bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical Correlates of Response to Anti-PD-1–based Therapy in Patients With Metastatic Melanoma
Authors: Davis Elizabeth J. , Perez Matthew C. , Ayoubi Noura , Zhao Shilin , Ye Fei , Wang Daniel Y. , Sosman Jeffrey A. , Al-Rohil Rami N. , Eroglu Zeynep , Johnson Douglas B.
Published: March 2019

Anti-PD-1 agents, alone or in combination with ipilimumab, produce durable responses in some melanoma patients. Tumor features that correlate with response are not well defined. We collected clinical data from metastatic melanoma patients treated at 2 centers who received anti-PD-1 (n=303) or anti-PD-1+ipilimumab (n=57). We correlated number of metastases, diameter of largest tumor (tumor bulk), and organ involvement with response rate (RR), progression-free survival (PFS), and overall survival (OS). Patients with diameter of largest tumor ≤2 cm had a 53% RR, whereas those with largest tumor >2 cm had a 38% RR (P=0.009). Those with liver metastases had lower RR (25% vs. 43%; P=0.002). RR to anti-PD-1 was greater in patients with ≤10 metastases compared with those with >10 (39% vs. 27%; P=0.027). In multivariable analyses, size of the largest tumor was independently associated with PFS (P=0.0005), OS (P<0.0001), and RR (P=0.02), whereas AJCC stage, lactate dehydrogenase, liver metastases, ECOG performance status, number of metastases, and prior therapies were not. In patients treated with anti-PD-1+ipilimumab, however, tumor bulk was not associated with outcomes, although number of metastases was associated with PFS (P=0.035) and RR (P=0.009) but not OS. Pathologic analysis did not reveal differences in T-cell infiltration in bulky versus small tumors. Tumor bulk, defined by diameter of largest tumor, was strongly and independently associated with clinical outcomes in anti-PD-1 but not in anti-PD-1+ipilimumab. In conjunction with molecular biomarkers, clinical predictors may help guide selection of immunotherapy agents.
Hypertension in menopausal women: the effect and role of estrogen
Authors: Srivaratharajah Kajenny , Abramson Beth L.
Published: March 2019

States of estrogen imbalance or deprivation are associated with higher risks of hypertension and cardiovascular disease in women; however, the effects of estrogen on hypertension are multifactorial, complex, and not completely understood. Although controversial, hormone therapy may improve cardiovascular outcomes when initiated by recently menopausal women. Improved screening for hypertension, especially in specific groups of younger women at higher risk, is recommended. Further study is needed to determine whether sex-specific differences exist in therapeutic response to pharmacologic management of hypertension.
The Effects of Radiation and Emitted Light Transport on the Positional Response of 11 cm × 42.5 cm × 5.5 cm NaI(Tl) Detectors
Authors: Noey Jordan D. , Xiao Jeffery B. , DiFulvio Angela , Sulieman Noor A. , Carmona Marco A. , Chung Long Kiu , El-Amir Issa N. , Frank Samuel J. , Liu Kevin , Schiefer Kai , Seekamp James M. , Sosa Charles S. , Trimas David J. , Vyas Archan P. , Kearfott Kimberlee J.
Published: March 2019

Experiments were performed with 30 11 cm × 42.5 cm × 5.5 cm NaI(Tl) detectors to better understand their positional response. Spectra were collected using 0.02 to 0.15 MBq point sources of 241Am, 137Cs, 60Co, and 133Ba positioned on lines parallel and perpendicular to the long axis of the crystal along both the narrow and wide detector faces as well as at different distances from them. A greater density of positions was sampled at the ends of the detector, and repeated measurements were made to examine potential gain drifts during the experiment. Spectroscopic peak counts, spectroscopic pulse heights, and net counts were analyzed. Empirical equations were fit to the aforementioned data for each specific source energy as a function of source position. In addition, a Monte Carlo radiation transport code was used to simulate the expected positionally variable response based solely upon radiation absorption. The simulated radiation transport efficiency functions were compared to the experimental data. The effects of the geometric radiation efficiency, the attenuation and scattering of emitted light within the scintillation crystal, and combined effects such as nonuniformity of the photomultiplier tube, photocathode response, and crystal irregularities were then distinguished. Functions describing each effect were derived. The results suggest potential new corrections to data obtained with large scintillation detectors as well as a novel approach to partial positional gamma-ray detection with minimal collimation, given that the energy resolution is within reason for particular photopeaks.
Clinical Characteristics of Saffold Virus Infection in Children
Authors: Ugai Satoko , Iwaya Atsushi , Taneichi Hiromichi , Hirokawa Chika , Aizawa Yuta , Hatakeyama Shuji , Saitoh Akihiko
Published: March 2019

Background:

Saffold virus (SAFV) is a novel human cardiovirus that was identified in 2007. Recently, SAFV has been isolated from nasal and stool specimens of infants presenting with respiratory and gastrointestinal symptoms and from cerebrospinal fluid (CSF) specimens of children with central nervous system infection. However, little is known regarding clinical characteristics of SAFV in children.

Methods:

We reviewed 5412 specimens from the database of the infectious agents surveillance system in Niigata prefecture, Japan, between January 2006 and December 2013, and identified SAFV-infected patients. Subsequently, we retrospectively reviewed their medical records and evaluated their clinical characteristics.

Results:

We identified 9 SAFV-infected patients (median age: 5 years; range: 2–16 years). Seven patients were diagnosed with pharyngitis, one with meningitis and one with fever of unknown origin. Dominant symptoms were high fever, appetite loss and headache. The median duration of the fevers was 2 days in patients with pharyngitis; however, the patient with meningitis remained febrile for 5 days. All blood tests available in this case series revealed leukocytosis with a predominance of neutrophils. CSF profiles showed mild lymphocytic pleocytosis. All patients recovered fully without complications.

Conclusions:

A few clinical characteristics of SAFV infection were clarified, including high fever of short duration in patients with pharyngitis, and neutrophil-dominant leukocytosis. The clinical course and CSF profiles of a case of meningitis were similar to those of other aseptic meningitis. SAFV needs to be included in the differential diagnosis of pharyngitis or meningitis when commonly identified viruses are not identified in such patients.
Progesterone relates to enhanced incisional acute pain and pinprick hyperalgesia in the luteal phase of female volunteers
Authors: Pogatzki-Zahn Esther M. , Drescher Christiane , Englbrecht Jan S. , Klein Thomas , Magerl Walter , Zahn Peter K.
Published: March 2019

The role of sex hormones on postsurgical pain perception is basically unclear. Here, we studied the role of endogenous gonadal hormones for pain and hyperalgesia in human volunteers after experimental incision. A 4-mm incision was made in the volar forearm of 15 female volunteers both in the follicular and the luteal phase (random block design). Somatosensory profiles were assessed at baseline and 1 to 72 hours after incision by quantitative sensory testing, compared between both cycle phases, and related to individual plasma levels of gonadal hormones. Sensory testing at baseline revealed significantly lower pain thresholds (25 vs 46 mN, P < 0.005) and increased pain ratings to pinprick (0.96 vs 0.47, P < 0.0001) in the luteal phase; similarly, 1 hour after incision, pain intensity to incision (38 vs 21/100, P < 0.005), pinprick hyperalgesia by rating (P < 0.05), and area of secondary hyperalgesia (P < 0.001) were enhanced in the luteal phase. Multiple regression analysis revealed that pinprick pain sensitivity at baseline was significantly predicted by progesterone (partial r = 0.67, P < 0.001), follicle-stimulating hormone (FSH) (partial r = 0.61, P < 0.005), and negatively by testosterone (partial r = −0.44, P < 0.05). Likewise, incision-induced pain and pinprick hyperalgesia (rating and area) were significantly predicted by progesterone (partial r = 0.70, r = 0.46, and r = 0.47, respectively; P < 0.05-0.0001) and in part by FSH; the contribution of estrogen, however, was fully occluded by progesterone for all measures. In conclusion, pinprick pain and incision-induced pain and mechanical hyperalgesia were greater in the luteal phase and predicted by progesterone, suggesting a major role for progesterone. Other hormones involved are testosterone (protective) and in part FSH.
Controlling Nutritional Status Score As a Predictive Marker for Patients With Implantable Left Ventricular Assist Device
Authors: Saito Akihito , Amiya Eisuke , Hatano Masaru , Shiraishi Yasuyuki , Nitta Daisuke , Minatsuki Shun , Maki Hisataka , Hosoya Yumiko , Tsuji Masaki , Bujo Chie , Nawata Kan , Kinoshita Osamu , Kimura Mitsutoshi , Endo Miyoko , Kagami Yukie , Nemoto Mariko , Ikeda Yuichi , Morita Hiroyuki , Ono Minoru , Komuro Issei
Published: March 2019

Although a correlation between the nutritional status and the prognosis of patients with heart failure has been suggested, a correlation between the nutritional status and outcomes after the left ventricular assist device (LVAD) implantation remains unclear. We aimed to investigate the efficacy of the Controlling Nutritional Status (CONUT) score (range 0–12, including serum albumin, total cholesterol, and lymphocytes) as a nutritional index in speculating the prognosis of patients undergoing LVAD implantation. We examined 63 consecutive patients who underwent the continuous-flow LVAD implantation. Using the preoperative CONUT score, patients were categorized into two groups: lower CONUT score (0–4: normal to mild malnutrition) and higher CONUT score (5–12: moderate to severe malnutrition). We compared for the backgrounds and the clinical events after LVAD implantation. The higher CONUT group exhibited a significantly higher mean right atrial pressure (10.9 ± 4.7 vs. 7.3 ± 4.1 mmHg; p = 0.0019). In that group, the mortality rate was significantly higher (25% vs. 2.6%; p = 0.0059) and the Kaplan–Meier analysis showed lower survival rate. Furthermore, more bleeding events significantly occurred in the higher CONUT group. The preoperative CONUT score may reflect systemic venous congestion and offer a useful prognostic index of clinical courses after LVAD implantation.
Partial Splenic Embolization Is a Safe and Effective Alternative in the Management of Portal Hypertension in Children
Authors: Vittorio Jennifer , Orellana Katherine , Martinez Mercedes , Ovchinsky Nadia , Schlossberg Peter , Griesemer Adam , Lobritto Steven
Published: March 2019

Objective:

There are multiple approaches to manage the clinical complications of portal hypertension (PHTN) to treat/prevent spontaneous hemorrhage by mitigating thrombocytopenia. No single approach is ideal for all patients given the heterogeneity of this population. Our goal was to determine whether partial splenic embolization (PSE) was safe and effective in the pediatric population.

Methods:

This is a retrospective review of our single‐center experience for all patients ages 0 to 21 who underwent PSE between January 2010 and August 2017. The embolized splenic volume targeted was 60% to 70%.

Results:

Twenty‐six patients underwent PSE due to thrombocytopenia and/or recurrent variceal bleeding. Patients ranged in age from 18 months to 20 years (mean 13.1 years). The median platelet count before PSE was 53.0 (×109/L). The platelet count improved after PSE with values >100,000 in 21 patients (80.8%). Children with prior esophageal varices showed improvement after PSE with only 9 (34.6%) requiring further endoscopic therapy. After PSE, patients developed transient abdominal pain, distention, fever, and perisplenic fluid collections. Serious complications such as splenic abscess, splenic rupture, bleeding, pancreatic infarction, opportunistic infection, or death were not observed. One patient experienced thrombotic complications after PSE and was later diagnosed with myelodysplastic syndrome.

Conclusions:

PSE is a safe and effective alternative in the management of pediatric PHTN in select populations. PSE may be a favorable alternative to splenectomy and portal systemic shunting because it preserves functional spleen mass and avoids postprocedure accelerated liver disease or encephalopathy.
Clinically Evident Portal Hypertension
Authors: Bass Lee M. , Shneider Benjamin L. , Henn Lisa , Goodrich Nathan P. , Magee John C. ,   Childhood Liver Disease Research Network (ChiLDReN)
Published: March 2019

Portal hypertension (PHT) is a major cause of morbidity and mortality in pediatric liver diseases. Thus, research into causes and disease modifiers in PHT in these conditions is vitally important. PHT is rarely directly or indirectly measured in the assessment of children with chronic liver disease. A straightforward, reproducible definition of PHT could be invaluable for consistently identifying patients with PHT and for grouping these patients according to their risk of complications from their disease. We propose the term Clinically Evident Portal Hypertension (CEPH) to denote clinical findings that demonstrate evidence of elevated portal pressure. When CEPH criteria are met, PHT is highly likely to be present, although it is likely that PHT exists for variable periods of time before meeting CEPH criteria. Use of this research definition of CEPH will allow for consistent identification of these patients by clinicians in nearly any clinical setting and serve as a clinical milepost that may dictate future prognosis in pediatric patients with cirrhosis.
Prospective Longitudinal Patient-Reported Satisfaction and Health-Related Quality of Life following DIEP Flap Breast Reconstruction: Relationship with Body Mass Index
Authors: Ochoa Oscar , Garza Ramon , Pisano Steven , Chrysopoulo Minas , Ledoux Peter , Arishita Gary , Ketchum Norma , Michalek Joel E. , Nastala Chet
Published: March 2019

Background:

Breast reconstruction plays a significant role in breast cancer treatment recovery. Introduction of the BREAST-Q questionnaire has facilitated quantifying patient-reported quality-of-life measures, promoting improved evidence-based clinical practice. Information regarding the effects of body mass index on patient-reported outcomes and health-related quality of life is significantly lacking.

Methods:

Consecutive deep inferior epigastric perforator (DIEP) flap breast reconstruction patients prospectively completed BREAST-Q questionnaires preoperatively and at two points postoperatively. The first (postoperative time point A) and second (postoperative time point B) postoperative questionnaires were completed 1 month postoperatively and following breast revision, respectively. Postoperative flap and donor-site complications were recorded prospectively. BREAST-Q scores were compared at all time points and stratified by body mass index group (≤25, >25 to 29.9, 30 to 34.9, and ≥35 kg/m2).

Results:

Between July of 2012 and August of 2016, 73 patients underwent 130 DIEP flap breast reconstructions. Breast satisfaction and psychosocial and sexual well-being scores increased significantly postoperatively. Chest and abdominal physical well-being scores returned to baseline levels by postoperative point B. Preoperatively, stratified by body mass index, breast satisfaction and psychosocial well-being scores were significantly lower among patients with body mass index of 35 or higher and of more than 30, respectively. After reconstruction, not only were breast satisfaction, psychosocial, and sexual well-being scores significantly improved in all body mass index groups versus baseline, but also between–body mass index group differences were no longer present. Outcome satisfaction, flap, and donor-site morbidity were similar irrespective of body mass index.

Conclusions:

Patient-reported outcomes demonstrate significant improvements in breast satisfaction and psychosocial and sexual well-being among patients following DIEP flap reconstruction. Preoperative differences in quality-of-life scores were improved in patients with obesity (body mass index ≥30 kg/m2).

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Risk, II.
Bioengineered Approach to the Design of a Fat Graft Based on Mathematical Modeling that Predicts Oxygen Delivery
Authors: Suszynski Thomas M. , Rohrich Rod J. , Sieber David A. , Boyd Travis G. , Thornton James F. , Teotia Sumeet S. , Cunningham Bruce L. , Van Beek Allen L.
Published: March 2019

Background:

Fat grafting is a common procedure in plastic surgery. A major limitation is unpredictable graft retention, in part caused by inadequate oxygen delivery during the early posttransfer period.

Methods:

The authors present a bioengineered approach to the design of a fat graft based on mathematical theory, which can estimate the limitations of oxygen delivery. To simplify the problem, four variables were defined: (1) recipient-site oxygen partial pressure; (2) adipose tissue oxygen permeability; (3) adipose tissue oxygen consumption rate; and (4) fat graft size. Recipient-site oxygen partial pressure and adipose tissue oxygen permeability were estimated from literature, whereas adipose tissue oxygen consumption rate was measured using stirred microchamber technology. Calculations were performed in both spherical and planar geometry to calculate the maximum allowable fat graft size from an oxygen delivery standpoint.

Results:

As expected, planar geometry is less favorable for oxygenation but represents a realistic configuration for a fat graft. Maximum allowable fat graft thickness is only approximately 1 to 2 mm at external oxygen partial pressures of 10 to 40 mm Hg; any thicker and an anoxic or necrotic core likely develops. Given a reasonably large surface area and assuming several planes of injection, the maximum allowable fat graft volume is tens of milliliters.

Conclusions:

A systematic bioengineered approach may help better design a fat graft. Applying principles of mass transfer theory can predict whether a fat graft has a favorable chance of surviving from an oxygen delivery standpoint and can direct the development of strategies for improved fat graft oxygenation.
How to Reduce the Probability of a Pollybeak Deformity in Primary Rhinoplasty: A Single-Center Experience
Authors: Hoehne Julius , Brandstetter Michael , Gubisch Wolfgang , Haack Sebastian
Published: March 2019

Being a very common and highly stigmatizing deformity following primary rhinoplasty, a pollybeak deformity should be avoided during any primary rhinoplasty, especially in patients with thick nasal skin. Two surgical techniques used in the authors’ department to decrease the probability of its development in at-risk patients are described in this article: the authors’ modification of the supratip suture initially described by Guyuron, and a direct excision of excessive skin that the authors term supratip excision, reserved for rare cases with massive skin excess. In addition, a brief overview of the results of the authors’ case series of 74 patients treated with the supratip suture technique, and 21 patients treated with the supratip excision technique over a 5-year period, is given. In the authors’ experience, very good aesthetic results are achieved using either of the two techniques in selected cases.
Agreement and Reproducibility of Proton Density Fat Fraction Measurements Using Commercial MR Sequences Across Different Platforms
Authors: Jang Jong Keon , Lee Seung Soo , Kim Bohyun , Cho Eun-Suk , Kim Yeong Jae , Byun Jae Ho , Park Beom Jin , Kim So Yeon , Kim Jin Hee
Published: March 2019

Objectives

The aim of this study was to evaluate the agreement and reproducibility of proton density fat fraction (PDFF) measurements using commercial magnetic resonance (MR) sequences across different imagers, vendors, and field strengths via a phantom experiment.

Materials and Methods

Eleven fat-water emulsion phantoms of varying fat proportions (ie, 0–50 weight%) were constructed. Phantom PDFFs were estimated using commercial chemical shift–based MR imaging sequences with Siemens 1.5 T and 3.0 T, Philips 3.0 T, and GE 1.5 T and 3.0 T imagers, and MR spectroscopic sequences (HISTO) with Siemens 1.5 T and 3.0 T imagers. Agreement among the estimated PDFF values between commercial sequences was evaluated using Bland-Altman analysis. Reproducibility of the PDFF measurements across commercial sequences was evaluated using the reproducibility coefficient. The test-retest repeatability of the PDFF measurements was evaluated using the repeatability coefficient.

Results

The repeatability coefficient of the PDFF measurements was 0.31% to 1.58% for the absolute PDFF value for commercial sequences. Statistically significant biases in the estimated PDFF were noted in 19 of 21 pairwise comparisons of commercial sequences (range of mean biases, −4.48% to 8.15% for the absolute PDFF value). The reproducibility coefficient of PDFF measurements was 9.0% for the absolute PDFF value over all commercial sequences and 10.6% for the absolute PDFF value over all chemical shift–based MR imaging sequences.

Conclusions

The measurement of the PDFF is highly repeatable with commercial MR sequences but is not reproducible across different sequences, imager vendors, and field strengths. The use of the same sequence and imager is therefore recommended for the longitudinal follow-up of hepatic steatosis using commercial MR sequences for PDFF measurements.
Familial Cavernous Hemangioma
Authors: Torres Guadalupe , Kini Ashwini T. , Al Othman Bayan , Lee Andrew G.
Published: March 2019

A 30-year-old woman presented with diplopia after resection of an intracranial cavernous malformation. Fundus examination showed an asymptomatic intraocular cavernous hemangioma of the retina. Clinicians should be aware of the potential coexistence of intraocular and intracranial cavernous malformations; the presence of both should suggest familial etiology. As with other intracranial and intraocular vascular lesions (e.g., arteriovenous malformation in Wyburn-Mason syndrome, retinal hemangioblastoma in von Hippel Lindau disease, and choroidal hemangioma in Sturge–Weber syndrome), the presence of a vascular lesion in either location should prompt evaluation for additional pathology.
Quality characteristics of muffin added with Elaeagnus multiflora powder
Authors: Hong Ju-Yeon
Published: March 2019

The purpose of this study is to evaluate quality and functionality of muffin added 0%, 3%, 6%, 9%, and 12% powder of Elaeagnus multiflora. The volume and specific volume of muffin decreased with the addition of Elaeagnus multiflora powder. The baking loss rate and moisture content of the muffin increased by the addition of Elaeagnus multiflora powder. The “L” values of muffin were decreased by the added amount of Elaeagnus multiflora powder, but the “a” and “b” values of muffin were increased. Internal appearance showed that the number and size of air cells decreased with the addition of Elaeagnus multiflora powder. The texture measurement result showed that the hardness, cohesiveness, chewiness and brittleness of all muffin was increased according to increase to the added amount of Elaeagnus multiflora powder. The springiness was the highest in control (0%), the muffin decreased by the addition of Elaeagnus multiflora powder. Electron donating ability and the total polyphenol content was increased with the addition of Elaeagnus multiflora powder. For these results, the quality of preservation of Elaeagnus multiflora powder added muffin was higher than those of control muffin.
The Dementias Platform UK (DPUK) Data Portal
Authors: Bauermeister S , Orton C , Thompson S , Barker R A , Bauermeister J R , Ben-Shlomo Y , Brayne C , Burn D , Campbell A , Calvin C , Chandran S , Chaturvedi N , Chene G , Chessell I P , Corbett A , Davis D H J , Denis M , Dufouil C , Elliott P , Fox N , Hill D , Hofer SM , Hu M T , Jindra C , Kee F , Kim C H , Kim C , Kivimaki M , Koychev I , Lawson R A , Linden G J , Lyons R A , Mackay C , Matthews P M , McGuiness B , Middleton L , Moody C , Moore K , Na D L , O’Brien J T , Ourselin S , Paranjothy S , Park K S , Porteous D J , Richards M , Ritchie C W , Rohrer J D , Rossor M N , Rowe J B , Scahill R , Schnier C , Schott J M , Seo S W , South M , Steptoe A , Tabrizi S J , Tales A , Tillin T , Timpson N J , Toga A W , Visser PJ , Wade-Martins R , Wilkinson T , Williams J , Wong A , Gallacher J E
Published: March 2019

The Dementias Platform UK (DPUK) Data Portal is a data repository facilitating access to data for 3 370 929 individuals in 42 cohorts. The Data Portal is an end-to-end data management solution providing a secure, fully auditable, remote access environment for the analysis of cohort data. All projects utilising the data are by default collaborations with the cohort research teams generating the data.

The Data Portal uses UK Secure eResearch Platform (UKSeRP) infrastructure to provide three core utilities: data discovery, access, and analysis. These are delivered using a 7 layered architecture comprising: data ingestion, data curation, platform interoperability, data discovery, access brokerage, data analysis and knowledge preservation. Automated, streamlined, and standardised procedures reduce the administrative burden for all stakeholders, particularly for requests involving multiple independent datasets, where a single request may be forwarded to multiple data controllers. Researchers are provided with their own secure ‘lab’ using VMware which is accessed using two factor authentication.

Over the last 2 years, 160 project proposals involving 579 individual cohort data access requests were received. These were received from 268 applicants spanning 72 institutions (56 academic, 13 commercial, 3 government) in 16 countries with 84 requests involving multiple cohorts. Project are varied including multi-modal, machine learning, and Mendelian randomisation analyses. Data access is usually free at point of use although a small number of cohorts require a data access fee.
Distribution of iridescent colours in hummingbird communities results from the interplay between selection for camouflage and communication
Authors: Gruson Hugo , Elias Marianne , Parra Juan L. , Andraud Christine , Berthier Serge , Doutrelant Claire , Gomez Doris
Published: March 2019

Identification errors between closely related, co-occurring, species may lead to misdirected social interactions such as costly interbreeding or misdirected aggression. This selects for divergence in traits involved in species identification among co-occurring species, resulting from character displacement. On the other hand, predation may select for crypsis, potentially leading co-occurring species that share the same environment and predators to have a similar appearance. However, few studies have explored how these antagonistic processes influence colour at the community level. Here, we assess colour clustering and overdispersion in 189 hummingbird communities, tallying 112 species, across Ecuador and suggest possible evolutionary mechanisms at stake by controlling for species phylogenetic relatedness. In hummingbirds, most colours are iridescent structural colours, defined as colours that change with the illumination or observation angle. Because small variations in the underlying structures can have dramatic effects on the resulting colours and because iridescent structures can produce virtually any hue and brightness, we expect iridescent colours to respond finely to selective pressures. Moreover, we predict that hue angular dependence – a specific aspect of iridescent colours – may be used as an additional channel for species recognition. In our hummingbird assemblages in Ecuador, we find support for colour overdispersion in ventral and facial patches at the community level even after controlling for the phylogeny, especially on iridescence-related traits, suggesting character displacement among co-occurring species. We also find colour clustering at the community level on dorsal patches, suspected to be involved in camouflage, suggesting that the same cryptic colours are selected among co-occurring species.

This article has been peer-reviewed and recommended byPeer Community In Evolutionary Biology
Application of Volumetric Absorptive Micro Sampling to Measure Multidimensional Anti-Influenza Hemagglutinin Igg Antibodies by MPlex-Flu Assay
Authors: Wang Jiong , Li Dongme , Wiltse Alexander , Emo Jason , Hilchey Shannon P. , Zand Martin S.
Published: March 2019

Recently, volumetric absorptive microsampling (VAMS) has been used for peripheral blood sampling and analyses in several fields. VAMS ensures accurate sampling by collecting a fixed blood volume (10 or 20µL) on a volumetric swab in blood spot format, and allows for long-term sample storage. The mPlex-Flu assay is a novel, multidimensional assay that measures the concentration of antibodies against multiple influenza virus hemagglutinins simultaneously strains with a small volume of serum (less than 5µL). Here we describe combining these two methods to measure multidimensional influenza antibody activity using a finger-stick and VAMS. In this study, we compared influenza antibody profiles measured from capillary blood obtained with a finger-stick, and venous whole blood collected by traditional phlebotomy from 20 subjects using the mPlex-Flu assay. We found that results with the two sampling methods were virtually identical across all influenza strains within the same subject (mean ofR2=0.9470), and that antibodies remained stable over three weeks when VAMS samples were stored at room temperature and transported using a variety of shipping methods. Additionally, VAMS sampling is an easy and highly reproducible process; when volunteers performed finger stick VAMS at home by themselves, the results of anti-HA antibody concentrations showed that they are highly consistent with sampling performed by study personnel on-site (R2=0.9496). This novel approach provides advantages for clinical influenza vaccine studies, including ease of sampling, low cost, and high accuracy. We conclude that these methods could provide an accurate and low-cost means for monitoring the influenza virus antibody responses in large population studies.
Direction of gait asymmetry following stroke determines acute response to locomotor task
Authors: Little Virginia L , Perry Lindsay A , Mercado Mae WV , Kautz Steven A , Patten Carolynn
Published: March 2019

Background

Given the prevalence of gait dysfunction following stroke, walking recovery is a primary goal of rehabilitation. However, current gait rehabilitation approaches fail to demonstrate consistent benefits. Furthermore, asymmetry is a prominent feature of gait dysfunction following stroke. Differential patterns of gait asymmetry may respond differently to gait training parameters.

Objective

The purpose of this study was to determine whether differential responses to locomotor task condition occur on the basis of direction of step length asymmetry (Symmetrical, NPshort, Pshort) observed during overground walking.

Methods

Participants first walked overground at their self-selected walking speed. Overground data were compared against three task conditions all tested during treadmill walking: self-selected speed with 0% body weight support (TM); self-selected speed with 30% body weight support (BWS); and fastest comfortable speed with 30% body weight support and nonparetic leg guidance (GuidanceNP). Our primary outcomes were: step length, single limb support duration, and stride length.

Results

We identified differences in the response to locomotor task conditions for each step length asymmetry subgroup. GuidanceNPinduced an acute spatial symmetry only in the NPshortgroup and temporal symmetry in the Symmetrical group.

Conclusions

Task conditions consistent with locomotor training do not produce uniform effects across subpatterns of gait asymmetry. We identified differential responses to locomotor task conditions between groups with distinct asymmetry patterns, suggesting these subgroups may require unique intervention strategies. Despite group differences in asymmetry characteristics, improvements in symmetry noted in the Symmetrical and NPshortgroups were driven by changes in both the paretic and nonparetic limbs.
Genomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia
Authors: Li Yan , Pulford Caisey V. , Díaz Paula , Perez-Sepulveda Blanca M. , Duarte Carolina , Predeus Alexander V. , Wiesner Magdalena , Heavens Darren , Low Ross , Schudoma Christian , Lipscombe James , Montaño Angeline , Hall Neil , Moreno Jaime , Hinton Jay C. D.
Published: March 2019

Salmonellosis is an endemic human infection, associated with both sporadic cases and outbreaks throughout Colombia. Typhimurium is the most common Colombian serovar ofSalmonella enterica, responsible for 32.5% of theSalmonellainfections. Whole genome sequencing (WGS) is being used increasingly in Europe and the USA to study the epidemiology ofSalmonella, but there has not yet been a WGS-based analysis ofSalmonellaassociated with bloodstream infection in Colombia. Here, we analysed 209 genome sequences of ColombianS. Typhimurium and monophasicS. 4,[5],12:i:-isolates from Colombia from 1999 to 2017. We used a core genome-based maximum likelihood tree to define seven distinct clusters which were predominantly Sequence Type (ST) 19 isolates. We also identified the first ST313 and monophasic ST34 isolates to be reported in Colombia. The history of each cluster was reconstructed with a Bayesian tree to reveal a timeline of evolution. Cluster 7 was closely related to European multidrug-resistant (MDR) DT104. Cluster 4 became the dominant variant ofSalmonellain 2016, and resistance to nalidixic acid was associated with a plasmid-encodedqnrB19gene. Our findings suggest multiple transfers ofS. Typhimurium between Europe and Colombia.

Author summary

The large-scale genome sequencing ofSalmonellaTyphimurium and monophasicSalmonella4,[5],12:i:-involved bloodstream isolates from Colombia. The two serovars were responsible for about 1/3 ofSalmonellainfections in Colombia in the past 20 years. To identify the population structure we used Whole Genome Sequencing, performedin silicosequence typing, obtained phylogenetic trees, inferred the evolutionary history, detected the plasmids and prophages, and associated the antibiotic resistance (AMR) genotype with phenotype. Different clusters showed temporal replacement. The Colombian sequence type 313 was distinct from African lineages due to the absence of a key virulence-related gene,bstA. One of the Colombian clusters is likely to belong to the global epidemic of DT104, according to the evolutionary history and the AMR profile. The most common cluster in recent years was resistant to nalidixic acid and carried a plasmid-mediated antibiotic resistant geneqnrB19. Our findings will inform the ongoing efforts to combat Salmonellosis by Colombian public health departments.
Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize
Authors: Xue Wei , Anderson Sarah N. , Wang Xufeng , Yang Liyan , Crisp Peter A. , Li Qing , Noshay Jaclyn , Albert Patrice S. , Birchler James A. , Bilinski Paul , Stitzer Michelle C. , Ross-Ibarra Jeffrey , Flint-Garcia Sherry , Chen Xuemei , Springer Nathan M. , Doebley John F.
Published: March 2019

In the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1plants appear similar to typical maize x teosinte F1s. However, upon backcrossing to maize, the BC1and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. Ade novoassembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 up-regulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation and sRNAs are similar between sickly plants and normal controls, although a few up-regulated transcripts and transposable elements are associated with altered sRNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon “hybrid decay” and present ideas on the mechanism that may underlie it.
Direct visualization of native CRISPR target search in live bacteria reveals Cascade DNA surveillance mechanism
Authors: Vink Jochem N.A. , Martens Koen J.A. , Vlot Marnix , McKenzie Rebecca E. , Almendros Cristóbal , Bonilla Boris Estrada , Brocken Daan J.W. , Hohlbein Johannes , Brouns Stan J.J.
Published: March 2019

CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels have remained unknown. Here we visualized individual Cascade complexes in a native type I CRISPR-Cas system. We uncovered an exponential relationship between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA (∼30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and impact CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment.

One sentence summary

The results from in vivo tracking of single CRISPR RNA-surveillance complexes in the native host cell explain their ability to rapidly recognize invader sequences.
PamgeneAnalyzeR open and reproducible pipeline for kinase profiling
Authors: Bekkar Amel , Nasrallah Anita , Guex Nicolas , Fajas Lluis , Xenarios Ioannis , Lopez-Mejia Isabel C.
Published: March 2019

Protein phosphorylation - catalyzed by protein kinases - is the most common post-translational modification. It increases the functional diversity of the proteome and influences various aspects of normal physiology and can be altered in disease states. High throughput profiling of kinases is becoming an essential experimental approach to investigate their activity and this can be achieved using technologies such as PamChip® arrays provided by PamGene for kinase activity measurement. Here we present “pamgeneAnalyzeR”, an R package developed as an alternative to the manual steps necessary to extract the data from PamChip® peptide microarrays images in a reproducible and robust manner. The extracted data can be directly used for downstream analysis.

Availability and implementation

PamgeneAnalyzeR is implemented in R and can be obtained from https://github.com/amelbek/pamgeneAnalyzeR.
Neural correlates of object and action naming practice
Authors: Delikishkina Ekaterina , Lingnau Angelika , Miceli Gabriele
Published: March 2019

Word retrieval deficits are a common problem in patients with stroke-induced brain damage. While complete recovery of language in chronic aphasia is rare, patients’ naming ability can be significantly improved by speech therapy. A growing number of neuroimaging studies have tried to pinpoint the neural changes associated with successful outcome of naming treatment. However, the mechanisms supporting naming practice in the healthy brain have received little attention. Yet, understanding these mechanisms is crucial for teasing them apart from functional reorganization following brain damage. To address this issue, we trained a group of healthy monolingual Italian speakers on naming pictured objects and actions for ten consecutive days and scanned them before and after training. Although activity during object vs. action naming dissociated in several regions (lateral occipitotemporal, parietal and left inferior frontal cortices), training effects for the two word classes were similar and included activation decreases in classical language regions of the left hemisphere (posterior inferior frontal gyrus, anterior insula), potentially due to decreased lexical selection demands. Additionally, MVPA revealed training-related activation changes in the left parietal and temporal cortices associated with the retrieval of knowledge from episodic memory (precuneus, angular gyrus) and facilitated access to phonological word forms (posterior superior temporal sulcus).
University student engagement in learning
Authors: Lau Patricia Yin Yin , Lee Christina Kwai Choi , Ho ChyeKok
Published: March 2019

Purpose

The purpose of this paper is to explore how university fieldtrips progressively deepen student engagement, and explain that stage-by-stage using the organismic integration theory.

Design/methodology/approach

Using reflective logs, follow-up focus groups after two years and facilitator observations, this Malaysian qualitative study followed 12 business students across two three-day rainforest fieldtrips.

Findings

Students progressed toward greater – and enduring – engagement, and transferable socio-cognitive skills, via three thematic stages. Voice and self-reflection – motivated by protecting group harmony – were key, enabled by facilitator and peer encouragement.

Research limitations/implications

This exploratory study invites research in specified education cultures. Further, a longitudinal, quantitative study could be designed to examine the conceptual framework developed in Figure 1.

Practical implications

University curricula, especially in collectivist high power distance cultures, should include fieldtrips as a particularly powerful form of experiential learning. Benefits of deeper engagement extend beyond present to future courses and the workplace. Higher student attraction/retention and employability may follow. Intrinsic motivation grows through the student–instructor interaction, watching theoretical principles in action, and having eureka moments through reflection, expression and exchange of ideas.

Originality/value

The research fills a gap by mapping student engagement progressively from extrinsic to intrinsic motivation along with socio-cognitive competencies. The authors reveal the centrality of voice and reflection to promote group harmony, explain the roles of facilitators and peers and show long-lasting transferable benefits to learning. Novelly, the authors provide empirical support for existing conceptual frameworks but also extend these.
Online grocery retailing – exploring local grocers beliefs
Authors: Kureshi Sonal , Thomas Sujo
Published: March 2019

Purpose

The purpose of this paper is to understand the beliefs of local grocery retailers about online grocery retailing. Using the theory of planned behavior (TPB), the study explores the outcome, normative and control beliefs held by the local grocers about online grocery retailing which would eventually translate into behavior. Factors influencing local grocers intention to participate or refusing to participate in the online grocery retailing was investigated.

Design/methodology/approach

In total, 20 in-depth interviews with local grocery retailers were conducted ranging from small to large sized retail stores from a city in the western part of India. The sample included two groups of local grocers – first, grocers who partnered with online retailers as suppliers. This group included those retailers who had partnered but discontinued later and second, grocers who had not partnered with online retailers. In-depth interviews with the local grocery retailers were conducted using TPB as a basis to uncover local grocers’ beliefs toward online grocery retailing and predict their behavior.

Findings

The outcome beliefs were classified into five broad heads – business expansion; gaining visibility and reputation; customer expectations; inventory management; and margins, costs and technical issues. The normative belief was that the actions and response to online grocery retailing would be governed by their referent group – the consumers. The main control belief was that partnering with online grocery retailing would result in loss of control regarding their business operations.

Research limitations/implications

The results indicated that in a country like India especially in small to medium size towns, online grocery retailers would have to think of creative ways to involve the local grocery retailers to grow their business. The local grocers due to their size were able to adapt to the requirements of their referent consumers without any additional cost. They were unlikely to give up control regarding how they run their business. The main limitation of this study was the exploratory nature of this study which makes it difficult to prioritize the importance given to each belief. The study sample was restricted to one city in India, and future studies could include other cities.

Practical implications

The findings have practical implications for online grocery retailers who wish to expand into emerging markets like India. It provides understanding about the local grocery retailers who were the major competitors of online grocery retailers. It provides direction to integrate and partner with the local grocers and utilize them for mutual benefits.

Originality/value

Given the absence of academic literature in the public domain, this study provides a platform for future studies in this area. This paper is a systematic attempt to uncover the underlying beliefs of local grocery retailers who were the key players in the grocery retailing business.