% prevalence was 70% (95% CI 55% to 85%). Staff distress, resident agitation, and prescription of psychotropic medications were associated with sleep disturbances. Studies with a higher percentage of males had a higher prevalence of sleep disturbance.

Conclusions

Clinically significant sleep disturbances are less common than those measured on actigraphy and are associated with residents and staff distress and the increased prescription of psychotropics. Actigraphy appears to offer no benefit over proxy reports in this population.
Does midlife aging impact women’s sleep duration, continuity, and timing?: A longitudinal analysis from the Study of Women’s Health Across the Nation
Authors: Matthews Karen A , Kravitz Howard M , Lee Laisze , Harlow Siobán D , Bromberger Joyce T , Joffe Hadine , Hall Martica H
Published: October 2019

Our study objectives were to evaluate the age-related changes in actigraphy measures of sleep duration, continuity, and timing across 12 years in midlife women as they traversed the menopause, and to take into account factors affecting women’s sleep that also change with age. Black, white, and Chinese women were recruited from the Study of Women’s Health Across the Nation (SWAN) to participate in an ancillary sleep study on two occasions over 3 years apart and a third assessment 12 years after the first (N = 300, mean ages, 52, 55, and 64 at the three assessments). Women had at least four consecutive nights of actigraphy (95% with 7 nights) and sleep diaries, and self-reported sleep complaints measured at each time point. Partial correlations adjusted for time between assessments across the 12 years were significant and moderate in size (r’s = .33–.58). PROC MIXED/GLIMMIX multivariate models showed that sleep duration increased over time; wake after sleep onset (WASO) declined, midpoint of sleep interval increased, and sleep latency and number of sleep complaints did not change between the first and third assessments. Blacks and whites had a greater increase in sleep duration than Chinese. Taken together, the results of this longitudinal study suggest that sleep may not worsen, in general, in midlife women. Perhaps, the expected negative effect of aging in midlife into early old age on sleep is overstated.
The adult guardianship dilemma in Hong Kong
Authors: Lee Rebecca
Published: October 2019

Today, there is worldwide consensus that ageing has become an issue of global concern. The frail elderly, together with other vulnerable sections of the community, may turn to adult guardianship, a mechanism for planning for and the protection of individuals with cognitive impairment. There is, however, an inherent tension at the heart of the legal institution of adult guardianship: although it protects individuals with cognitive impairment from potential abuse and exploitation, that protection is often provided by subjecting individuals to the plenary authority of their guardians. Against this backdrop, this article critically examines the struggle with the tension within the adult guardianship regime in Hong Kong and, drawing on reforms in major jurisdictions with long-standing experience of guardianship experimentation, explores the features of a guardianship system that tackles this dilemma.
Modulation of the metabolic response using dexamethasone in beef steers vaccinated with a multivalent respiratory vaccine1
Authors: Burdick Sanchez Nicole C , Carroll Jeffery A , May Nathan D , Hughes Heather D , Roberts Shelby L , Broadway Paul R , Ballou Michael A , Richeson John T
Published: October 2019

Available energy plays a critical role in the initiation and maintenance of an immune response to a pathogen, a process that is further altered by activation of the stress system. This study was designed to determine the effect of an acute vs chronic stress model on the metabolic response to vaccination in naïve beef steers. Steers (n = 32; 209 ± 8 kg) were blocked by body weight (BW) and randomly assigned to one of three treatments: 1) Chronic stress (CHR), 0.5 mg/kg BW dexamethasone (DEX) administered i.v. at 1000 h on day 3 to day 0; 2) Acute stress (ACU), 0.5 mg/kg BW DEX administered i.v. at 1000 h on day 0 only; or 3) Control (CON), no DEX. On day −4, steers were fitted with jugular vein catheters and moved into individual bleeding stalls in an environmentally-controlled facility. Blood samples were collected at −74, −50, and −26 h, at 0.5-h intervals from −4 to 6 h, and at 12, 24, 36, 48, and 72 h relative to vaccination with a combination vaccine (Pyramid 5 + Presponse SQ, Boehringer Ingelheim Animal Health USA, Duluth, GA) at 1200 h on day 0. Data were analyzed by the MIXED procedure of SAS specific for repeated measures. There was a treatment × time interaction (P < 0.001) for serum glucose concentrations. Specifically, glucose concentrations increased at −50 h in CHR steers and at 1200 h in ACU steers and remained elevated through 72 h postvaccination period in these two treatments compared to CON steers. The change in nonesterified fatty acid (NEFA) concentrations relative to baseline values was affected by treatment and time (P < 0.001) such that the change in NEFA was greater in CHR (0.06 ± 0.01 mmol/L), followed by CON (−0.01 ± 0.01 mmol/L) and ACU steers (−0.04 ± 0.01 mmol/L). There was a tendency (P = 0.08) for a treatment × time interaction for change in serum NEFA concentrations. Serum urea nitrogen (SUN) was affected by treatment and time (P < 0.001) such that SUN concentrations were greatest in CHR (12.0 ± 0.1 mg/dL) followed by ACU (10.4 ± 0.1 mg/dL) and CON steers (9.6 ± 0.1 mg/dL); however, the treatment × time interaction was not significant (P = 0.12). These data demonstrate that activation of the stress and immune axes using an acute or chronic stress model can increase energy mobilization prior to and following vaccination in naïve steers, potentially affecting available energy needed to mount an adequate antibody response to vaccination.
Use of barley or corn silage when fed with barley, corn, or a blend of barley and corn on growth performance, nutrient utilization, and carcass characteristics of finishing beef cattle
Authors: Johnson Jordan A , Sutherland Brittney D , McKinnon John J , McAllister Tim A , Penner Gregory B
Published: October 2019

The objective of this study was to evaluate the effects of the source of silage, cereal grain, and their interaction on growth performance, digestibility, and carcass characteristics of finishing beef cattle. Using a completely randomized design within an 89-d finishing study, 288 steers were randomly assigned to 1 of 24 pens (12 steers/pen) with average steer body weight (BW) within a pen of 464 kg ± 1.7 kg (mean ± SD). Diets were arranged in a 2 × 3 factorial with corn silage (CS) or barley silage (BS) included at 8% (dry matter [DM] basis). Within each silage source, diets contained dry-rolled barley grain (BG; 86% of DM), dry-rolled corn grain (CG; 85% of DM), or an equal blend of BG and CG (BCG; 85% of DM). Total tract digestibility of nutrients was estimated from fecal samples using near-infrared spectroscopy. Data were analyzed with pen as the experimental unit using the Mixed Model of SAS with the fixed effects of silage, grain, and the two-way interaction. Carcass and fecal kernel data were analyzed using GLIMMIX utilizing the same model. There were no interactions detected between silage and grain source. Feeding CG increased (P < 0.01) DM intake by 0.8 and 0.6 kg/d relative to BG and BCG, respectively. Gain-to-feed ratio was greater (P = 0.04) for BG (0.172 kg/kg) than CG (0.162 kg/kg) but did not differ from BCG (0.165 kg/kg). Furthermore, average daily gain (2.07 kg/d) and final body weight did not differ among treatments (P ≥ 0.25). Hot carcass weight (HCW) was 6.2 kg greater (372.2 vs. 366.0 kg; P < 0.01) and dressing percentage was 0.57 percentage units greater (59.53 vs. 58.96 %; P = 0.04) for steers fed CS than BS, respectively. There was no effect of dietary treatment on the severity of liver abscesses (P ≥ 0.20) with 72.0% of carcasses having clear livers, 24.4% with minor liver abscesses, and 3.6% with severe liver abscesses. Digestibility of DM, organic matter, crude protein, neutral detergent fiber, and starch were greater for BG (P < 0.01) than CG or BCG. As expected, grain source affected the appearance of grain kernels in the feces (P ≤ 0.04). Feeding CS silage increased the appearance of fractured corn kernels (P = 0.04), while feeding BS increased fiber appearance in the feces (P = 0.02). Current results indicate that when dry rolled, feeding BG resulted in improved performance and digestibility compared with CG and BCG. Even at low inclusion levels (8% of DM), CS resulted in improved carcass characteristics relative to BS.
Examining the association between religiosity and medical mistrust among churchgoing Latinos in Long Beach, CA
Authors: López-Cevallos Daniel F , Flórez Karen R , Derose Kathryn P
Published: October 2019

Medical mistrust among racial/ethnic minorities has been associated with decreases in health care utilization, whereas religiosity has been separately linked with increases in this behavior. However, very few studies have examined the relationship between religiosity and medical mistrust among Latinos, a group with strong religious connections and potentially high mistrust. In-person, self-administered surveys were collected among 767 adult Latinos attending three Latino churches (one Catholic and two Pentecostal) in Long Beach, CA. Measures included a previously validated 12-item medical mistrust scale, religiosity (religious denomination, length and frequency of attendance, and number of groups or ministries involved in), health care access, and sociodemographic factors. Medical mistrust score was 2.47 (standard deviation [SD] = 0.77; range 1–5). Almost two-thirds of participants (62%) attended religious services frequently (once a week or more), and the majority attended a Catholic church (80%). About half of the participants had attended their church for ≥5 years (50%) and participated in one to two church groups or ministries (53%). Multivariable analyses show that Pentecostal church congregation and those identifying as Mexican/Chicano were negatively associated with medical mistrust. On the contrary, participating in church groups or ministries and having an immigrant parent were positively associated with medical mistrust. Our findings suggest that church-based health initiatives should consider church denomination, length of attendance, participation in groups or ministries, and ethnic differences to address medical mistrust issues among Latino congregants.
Booms, Busts, and Household Enterprise: Evidence from Coffee Farmers in Tanzania
Authors: Adhvaryu Achyuta , Kala Namrata , Nyshadham Anant
Published: October 2019

Smallholder agricultural commodity suppliers in developing countries are often vulnerable to global commodity price fluctuations. Using panel data on farmers from an area of Tanzania where most farmers grow coffee, this study finds that global coffee prices matter for household outcomes, through their effects on farmgate prices, coffee sales and revenues, and household expenditures. The article documents that households cope with coffee price busts by increasing enterprise ownership, an effect that is greater for households without access to other means of coping. Comparisons of mean outcomes of enterprises operated by coper households (which operated an enterprise only in periods of low coffee price) with those of stayer households (which operated an enterprise throughout the sample period) indicate that the former are less likely to be profitable or to hire workers.
Biomes, geology and past climate drive speciation of laminate-toothed rats on South African mountains (Murinae: Otomys)
Authors: Taylor Peter John , Kearney Teresa , Dalton Desire Lee , Chakona Gamuchirai , Kelly Christopher M R , Barker Nigel P
Published: October 2019

Mitochondrial DNA sequences (1137 bp) of the cytochrome b gene and craniodental and craniometric data were used to investigate the evolutionary relationships of six putative rodent taxa of Otomys (family Muridae: subfamily Murinae: tribe Otomyini) co-occurring in the Western Cape and Eastern Cape provinces of South Africa. Phylogenetic analysis of 20 new sequences together with craniodental and craniometric characters of 94 adult skulls reveal the existence of a unique lineage of Otomys cf. karoensis (named herein Otomys willani sp. nov.) from the Sneeuberg Centre of Floristic Endemism in the southern Drakensberg Mountain Range. Craniometric analysis distinguished O. karoensis from O. willani and identified a further four localities in the range of the latter species. We document southern range extensions of both Sloggett’s ice rat, Otomys sloggetti, and the vlei rat Otomys auratus to the Sneeuberg Mountain Range, in addition to appreciable genetic divergence between Sneeuberg and southern and central Drakensberg populations of O. sloggetti. Our results demonstrate parallel patterns of cryptic speciation in two co-occurring species complexes (Otomys irroratus s.l. and O. karoensis s.l.) associated closely with the boundaries of biomes (fynbos vs. grassland biomes) and geological formations (Cape Fold Belt vs. Great Escarpment).
The weakest link: uncertainty and sensitivity analysis of extinction probability estimates for tsetse (Glossina spp) populations
Authors: Are Elisha B. , Hargrove John W.
Published: October 2019

Background

A relatively simple life history allows us to derive an expression for the extinction probability of populations of tsetse, vectors of African sleeping sickness. We present the uncertainty and sensitivity analysis of extinction probability for tsetse population, to offer key insights into parameters in the control/eradication of tsetse populations.

Methods

We represent tsetse population growth as a branching process, and derive closed form estimates of population extinction from that model. Statistical and mathematical techniques are used to analyse the uncertainties in estimating extinction probability, and the sensitivity of the extinction probability to changes in input parameters representing the natural life history and vital dynamics of tsetse populations.

Results

For fixed values of input parameters, the sensitivity of extinction probability depends on the baseline parameter values. For example, extinction probability is more sensitive to the probability that a female is inseminated by a fertile male when daily pupal mortality is low, whereas the extinction probability is more sensitive to daily mortality rate for adult females when daily pupal mortality, and extinction probabilities, are high. Global uncertainty and sensitivity analysis showed that daily mortality rate for adult females has the highest impact on the extinction probability.

Conclusions

The strong correlation between extinction probability and daily female adult mortality gives a strong argument that control techniques to increase daily female adult mortality may be the single most effective means of ensuring eradication of tsetse population.

Author summary

Tsetse flies (Glossina spp) are vectors of Trypanosomiasis, a deadly disease commonly called sleeping sickness in humans and nagana in livestock. The relatively simple life history of tsetse enabled us to model its population growth as a stochastic branching process. We derived a closed-form expression for the probability that a population of tsetse goes extinct, as a function of death, birth, development and insemination rates in female tsetse. We analyzed the sensitivity of the extinction probability to the different input parameters, in a bid to identify parameters with the highest impact on extinction probability. This information can, potentially, inform policy direction for tsetse control/elimination. In all the scenarios we considered, the daily mortality rate for adult females has the greatest impact on the magnitude of extinction probability. Our findings suggest that the mortality rate in the adult females is the weakest link in tsetse life history, and this fact should be exploited in achieving tsetse population control, or even elimination.
Diotic and dichotic frequency discrimination thresholds in musicians and non-musicians: relationships between perception, musical ability and self-evaluated competence
Authors: Musacchia Gabriella , Inabinet Devin , De La Cruz Jan , Cha Justin , Ng Kevin
Published: October 2019

Pitch perception provides important information for musical and vocal communication. Numerous studies have shown that musical training and expertise are associated with better pitch processing, however, it is unclear what types of pitch percepts are plastic with music training. The current study addresses this issue by measuring discrimination thresholds of Musicians (n=20) and Non-musicians (n=18) to diotic (same sound to both ears) and dichotic (different sounds to each ear) stimuli created from four types of acoustic computations:1) pure sinusoidal tones, PT; 2) four-harmonic complex tones, CT; 3) iterated rippled noise, IRN; and 4) interaurally correlated broadband noise, called “Huggins” or “dichotic” pitch sounds, DP. Frequency Difference Limens (DLF) in each condition were obtained via a 3-alternative-forced-choice adaptive task requiring selection of the interval with the highest pitch, yielding the smallest perceptible fundamental frequency (F0) distance (in Hz) between two sounds. Music skill was measured by an online test of musical Pitch, Melody and Timing (International Laboratory for Brain Music and Sound Research, https://www.brams.org/en/onlinetest/). Musicianship, length of music experience and self-evaluation of musical skill were assessed by questionnaire. Results showed musicians had smaller DLFs in all four conditions and that thresholds were related to subjective and objective musical ability. In addition, self-report of musical ability was shown to be a significant variable in group classification, suggesting that the neurobehavioral profile of musicians includes self-evaluation of musical competence.
A Complex Regulatory Landscape Involved In The Development Of External Genitals
Authors: Amândio Ana Rita , Lopez-Delisle Lucille , Bolt Christopher Chase , Mascrez Bénédicte , Duboule Denis
Published: October 2019

In vertebrates, developmental genes are often controlled by large regulatory landscapes matching the dimensions of topologically associating domains (TADs). In various ontogenic contexts, the associated constitutive chromatin backbone is modified by fine-tuned specific variations in enhancer-enhancer and enhancer-promoter interaction profiles. In this work, we take one of the TADs flanking theHoxDgene cluster as a paradigm to address the question of how these complex regulatory architectures are formed and how they are de-constructed once their function has been achieved. We suggest that this TAD can be considered as a coherent functional unit in itself, with several regulatory sequences acting together to elicit a transcriptional response. With one notable exception, the deletion of each of these sequences in isolation did not produce any substantial modification in the global transcriptional outcome of the system, a result at odds with a conventional view of long-range enhancer function. Likewise, both the deletion and inversion of a supposedly critical CTCF site located in a region rich in such sequences did not affect transcription of the target gene. In the latter case, however, slight modifications were observed in interaction profilesin vivoin agreement with the loop extrusion model, despite no apparent functional consequences. We discuss these unexpected results by considering both conventional explanations and an alternative possibility whereby a rather unspecific accumulation of particular factors within the TAD backbone may have a global impact upon transcription.
Integrative Modeling of a Sin3/HDAC Complex Sub-structure
Authors: Banks Charles A. S. , Zhang Ying , Miah Sayem , Hao Yan , Adams Mark K. , Wen Zhihui , Thornton Janet L. , Florens Laurence , Washburn Michael P.
Published: October 2019

Sin3/HDAC complexes function by deacetylating histones, which makes chromatin more compact and modulates gene expression. Although components used to build these complexes have been well defined, we still have only a limited understanding of the structure of the Sin3/HDAC subunits as they are assembled around the scaffolding protein SIN3A. To characterize the spatial arrangement of Sin3 subunits, we combined Halo affinity capture, chemical cross-linking and high-resolution mass spectrometry (XL-MS) to determine intersubunit distance constraints, identifying 66 high-confidence interprotein and 63 high-confidence self cross-links for 13 Sin3 subunits. To validate our XL-MS data, we first mapped self cross-links onto existing structures to verify that cross-link distances were consistent with cross-linker length and subsequently deleted crosslink hotspot regions within the SIN3A scaffolding protein which then failed to capture crosslinked partners. Having assessed cross-link authenticity, we next used distance restraints from interprotein cross-links to guide assembly of a Sin3 complex substructure. We identified the relative positions of subunits SAP30L, HDAC1, SUDS3, HDAC2, and ING1 around the SIN3A scaffold. The architecture of this subassembly suggests that multiple factors have space to assemble to collectively influence the behavior of the catalytic subunit HDAC1.
Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein
Authors: Wych David C. , Fraser James S. , Mobley David L. , Wall Michael E.
Published: October 2019

To gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2×2×2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquid-like motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intra-protein) and between different protein molecules (inter-protein). The inter-protein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intra-protein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall our findings increase our understanding of the connection between molecular motions and diffraction data, and therefore advance efforts to extract information about functionally important motions from crystallography experiments.
Interactions of encoding and decoding problems to understand motor control
Authors: Wen Shixian , Yin Allen , Zheng Li , Itti Laurent
Published: October 2019

Learning a map from movement to neural data (Encoding Problem) and vice versa (Decoding Problem) are crucial to understanding motor control. A principled encoding model that understands underlying neural dynamics can help better solve the decoding problem. Here, we develop a new generative encoding model leveraging deep learning that autonomously captures neural dynamics. After training, the model can synthesize spike trains given any observed kinematics, under the guidance of the learned neural dynamics. When neural data from other sessions or subjects are limited, synthesized spike trains can improve cross-session and cross-subject decoding performance of a Brain Computer Interface decoder. For cross-subject, even with ample data for both subjects, neural dynamics learned from a previous subject can transfer useful knowledge that improves the best achievable decoding performance for the new subject. The approach is general and fully data-driven, and hence could apply to neuroscience encoding and decoding problems beyond motor control.
Cleavage, down-regulation and aggregation of serum amyloid A
Authors: Wang Wenhua , Khatua Prabir , Hansmann Ulrich H.E.
Published: October 2019

Various diseases cause over-expression of the serum amyloid A protein (SAA), which leads in some, but not all, cases to amyloidosis as a secondary disease. The response to the over-expression involves dissociation of SAA hexamer and subsequent cleavage of the released monomers, most commonly yielding fragments SAA1−76 of the full-sized SAA1−104. We report results from molecular dynamic simulations that probe the role of this cleavage for down-regulating activity and the concentration of SAA. We propose a mechanism that relies on two elements. First, the probability to assemble into hexamers is lower for the fragments than it is for the full-sized protein. Second, unlike other fragments SAA1−76 can switch between two distinct configurations. The first kind is easy to proteolyze (allowing a fast reduction of SAA concentration) but prone to aggregation, while the situation is opposite for the second kind. If the time scale for amyloid formation is longer than the one for proteolysis, the aggregation-prone species dominates. However, if environmental conditions such as low pH increase the risk of amyloid formation, the ensemble shifts toward the more protected form. We speculate that SAA amyloidosis is a failure of the switching mechanism leading to accumulation of the aggregation-prone species and subsequent amyloid formation.
Correlates of non-random patterns of capsule switching in pneumococcus
Authors: Joshi Shreyas S. , Al-Mamun M. A. , Weinberger Daniel M.
Published: October 2019

Background

Pneumococcus is a diverse pathogen, with >90 serotypes, each of which has a distinct polysaccharide capsule. Pneumococci can switch capsules, evading vaccine pressure. Certain serotype pairs are more likely to switch, but the drivers of these patterns are not well understood.

Methods

We used the PubMLST and Global Pneumococcal Sequencing (GPS) databases to quantify the number of genetic lineages on which different serotype pairs co-occur. We also quantified the genetic diversity of each serotype. Regression models evaluated the relationship between shared polysaccharide structural components and the frequency of serotype switching and diversity.

Results

A number of serotype pairs co-occurred on the same genetic lineage more commonly than expected. Co-occurrence of between-serogroup pairs was more common when both serotypes had glucose as a component of the capsule (and, potentially, glucuronic acid). Diversity also varied markedly by serotype and was lower for serotypes with glucuronic acid in the capsule and higher for those with galactose in the capsule.

Conclusions

Certain pairs of serotypes are more likely to occur on the same genetic background, and these patterns were correlated with shared polysaccharide components. This might indicate adaptation of strains to produce capsules with particular characteristics.
Protein Phosphatase 1 activity controls a balance between collective and single cell modes of migration
Authors: Chen Yujun , Kotian Nirupama , Aranjuez George , Chen Lin , Messer C. Luke , Burtscher Ashley , Sawant Ketki , Ramel Damien , Wang Xiaobo , McDonald Jocelyn A.
Published: October 2019

Collective cell migration is central to many developmental and pathological processes. However, the mechanisms that keep cell collectives together and coordinate movement of multiple cells are poorly understood. Using theDrosophilaborder cell migration model, we find that Protein phosphatase 1 (Pp1) activity controls collective cell cohesion and migration. Inhibition of Pp1 causes border cells to round up, dissociate, and move as single cells with altered motility. We present evidence that Pp1 promotes proper levels of cadherin-catenin complex proteins at cell-cell junctions within the cluster to keep border cells together. Pp1 further restricts actomyosin contractility to the cluster periphery rather than at internal cell-cell contacts. We show that the myosin phosphatase Pp1 complex, which inhibits non-muscle myosin-II (Myo-II) activity, coordinates border cell shape and cluster cohesion. Given the high conservation of Pp1 complexes, this study identifies Pp1 as a major regulator of collective versus single cell migration.
Integrating multiple dimensions of biodiversity to inform global parrot conservation
Authors: Burgio Kevin R. , Davis Katie E. , Dreiss Lindsay M. , Cisneros Laura M. , Klingbeil Brian T. , Presley Steven J. , Willig Michael R.
Published: October 2019

Because biodiversity is increasingly threatened by habitat destruction and climate change, conservation agencies face challenges associated with an uncertain future. In addition to changes associated with climate and land use, parrots are threatened by hunting and capture for the pet trade, making them the most at-risk order of birds in the world. Parrots provide key ecosystem services, but remain understudied compared to other major bird orders despite their high extinction risk and ecological importance. Species richness is often used to identify high priority areas for conserving biodiversity. By definition, richness considers all species to be equally different. However, ongoing research emphasizes the importance of incorporating ecological functions (functional diversity) or evolutionary relationships (phylogenetic diversity) to more fully understand patterns of biodiversity, suggesting that using functional and phylogenetic information could improve conservation strategies. These distinctions among dimensions of biodiversity are important, because (1) areas of high species richness do not always represent areas of high functional or phylogenetic diversity, and (2) functional or phylogenetic diversity may better predict ecosystem function and evolutionary potential, which are essential for effective long-term conservation policy and management.

Our objective was to create a framework for identifying areas of high species richness, functional diversity, and phylogenetic diversity within the global distribution of parrots We combined species richness, functional diversity, and phylogenetic diversity into an Integrated Biodiversity Index (IBI) to identify global biodiversity hotspots for parrots. We found important spatial mismatches among dimensions, which demonstrate that species richness is not always an effective proxy for other dimensions of parrot biodiversity. The IBI is an integrative and flexible index that can incorporate multiple dimensions of biodiversity, resulting in an intuitive and more direct way of assessing comprehensive goals in conservation planning (i.e., healthy ecosystem functioning and climate change resilience).