bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk of Fractures in Inflammatory Bowel Diseases
Authors: Komaki Yuga , Komaki Fukiko , Micic Dejan , Ido Akio , Sakuraba Atsushi
Published: April 2018

Background:

Studies assessing the risk of fractures in inflammatory bowel diseases (IBD) have shown controversial results.

Goals:

We performed a systematic review and meta-analysis to assess the risk of fractures in IBD.

Study:

Electronic databases were searched for cohort studies assessing the risk of fractures in IBD. The outcomes were the risk of overall fractures and at specific sites, and the association between the risk of fractures and the proportion of patients with corticosteroid use or osteoporosis.

Results:

Ten studies including 470,541 patients were identified. The risk of overall fractures in IBD patients was similar to controls [odds ratio (OR), 1.08; P=0.70; 95% confidence interval (CI), 0.72-1.62) with moderate heterogeneity (I
2=74.4%) which appeared to be due to the variable power and outcomes among the studies. The OR of fractures at the spine was significantly elevated at 2.21 (P<0.0001; 95% CI, 1.39-3.50) with low heterogeneity (I
2=26.1%). Meta-regression showed a correlation with the proportion of patients with steroid use. Risks of fractures at other sites (hip, rib, and wrist) were not elevated. Patients with fractures were more commonly on steroids compared with those without fractures (OR, 1.47; P=0.057; 95% CI, 0.99-2.20; I

2
<0.0001%), but there was no correlation with osteoporosis.

Conclusions:

IBD patients had no increased risk of overall fractures, but were at significantly increased risk of fractures at the spine, which was associated with steroid use. Strict surveillance and prevention of spine fractures are indicated in patients with IBD.
Refugee Children's Participation in the Women, Infants, and Children Supplemental Nutrition (WIC) Program in Massachusetts, 1998-2010
Authors: Smock Laura , Nguyen Thinh , Metallinos-Katsaras Elizabeth , Magge Hema , Cochran Jennifer , Geltman Paul L.
Published: April 2018

Objectives:

To (1) describe prevalence of growth abnormalities and anemia in refugee children; (2) describe the proportion of age-eligible refugee children enrolled in Special Supplemental Nutrition Program for Women, Infants, and Children (WIC); and (3) identify risk factors for lack of enrollment in WIC.

Design:

Data were collected from 1731 health screenings for refugee children younger than 5 years in Massachusetts in 1998-2010 and matched to WIC program records. Risk factors for lack of WIC enrollment were analyzed in SAS using multivariate logistic regression.

Setting:

Massachusetts.

Participants:

Refugee children under age 5 years.

Main Outcome Measures:

(1) prevalence of growth abnormalities and anemia in refugee children, (2) proportion of age-eligible refugee children enrolled in WIC, and (3) association of risk factors with lack of WIC enrollment.

Results:

Overall, 33% of refugee children under age 5 in Massachusetts had at least 1 growth and nutrition problem, including anemia (31%), stunting (10%), wasting (8%), and low weight for age (10%). WIC enrollment among refugee children under 5 years of age was only 62%, lower than that of all eligible children under 5 in Massachusetts (86%). Risk factors for lack of WIC enrollment among refugee children included age, world region of origin, and arrival cohort.

Conclusions:

Although many refugee children under age 5 experience growth or nutrition problems, one-third of refugee children in Massachusetts were not enrolled in WIC for nutrition assistance, representing a failure of the system. Agencies providing services at the local level should be supported to facilitate enrollment and participation for shared clients.
Evaluating Quality Metrics and Cost After Discharge
Authors: de Mestral Charles , Salata Konrad , Hussain Mohamad A. , Kayssi Ahmed , Al-Omran Mohammed , Roche-Nagle Graham
Published: April 2018

Background:

Early readmission to hospital after surgery is an omnipresent quality metric across surgical fields. We sought to understand the relative importance of hospital readmission among all health services received after hospital discharge.

Objective:

The aim of this study was to characterize 30-day postdischarge cost and risk of an emergency department (ED) visit, readmission, or death after hospitalization for elective major vascular surgery.

Methods:

This is a population-based retrospective cohort study of patients who underwent elective major vascular surgery - carotid endarterectomy, EVAR, open AAA repair, bypass for lower extremity peripheral arterial disease - in Ontario, Canada, between 2004 and 2015. The outcomes of interest included quality metrics - ED visit, readmission, death - and cost to the Ministry of Health, within 30 days of discharge. Costs after discharge included those attributable to hospital readmission, ED visits, rehab, physician billing, outpatient nursing and allied health care, medications, interventions, and tests. Multivariable regression models characterized the association of pre-discharge characteristics with the above-mentioned postdischarge quality metrics and cost.

Results:

A total of 30,752 patients were identified. Within 30 days of discharge, 2588 (8.4%) patients were readmitted to hospital and 13 patients died (0.04%). Another 4145 (13.5%) patients visited an ED without requiring admission. Across all patients, over half of 30-day postdischarge costs were attributable to outpatient care. Patients at an increased risk of an ED visit, readmission, or death within 30 days of discharge differed from those patients with relatively higher 30-day costs.

Conclusion:

Events occurring outside the hospital setting should be integral to the evaluation of quality of care and cost after hospitalization for major vascular surgery.
Association of Hospital Network Participation With Surgical Outcomes and Medicare Expenditures
Authors: Sheetz Kyle H. , Ryan Andrew M. , Ibrahim Andrew M. , Dimick Justin B.
Published: April 2018

Objective:

The aim of this study was to evaluate whether hospital network participation is associated with improvement in surgical outcomes and spending compared to control hospitals not participating in a network.

Summary Background Date:

Hospitals face significant financial and organizational pressures to integrate into networks. It remains unclear whether these business arrangements impact clinical quality or healthcare expenditures.

Methods:

We conducted a longitudinal, quasi-experimental study of 1,981,095 national Medicare beneficiaries (2007–2014) undergoing general, vascular, cardiac, or orthopedic surgery at a network (n = 1868) or non-network (n = 2734) hospital. We tested whether joining a network was associated with improvement in the study outcomes after accounting for overall trends toward better outcomes. We used hierarchical multivariable logistical and linear regression to adjust for patient factors, procedural characteristics, type of admission, and hospital factors.

Results:

After accounting for patient factors and existing trends toward better outcomes, there was no association between network participation and surgical outcomes. For example, the rates of serious complications were similar between network [11.4%, 95% confidence interval (CI) 11.1%–11.5%] and non-network hospitals (11.2%; 95% CI 11.0%–11.3%; odds ratio 1.00, 95% CI 0.97–1.03, P = 0.92). There was no association between time-in-network and improvement in rates of serious complications during the 8-year study period. For example, after 7 years of network participation, the rate of serious complications in 2014 was 9.6% (95% CI 8.8%–10.4%) in network hospitals versus 9.2% (95% CI 8.5%–9.9%, P = 0.11) in non-network hospitals.

Conclusions:

Hospital network participation was not associated with improvements in patient outcomes or lower episode payments among Medicare beneficiaries undergoing inpatient surgery.
Clinical Outcomes of Single-port Surgery for Colon Cancer in Octogenarians
Authors: Tei Mitsuyoshi , Otsuka Masahisa , Suzuki Yozo , Kishi Kentaro , Tanemura Masahiro , Akamatsu Hiroki
Published: April 2018

Aim:

The aim of this study was to evaluate the clinical outcomes of single-port surgery for colon cancer in octogenarians.

Materials and Methods:

A retrospective cohort study was performed on patients who underwent single-port surgery for colon cancer from 2010 to 2014 at a single institution. Patients were categorized into the following 3 groups according to age: ≤69 years (n=196), 70 to 79 years (n=143), and ≥80 years (n=86). Short-term and long-term outcomes were assessed among 3 groups.

Results:

The rate of overall postoperative complications in the octogenarian group did not differ significantly, compared with the other groups (20.9% in the octogenarians group vs. 14.3% in the ≤69 y group and 15.4% in the 70 to 79 y group, P=0.363). The 3-year relapse-free survival rates were similar among groups (83.9% in the octogenarians group vs. 87.8% in the ≤69 y group and 87.5% in the 70 to 79 y group, P=0.754). The 5-year overall survival rates were 79.8% in the octogenarians group, 89.9% in the ≤69 years group, and 81.7% in the 70 to 79 years group (P=0.063).

Conclusion:

Single-port surgery is safe, feasible, and can provide satisfactory oncological outcomes in octogenarians with colon cancer.
Assessing Consensus Between UK Renal Clinicians on Listing for Kidney Transplantation: A Modified Delphi Study
Authors: Tonkin-Crine Sarah , Pruthi Rishi , Taylor Dominic M. , Leydon Geraldine M. , Calestani Melania , Oniscu Gabriel C. , Bradley J. Andrew , Tomson Charles R. , Bradley Clare , Dudley Christopher , Watson Christopher J.E. , Draper Heather , Johnson Rachel J. , Metcalfe Wendy , Fogarty Damian G. , Ravanan Rommel , Roderick Paul
Published: April 2018

Background

It is well recognized that there is significant variation between centers in access to kidney transplantation. In the absence of high-grade evidence, it is unclear whether variation is due to patient case mix, other center factors, or individual clinician decisions. This study sought consensus between UK clinicians on factors that should influence access to kidney transplantation.

Methods

As part of the Access to Transplantation and Transplant Outcome Measures project, consultant nephrologists and transplant surgeons in 71 centers were invited to participate in a Delphi study involving 2 rounds. During rounds 1 and 2, participants rated their agreement to 29 statements covering 8 topics regarding kidney transplantation. A stakeholder meeting was used to discuss statements of interest after the 2 rounds.

Results

In total, 122 nephrologists and 16 transplant surgeons from 45 units participated in rounds 1 and 2. After 2 rounds, 12 of 29 statements reached consensus. Fifty people participated in the stakeholder meeting. After the stakeholder meeting, a further 4 statements reached agreement. Of the 8 topics covered, consensus was reached in 6: use of a transplant protocol, patient age, body mass index, patient compliance with treatment, cardiac workup, and use of multidisciplinary meetings. Consensus was not reached on screening for malignancy and use of peripheral Doppler studies.

Conclusions

The Delphi process identified factors upon which clinicians agreed and areas where consensus could not be achieved. The findings should inform national guidelines to support decision making in the absence of high quality evidence and to guide areas that warrant future research.
Wing scale ultrastructure underlying convergent and divergent iridescent colours in mimeticHeliconiusbutterflies
Authors: Parnell Andrew J. , Bradford James E. , Curran Emma V. , Washington Adam L. , Adams Gracie , Brien Melanie N. , Burg Stephanie L. , Morochz Carlos , Fairclough J. Patrick A. , Vukusic Pete , Martin Simon J. , Doak Scott , Nadeau Nicola J.
Published: April 2018

Iridescence is an optical phenomenon whereby colour changes with the illumination and viewing angle. It can be produced by thin film interference or diffraction. Iridescent optical structures are fairly common in nature, but relatively little is known about their production or evolution. Here we describe the structures responsible for producing blue-green iridescent colour inHeliconiusbutterflies. Overall the wing scale structures of iridescent and non-iridescentHeliconiusspecies are very similar, both having longitudinal ridges joined by cross-ribs. However, iridescent scales have ridges composed of layered lamellae, which act as multilayer reflectors. Differences in brightness between species can be explained by the extent of overlap of the lamellae and their curvature as well as the density of ridges on the scale.Heliconiusare well known for their Müllerian mimicry. We find that iridescent structural colour is not closely matched between co-mimetic species. Differences appear less pronounced in models ofHeliconiusvision than models of avian vision, suggesting that they are not driven by selection to avoid heterospecific courtship by co-mimics. Ridge profiles appear to evolve relatively slowly, being similar between closely related taxa, while ridge density evolves faster and is similar between distantly related co-mimics.
Membrane protein-based biosensors
Authors: Misawa Nobuo , Osaki Toshihisa , Takeuchi Shoji
Published: April 2018

This review highlights recent development of biosensors that use the functions of membrane proteins. Membrane proteins are essential components of biological membranes and have a central role in detection of various environmental stimuli such as olfaction and gustation. A number of studies have attempted for development of biosensors using the sensing property of these membrane proteins. Their specificity to target molecules is particularly attractive as it is significantly superior to that of traditional human-made sensors. In this review, we classified the membrane protein-based biosensors into two platforms: the lipid bilayer-based platform and the cell-based platform. On lipid bilayer platforms, the membrane proteins are embedded in a lipid bilayer that bridges between the protein and a sensor device. On cell-based platforms, the membrane proteins are expressed in a cultured cell, which is then integrated in a sensor device. For both platforms we introduce the fundamental information and the recent progress in the development of the biosensors, and remark on the outlook for practical biosensing applications.
Sost
deficiency leads to reduced mechanical strains at the tibia midshaft in strain-matched
in vivo
loading experiments in mice
Authors: Albiol Laia , Cilla Myriam , Pflanz David , Kramer Ina , Kneissel Michaela , Duda Georg N. , Willie Bettina M. , Checa Sara
Published: April 2018

Sclerostin, a product of the
Sost
gene, is a Wnt-inhibitor and thus negatively regulates bone accrual. Canonical Wnt/β-catenin signalling is also known to be activated in mechanotransduction. Sclerostin neutralizing antibodies are being tested in ongoing clinical trials to target osteoporosis and osteogenesis imperfecta but their interaction with mechanical stimuli on bone formation remains unclear.
Sost
knockout (KO) mice were examined to gain insight into how long-term
Sost
deficiency alters the local mechanical environment within the bone. This knowledge is crucial as the strain environment regulates bone adaptation. We characterized the bone geometry at the tibial midshaft of young and adult
Sost
KO and age-matched littermate control (LC) mice using microcomputed tomography imaging. The cortical area and the minimal and maximal moment of inertia were higher in
Sost
KO than in LC mice, whereas no difference was detected in either the anterior–posterior or medio-lateral bone curvature. Differences observed between age-matched genotypes were greater in adult mice. We analysed the local mechanical environment in the bone using finite-element models (FEMs), which showed that strains in the tibiae of
Sost
KO mice are lower than in age-matched LC mice at the diaphyseal midshaft, a region commonly used to assess cortical bone formation and resorption. Our FEMs also suggested that tissue mineral density is only a minor contributor to the strain distribution in tibial cortical bone from
Sost
KO mice compared to bone geometry. Furthermore, they indicated that although strain gauging experiments matched strains at the gauge site, strains along the tibial length were not comparable between age-matched
Sost
KO and LC mice or between young and adult animals within the same genotype.
Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis inStreptococcus pneumoniae
Authors: Han Xiao , Sun Renhua , Sandalova Tatyana , Achour Adnane
Published: April 2018

Spr1654 fromStreptococcus pneumoniaeplays a key role in the production of unusual sugars, presumably functioning as a pyridoxal-5′-phosphate (PLP)-dependent aminotransferase. Spr1654 was predicted to catalyse the transferring of amino group to form the amino sugar 2-acetamido-4-amino-2, 4, 6-trideoxygalactose moiety (AATGal), representing a crucial step in biosynthesis of teichoic acids inS. pneumoniae. We have determined the crystal structures of the apo-, PLP- and PMP-bound forms of Spr1654. Spr1654 forms a homodimer, in which each monomer contains one active site. Using spectrophotometry and based on absorbance profiles of PLP- and PMP-formed enzymes, our results indicate thatl-glutamate is most likely the preferred amino donor. Structural superposition of the crystal structures of Spr1654 on previously determined structures of other sugar aminotransferases in complex with glutamate and/or UDP-activated sugar allowed us to identify key Spr1654 residues for ligand binding and catalysis. The crystal structures of Spr1654 and in complex with PLP and PMP can direct the future rational design of novel therapeutic compounds againstS. pneumoniae.
Environmentally friendly and breathable wet-laid hydroentangled nonwovens for personal hygiene care with excellent water absorbency and flushability
Authors: Deng Chao , Liu Wanjun , Zhang Yinjiang , Huang Chen , Zhao Yi , Jin Xiangyu
Published: April 2018

Developing wet-laid papers with a good wet strength remains a longstanding challenge in the papermaking industry. In this study, hydroentanglement, a mechanical bonding technique is developed to consolidate the wet-laid fibre web. The results indicate that wet tensile strength, ductile stretching property, softness, air permeability and water absorbency of the wet-laid fibre web are significantly improved by hydroentanglement. In addition, the abrasion test shows that the dusting off rate of wet-laid fibre web can be effectively reduced through hydroentanglement. Moreover, the disintegration experiment proves that wet-laid hydroentangled nonwovens could be easily dispersed when compared with conventional carded hydroentangled nonwovens. Therefore, the new wet-laid hydroentangled nonwovens can maintain excellent performance in a wet state, showing a great potential for personal hygiene applications.
Vibrational spectroscopy of metal methanesulfonates: M = Na, Cs, Cu, Ag, Cd
Authors: Parker Stewart F. , Zhong Lisha
Published: April 2018

In this work, we have used a combination of vibrational spectroscopy (infrared, Raman and inelastic neutron scattering) and periodic density functional theory to investigate six metal methanesulfonate compounds that exhibit four different modes of complexation of the methanesulfonate ion: ionic, monodentate, bidentate and pentadentate. We found that the transition energies of the modes associated with the methyl group (C–H stretches and deformations, methyl rock and torsion) are essentially independent of the mode of coordination. The SO
3
modes in the Raman spectra also show little variation. In the infrared spectra, there is a clear distinction between ionic (i.e. not coordinated) and coordinated forms of the methanesulfonate ion. This is manifested as a splitting of the asymmetric S–O stretch modes of the SO
3
moiety. Unfortunately, no further differentiation between the various modes of coordination: unidentate, bidentate etc … is possible with the compounds examined. While it is likely that such a distinction could be made, this will require a much larger dataset of compounds for which both structural and spectroscopic data are available than that available here.
Vascularization of the trachea in the bottlenose dolphin: comparison with bovine and evidence for evolutionary adaptations to diving
Authors: Ballarin Cristina , Bagnoli Paola , Peruffo Antonella , Cozzi Bruno
Published: April 2018

The rigid structure of the mammalian trachea is functional to maintain constant patency and airflow during breathing, but no gas exchange takes place through its walls. The structure of the organ in dolphins shows increased rigidity of the tracheal cartilaginous rings and the presence of vascular lacunae in the submucosa. However, no actual comparison was ever made between the size and capacity of the vascular lacunae of the dolphin trachea and the potentially homologous structures of terrestrial mammals. In the present study, the extension of the lacunae has been compared between the bottlenose dolphin and the bovine, a closely related terrestrial Cetartiodactyla. Our results indicate that the extension of the blood spaces in the submucosa of dolphins is over 12 times larger than in the corresponding structure of the bovines. Furthermore, a microscopic analysis revealed the presence of valve-like structures in the walls of the cetacean lacunae. The huge difference in size suggests that the lacunae are not merely a product of individual physiological plasticity, but may constitute a true adaptive evolutionary character, functional to life in the aquatic environment. The presence of valve-like structures may be related to the regulation of blood flow, and curtail excessive compression under baric stress at depth.
Glucocorticoids modulate gastrointestinal microbiome in a wild bird
Authors: Noguera José C. , Aira Manuel , Pérez-Losada Marcos , Domínguez Jorge , Velando Alberto
Published: April 2018

It has recently been hypothesized that stress exposure (e.g. via glucocorticoid secretion) may dysregulate the bacterial gut microbiome, a crucial ‘organ' in animal health. However, whether stress exposure (e.g. via glucocorticoid secretion) affects the bacterial gut microbiome of natural populations is unknown. We have experimentally altered the basal glucocorticoid level (corticosterone implants) in a wild avian species, the yellow-legged gullLarus michahellis, to assess its effects on the gastrointestinal microbiota. Our results suggest underrepresentation of several microbial taxa in the corticosterone-implanted birds. Importantly, such reduction included potentially pathogenic avian bacteria (e.g.MycoplasmaandMicrovirga) and also some commensal taxa that may be beneficial for birds (e.g. Firmicutes). Our findings clearly demonstrate a close link between microbiome communities and glucocorticoid levels in natural populations. Furthermore, they suggest a beneficial effect of stress in reducing the risk of infection that should be explored in future studies.
A novel non-sequencing approach for rapid authentication of Testudinis Carapax et Plastrum and Trionycis Carapax by species-specific primers
Authors: Yang Huan , Yu Pingtian , Lu Yi , Jiao Zhaoqun , Chen Liqun , Zhou Ying , Shen Yuping , Jia Xiaobin
Published: April 2018

A novel non-sequencing approach was developed to detect short DNA fragments (
ca
100 bp) for rapid authentication of two natural products, namely Testudinis Carapax et Plastrum and Trionycis Carapax, based on the difference in mitochondrial genome. Five specifically designed primer reactions were established to target species for reliable identification of their commercial products. They were confirmed to have a high level of inter-species-specificity and good intra-species stability. The limit of detection was estimated to be 1 ng of genomes for all of five assays. Also, the validation results demonstrated that the raw materials and processed products in addition to some of the highly processed products can be conveniently authenticated with good sensitivity and precision by this newly proposed approach. Especially, when reference sample mixtures were assayed, these primer sets have still performed well but not the prevailing COI barcoding technology. These could assist in the discrimination and identification of other animal-derived medicines for their form of raw material, the pulverized and the complex.
Family ties: the multilevel effects of households and kinship on the networks of individuals
Authors: Koster Jeremy
Published: April 2018

Among social mammals, humans uniquely organize themselves into communities of households that are centred around enduring, predominantly monogamous unions of men and women. As a consequence of this social organization, individuals maintain social relationships both within and across households, and potentially there is conflict among household members about which social ties to prioritize or de-emphasize. Extending the logic of structural balance theory, I predict that there will be considerable overlap in the social networks of individual household members, resulting in a pattern of group-level reciprocity. To test this prediction, I advance the Group-Structured Social Relations Model, a generalized linear mixed model that tests for group-level effects in the inter-household social networks of individuals. The empirical data stem from social support interviews conducted in a community of indigenous Nicaraguan horticulturalists, and model results show high group-level reciprocity among households. Although support networks are organized around kinship, covariates that test predictions of kin selection models do not receive strong support, potentially because most kin-directed altruism occurs within households, not between households. In addition, the models show that households with high genetic relatedness in part from children born to adulterous relationships are less likely to assist each other.
Drivers of temporal beta diversity of a benthic community in a seasonally hypoxic fjord
Authors: Chu Jackson W. F. , Curkan Curtis , Tunnicliffe Verena
Published: April 2018

Global expansion of oxygen-deficient (hypoxic) waters will have detrimental effects on marine life in the Northeast Pacific Ocean (NEP) where some of the largest proportional losses in aerobic habitat are predicted to occur. However, few
in situ
studies have accounted for the high environmental variability in this region while including natural community-assembly dynamics. Here, we present results from a 14-month deployment of a benthic camera platform tethered to the VENUS cabled observatory in the seasonally hypoxic Saanich Inlet. Our time series continuously recorded natural cycles of deoxygenation and reoxygenation that allowed us to test whether a community from the NEP showed hysteresis in its recovery compared to hypoxia-induced decline, and to address the processes driving temporal beta diversity under variable states of hypoxia. Using high-frequency ecological time series, we reveal (i) differences in the response and recovery of the epibenthic community are rate-limited by recovery of the sessile species assemblage; (ii) both environmental and biological processes influence community assembly patterns at multiple timescales; and (iii) interspecific processes can drive temporal beta diversity in seasonal hypoxia. Ultimately, our results illustrate how different timescale-dependent drivers can influence the response and recovery of a marine habitat under increasing stress from environmental change.
Salishicetus meadi, a new aetiocetid from the late Oligocene of Washington State and implications for feeding transitions in early mysticete evolution
Authors: Peredo Carlos Mauricio , Pyenson Nicholas D.
Published: April 2018

Living baleen whales, or Mysticeti, lack teeth and instead feed using keratinous baleen plates to sieve prey-laden water. This feeding strategy is profoundly different from that of their toothed ancestors, which processed prey using the differentiated dentition characteristic of mammals. The fossil record of mysticetes reveals stem members that include extinct taxa with dentition, illuminating the morphological states that preceded the loss of teeth and the subsequent origin of baleen. The relationships among stem mysticetes, including putative clades such as Mammalodontidae and Aetiocetidae, remain debatable. Aetiocetids are among the more species-rich clade of stem mysticetes, and known only from fossil localities along the North Pacific coastline. Here, we report a new aetiocetid,Salishicetus meadigen. et sp. nov, from the late Oligocene of Washington State, USA.Salishicetuspreserves a near-complete lower dentition with extensive occlusal wear, indicating that it processed prey using shearing cheek teeth in the same way as its stem cetacean ancestors. Using a matrix with all known species of aetiocetids, we recover a monophyletic Aetiocetidae, crownward of a basal clade of Mammalodontidae. The description ofSalishicetusresolves phylogenetic relationships among aetiocetids, which provides a basis for reconstructing ancestral feeding morphology along the stem leading to crown Mysticeti.
Clawed forelimbs allow northern seals to eat like their ancient ancestors
Authors: Hocking David P. , Marx Felix G. , Sattler Renae , Harris Robert N. , Pollock Tahlia I. , Sorrell Karina J. , Fitzgerald Erich M. G. , McCurry Matthew R. , Evans Alistair R.
Published: April 2018

Streamlined flippers are often considered the defining feature of seals and sea lions, whose very name ‘pinniped’ comes from the Latin
pinna
and
pedis
, meaning ‘fin-footed’. Yet not all pinniped limbs are alike. Whereas otariids (fur seals and sea lions) possess stiff streamlined forelimb flippers, phocine seals (northern true seals) have retained a webbed yet mobile paw bearing sharp claws. Here, we show that captive and wild phocines routinely use these claws to secure prey during processing, enabling seals to tear large fish by stretching them between their teeth and forelimbs. ‘Hold and tear’ processing relies on the primitive forelimb anatomy displayed by phocines, which is also found in the early fossil pinniped
Enaliarctos
. Phocine forelimb anatomy and behaviour therefore provide a glimpse into how the earliest seals likely fed, and indicate what behaviours may have assisted pinnipeds along their journey from terrestrial to aquatic feeding.
The cascading pathogenic consequences ofSarcoptes scabieiinfection that manifest in host disease
Authors: Martin Alynn M. , Fraser Tamieka A. , Lesku John A. , Simpson Kellie , Roberts Georgia L. , Garvey Jillian , Polkinghorne Adam , Burridge Christopher P. , Carver Scott
Published: April 2018

Sarcoptic mange, caused by the parasitic miteSarcoptes scabiei, causes a substantive burden of disease to humans, domestic animals and wildlife, globally. There are many effects ofS. scabieiinfection, culminating in the disease which hosts suffer. However, major knowledge gaps remain on the pathogenic impacts of this infection. Here, we focus on the bare-nosed wombat host (Vombatus ursinus) to investigate the effects of mange on: (i) host heat loss and thermoregulation, (ii) field metabolic rates, (iii) foraging and resting behaviour across full circadian cycles, and (iv) fatty acid composition in host adipose, bone marrow, brain and muscle tissues. Our findings indicate that mange-infectedV. ursinuslose more heat to the environment from alopecia-affected body regions than healthy individuals. Additionally, mange-infected individuals have higher metabolic rates in the wild. However, these metabolic demands are difficult to meet, because infected individuals spend less time foraging and more time inactive relative to their healthy counterparts, despite being outside of the burrow for longer. Lastly, mange infection results in altered fatty acid composition in adipose tissue, with increased amounts of omega-6 acids, and decreased amounts of omega-3 acids, a consequence of chronic cutaneous inflammation and inhibition of anti-inflammatory responses. These findings highlight the interactions of mange-induced physiological and behavioural changes, and have implications for the treatment and rehabilitation of infected individuals.
Wrinkles and creases in the bending, unbending and eversion of soft sectors
Authors: Sigaeva Taisiya , Mangan Robert , Vergori Luigi , Destrade Michel , Sudak Les
Published: April 2018

We study what is clearly one of the most common modes of deformation found in nature, science and engineering, namely the large elastic bending of curved structures, as well as its inverse, unbending, which can be brought beyond complete straightening to turn into eversion. We find that the suggested mathematical solution to these problems always exists and is unique when the solid is modelled as a homogeneous, isotropic, incompressible hyperelastic material with a strain-energy satisfying the strong ellipticity condition. We also provide explicit asymptotic solutions for thin sectors. When the deformations are severe enough, the compressed side of the elastic material may buckle and wrinkles could then develop. We analyse, in detail, the onset of this instability for the Mooney–Rivlin strain energy, which covers the cases of the neo-Hookean model in exact nonlinear elasticity and of third-order elastic materials in weakly nonlinear elasticity. In particular, the associated theoretical and numerical treatment allows us to predict the number and wavelength of the wrinkles. Guided by experimental observations, we finally look at the development of creases, which we simulate through advanced finite-element computations. In some cases, the linearized analysis allows us to predict correctly the number and the wavelength of the creases, which turn out to occur only a few per cent of strain earlier than the wrinkles.
Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability
Authors: Parsons Kevin J. , Son Young H. , Crespel Amelie , Thambithurai Davide , Killen Shaun , Harris Matthew P. , Albertson R. Craig
Published: April 2018

Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have little understanding of its genetic basis and its temporal dynamics over generations. To address these open questions, we compared patterns of craniofacial modularity among laboratory strains, defined mutant lines and a wild population of zebrafish (Danio rerio). Our findings suggest that relatively simple genetic changes can have profound effects on covariance, without greatly affecting craniofacial shape. Moreover, we show that instead of completely deconstructing the covariance structure among sets of traits, mutations cause shifts among seemingly latent patterns of modularity suggesting that the skull may be predisposed towards a limited number of phenotypes. This new insight may serve to greatly increase the evolvability of a population by providing a range of ‘preset’ patterns of modularity that can appear readily and allow for rapid evolution.
Genome-wide single nucleotide polymorphism scan suggests adaptation to urbanization in an important pollinator, the red-tailed bumblebee (
Bombus lapidarius
L.)
Authors: Theodorou Panagiotis , Radzevičiūtė Rita , Kahnt Belinda , Soro Antonella , Grosse Ivo , Paxton Robert J.
Published: April 2018

Urbanization is considered a global threat to biodiversity; the growth of cities results in an increase in impervious surfaces, soil and air pollution, fragmentation of natural vegetation and invasion of non-native species, along with numerous environmental changes, including the heat island phenomenon. The combination of these effects constitutes a challenge for both the survival and persistence of many native species, while also imposing altered selective regimes. Here, using 110 314 single nucleotide polymorphisms generated by restriction-site-associated DNA sequencing, we investigated the genome-wide effects of urbanization on putative neutral and adaptive genomic diversity in a major insect pollinator,
Bombus lapidarius
, collected from nine German cities and nine paired rural sites. Overall, genetic differentiation among sites was low and there was no obvious genome-wide genetic structuring, suggesting the absence of strong effects of urbanization on gene flow. We nevertheless identified several loci under directional selection, a subset of which was associated with urban land use, including the percentage of impervious surface surrounding each sampling site. Overall, our results provide evidence of local adaptation to urbanization in the face of gene flow in a highly mobile insect pollinator.
An avian seed dispersal paradox: New Zealand's extinct megafaunal birds did not disperse large seeds
Authors: Carpenter Joanna K. , Wood Jamie R. , Wilmshurst Janet M. , Kelly Dave
Published: April 2018

Often the mutualistic roles of extinct species are inferred based on plausible assumptions, but sometimes palaeoecological evidence can overturn such inferences. We present an example from New Zealand, where it has been widely assumed that some of the largest-seeded plants were dispersed by the giant extinct herbivorous moa (Dinornithiformes). The presence of large seeds in preserved moa gizzard contents supported this hypothesis, and five slow-germinating plant species (
Elaeocarpus dentatus, E. hookerianus, Prumnopitys ferruginea, P. taxifolia, Vitex lucens
) with thick seedcoats prompted speculation about whether these plants were adapted for moa dispersal. However, we demonstrate that all these assumptions are incorrect. While large seeds were present in 48% of moa gizzards analysed, analysis of 152 moa coprolites (subfossil faeces) revealed a very fine-grained consistency unparalleled in extant herbivores, with no intact seeds larger than 3.3 mm diameter. Secondly, prolonged experimental mechanical scarification of
E. dentatus
and
P. ferruginea
seeds did not reduce time to germination, providing no experimental support for the hypothesis that present-day slow germination results from the loss of scarification in moa guts. Paradoxically, although moa were New Zealand's largest native herbivores, the only seeds to survive moa gut passage intact were those of small-seeded herbs and shrubs.
Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860
Authors: Rosa Leonardo T. , Springthorpe Vicki , Bianconi Matheus E. , Thomas Gavin H. , Kelly David J.
Published: April 2018

Lineage-specific expansion (LSE) of protein families is a widespread phenomenon in many eukaryotic genomes, but is generally more limited in bacterial genomes. Here, we report the presence of 434 genes encoding solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family, within the 8.2 Mb genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860, a gene family over-representation of unprecedented abundance in prokaryotes. Representing over 6 % of the total number of coding sequences, the SBP genes are distributed across the whole genome but are found rarely in low-GC islands, where the gene density for this family is much lower. This observation, and the much higher sequence identity between the 434 Rhodoplanes TTT SBPs compared with the average identity between homologues from different species, is indicative of a key role for LSE in the expansion. The TTT SBP genes were found in the vicinity of genes encoding membrane components of transport systems from different families, as well as regulatory proteins such as histidine-kinases and transcription factors, indicating a broad range of functions around the sensing, response and transport of organic compounds. A smaller expansion of TTT SBPs is known in some species of the β-proteobacteria Bordetella and we observed similar expansions in other β-proteobacterial lineages, including members of the genus Comamonas and the industrial biotechnology organism Cupriavidus necator, indicating that strong environmental selection can drive SBP duplication and specialisation from multiple evolutionary starting points.
Isolation, Detection and Characterization of Aerobic Bacteria from Honey Samples of Bangladesh
Authors: Saha Sarbojoy
Published: April 2018

Honey is a sweet substance made from the nectar of flowers and other chemical secretions from the bees’ bodies who collect nectar from the flowers and bring it to their hives to transform it to the thick, golden and sweet liquid that we call honey. The benefits of honey are not just limited to its basic use as a natural sweetener, but also its medicinal properties. The purpose of this study was to identify the bacteria that are present in honey commonly found in Bangladesh, which can tolerate the antimicrobial conditions of honey and survive in it. Fortunately, such bacteria could be detected, isolated and characterized by morphological and biochemical tests. The predominant type of bacteria commonly found in both raw and commercial honeys of Bangladesh are gram positive cocci such as streptococci, staphylococci, micrococci, bacilli and lactobacilli. Few gram negative bacteria were also isolated like Escherichia coli (8%) and Klebsiella pneumonia (8%) and some gram negative/gram variable Micrococcus luteus (75%). Hopefully, such knowledge would benefit people in the future as they will know more about the microorganisms present in honey and about the safety and quality of the honey they are about to buy or consume.
MaSS-Simulator: A highly configurable MS/MS simulator for generating test datasets for big data algorithms
Authors: Awan Muaaz Gul , Saeed Fahad
Published: April 2018

Mass Spectrometry (MS) based proteomics has become an essential tool in the study of proteins. The big data from MS machines has led to the development of novel serial and parallel algorithmic tools. However, the absence of data benchmarks and ground truth makes the algorithmic integrity testing and reproducibility a challenging problem. To this end, we present MaSS-Simulator, which is an easy to use simulator and can be configured to generate MS/MS datasets for a wide variety of conditions with known ground truths. MaSS-Simulator offers a large number of configuration options to simulate control datasets with desired properties thus enabling rigorous and large scale algorithmic testing. We assessed 8,031 spectra generated by MaSS-Simulator by comparing them against the experimentally generated spectra of same peptides. Our results showed that MaSS-Simulator generated spectra were very close to the real-experimental spectra and had a relative-error distribution centered around 25%. In contrast the theoretical spectra for same peptides had relative-error distribution centered around 150%. Source code, executables and a user manual can be downloaded from https://github.com/pcdslab/MaSS-Simulator
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data
Authors: Chen Huidong , Albergante Luca , Hsu Jonathan Y , Lareau Caleb A , Bosco Giosue` Lo , Guan Jihong , Zhou Shuigeng , Gorban Alexander N , Bauer Daniel E , Aryee Martin J , Langenau David M , Zinovyev Andrei , Buenrostro Jason D , Yuan Guo-Cheng , Pinello Luca
Published: April 2018

Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data.
Hair regeneration by small molecules that activate autophagy
Authors: Chai Min , Jiang Meisheng , Vergnes Laurent , Fu Xudong , de Barros Stephanie C , Jiao Jing , Herschman Harvey R , Crooks Gay M , Reue Karen , Huang Jing
Published: April 2018

Hair plays important roles, ranging from the conservation of body heat to the preservation of psychological well-being. Hair loss or alopecia affects millions worldwide and can occur because of aging, hormonal dysfunction, autoimmunity, or as a side effect of cancer treatment (Gilhar et al., 2012; Petukhova et al., 2010). Methods that can be used to regrow hair are highly sought after, but lacking. Here we report that hair regeneration can be stimulated by small molecules that activate autophagy, including the longevity metabolites α-ketoglutarate and α-ketobutyrate, and the prescription drugs rapamycin and metformin which impinge on TOR and AMPK signaling.
Infectivity of dengue virus serotypes 1 and 2 is correlated to E protein intrinsic dynamics but not to envelope conformations
Authors: SHARMA Kamal Kant , LIM Xin-Xiang , TANTIRIMUDALIGE Sarala Neomi , Gupta Anjali , MARZINEK Jan K , HOLDBROOK Daniel , LIM Xin Ying Elisa , BOND Peter J , ANAND Ganesh S , WOHLAND Thorsten
Published: April 2018

Dengue is a mosquito-borne virus with dire health and economic impact. Dengue is responsible for an estimated ~390 million infections per year, with Dengue 2 (DENV2) being the most virulent strain among the four serotypes. Interestingly, it is also for strains of this serotype that temperature-dependent large scale morphological changes, termed as 'breathing', have been observed. Although, the structure of these morphologies has been solved to 3.5 Angstrom resolution, the dynamics of the viral envelope are unknown. Here, we combine fluorescence and mass spectrometry and molecular dynamics simulations to provide insights into DENV2 structural dynamics in comparison to DENV1. We observe hitherto unseen conformational changes and structural dynamics of the DENV2 envelope that are influenced by both temperature and divalent cations. Our results show that for DENV2 and DENV1 the intrinsic dynamics but not the specific morphologies are correlated to viral infectivity.