bluuebunny/crossref_metadata_2025_split huggingface dataset:
The plant secondary compound swainsonine reshapes gut microbiota in plateau pikas (Ochotona curzoniae)
Authors: Ren Shien , Fan Chao , Zhang Liangzhi , Tang Xianjiang , Fu Haibo , Liu Chuanfa , Jia Shangang , Zhang Yanming 
Published: August 2021

Abstract
Plants produce various plant secondary compounds (PSCs) to deter the foraging of herbivorous mammals. However, little is known about whether PSCs can reshape gut microbiota and promote gut homeostasis of hosts. Using 16S rDNA sequencing to investigate the effects of PSCs on the gut microbiota of small herbivorous mammals, we studied plateau pikas (Ochotona curzoniae) fed diets containing swainsonine (SW) extracted from Oxytropis ochrocephala. Our results showed that both long- and short-term treatment of a single artificial diet in the laboratory significantly reduced alpha diversity and significantly affected beta diversity, core bacteria abundance, and bacterial functions in pikas. After SW was added to the artificial diet, the alpha diversity significantly increased in the long-term treatment, and core bacteria (e.g., Akkermansiaceae) with altered relative abundances in the two treatments showed no significant difference compared with pikas in the wild. The complexity of the co-occurrence network structure was reduced in the artificial diet, but it increased after SW was added in both treatments. Further, the abundances of bacteria related to altered alanine, aspartate, and glutamate metabolism in the artificial diet were restored in response to SW. SW further decreased the concentration of short-chain fatty acids (SCFAs) in both treatments. Our results suggest that PSCs play a key role in regulating gut microbiota community and intestinal homeostasis, thereby maintaining host health.

Key points
• Swainsonine improves the intestinal bacterial diversity of plateau pikas.
• Swainsonine promotes the recovery of core bacterial abundances in the gut of plateau pikas.
• Swainsonine promotes the restoration of intestinal bacterial functions of plateau pikas.
Mucoepidermoid carcinoma of the head and neck: CRTC1/3 MAML 2 translocation and its prognosticators
Authors: van Weert Stijn , Lissenberg-Witte Birgit I. , Bloemena Elisabeth , Leemans C. René 
Published: August 2021

Abstract
Purpose
Mucoepidermoid carcinoma (MEC) of the head and neck is a prevalent malignant salivary gland tumour with a reported good outcome. The aim of this study was to report the outcome in our centre.

Methods
A retrospective chart analysis with survival analyses was performed combined with fluorescence in situ hybridization (FISH) analysis to assess CRTC1/3 MAML 2 fusion gene presence.

Results
Sixty-four cases of MEC were identified. Median age at presentation was 51.4 years with a predominance for parotid gland involvement. Five, 10- and 20- year disease-free survival was 98%, 90% and 68%, respectively. Overall survival was 94%, 90% and 64%, respectively. Local recurrence was seen up to 14 years after primary diagnosis; distant metastases were diagnosed up to 17 years later. The overall recurrence rate was less than 20 per cent. CRTC1/3 MAML 2 fusion gene presence showed no survival benefit.

Conclusion
MEC of the head and neck has a favorable outcome with the exception of high-grade MEC. PNI and nodal involvement are not rare. CRTC1/3 MAML 2 fusion gene presence showed no survival benefit. The tendency for late onset of loco-regional and distant recurrence should not be underestimated.
Clinical efficacy and safety of oral and intravenous vitamin C use in patients with malignant diseases
Authors: Hoppe Catalina , Freuding Maren , Büntzel Jens , Münstedt Karsten , Hübner Jutta 
Published: August 2021

Abstract
Background
Vitamin C, also called ascorbic acid, is a water-soluble antioxidant and free radical scavenger. It is required in the body for numerous metabolic functions and is involved in the development of proteins and connective tissue.

Methods
In April 2020, a systematic search was carried out on five electronic databases (Medline, Embase, Cochrane, Cinahl, PsycINFO) to find studies on the use, efficacy and safety of a complementary therapy with vitamin C in oncological patients.

Results
Out of the initial 23,195 search results, 21 studies with 1961 patients were included in this review. Five of the included studies (n = 417) were randomized controlled trials (RCTs). The remaining 16 studies belonged to a lower class of evidence. The patients who were treated with vitamin C suffered from various malignant diseases, some in an advanced and palliative stage. Vitamin C was applied intravenously or orally. It was either the only treatment or was combined with chemo- or radiotherapy. Endpoints included the development of the disease-related symptoms, quality of life, mortality, progression-free survival and safety of vitamin C. The studies were of moderate quality and showed either no effect of vitamin C or a positive trend, although this has rarely been statistically proven in group comparisons. No or only slight side effects with both oral and intravenous administration of vitamin C were reported.

Conclusion
Oral intake of vitamin C does not appear to have any effect in patients with malignancies. Data are heterogeneous for intravenous administration. There are no RCTs with statistical group comparisons.
Development and validation of a preoperative “difficulty score” for laparoscopic transabdominal adrenalectomy: a multicenter retrospective study
Authors: Alberici Laura , Paganini Alessandro M. , Ricci Claudio , Balla Andrea , Ballarini Zeno , Ortenzi Monica , Casole Giovanni , Quaresima Silvia , Di Dalmazi Guido , Ursi Pietro , Alfano Marie Sophie , Selva Saverio , Casadei Riccardo , Ingaldi Carlo , Lezoche Giovanni , Guerrieri Mario , Minni Francesco , Tiberio Guido Alberto Massimo 
Published: August 2021

AbstractBackgroundA difficulty score for laparoscopic adrenalectomy (LA) is lacking in the literature. A retrospective cohort study was designed to develop a preoperative “difficulty score” for LA.MethodsA multicenter study was conducted involving four Italian tertiary centers for adrenal disease. The population was randomly divided into two subsets: training group and validation one. A multicenter study was undertaken, including 964 patients. Patient, adrenal lesion, surgeon’s characteristics, and the type of procedure were studied as potential predictors of target events. The operative time (pOT), conversion rate (cLA), or both were used as indicators of the difficulty in three multivariate models. All models were developed in a training cohort (70% of the sample) and validated using 30% of patients. For all models, the ability to predict complicated postoperative course was reported describing the area under the curve (AUCs). Logistic regression, reporting odds ratio (OR) withp-value, was used.ResultsIn model A, gender (OR 2.04,p = 0.001), BMI (OR 1.07,p = 0.002), previous surgery (OR 1.29,p = 0.048), site (OR 21.8,p < 0.001) and size of the lesion (OR 1.16,p = 0.002), cumulative sum of procedures (OR 0.99,p < 0.001), extended (OR 26.72,p < 0.001) or associated procedures (OR 4.32,p = 0.015) increased the pOT. In model B, ASA (OR 2.86,p = 0.001), lesion size (OR 1.20,p = 0.005), and extended resection (OR 8.85,p = 0.007) increased the cLA risk. Model C had similar results to model A. All scores obtained predicted the target events in validation cohort (OR 1.99,p < 0.001; OR 1.37,p = 0.007; OR 1.70,p < 0.001, score A, B, and C, respectively). The AUCs in predicting complications were 0.740, 0.686, and 0.763 for model A, B, and C, respectively.ConclusionA difficulty score based on both pOT and cLA (Model C) was developed using 70% of the sample. The score was validated using a second cohort. Finally, the score was tested, and its results are able to predict a complicated postoperative course.
Archaeological and Contemporary Evidence Indicates Low Sea Otter Prevalence on the Pacific Northwest Coast During the Late Holocene
Authors: Slade Erin , McKechnie Iain , Salomon Anne K. 
Published: August 2021

AbstractThe historic extirpation and subsequent recovery of sea otters (Enhydra lutris) have profoundly changed coastal social-ecological systems across the northeastern Pacific. Today, the conservation status of sea otters is informed by estimates of population carrying capacity or growth rates independent of human impacts. However, archaeological and ethnographic evidence suggests that for millennia, complex hunting and management protocols by Indigenous communities limited sea otter abundance near human settlements to reduce the negative impacts of this keystone predator on shared shellfish prey. To assess relative sea otter prevalence in the Holocene, we compared the size structure of ancient California mussels (Mytilus californianus) from six archaeological sites in two regions on the Pacific Northwest Coast, to modern California mussels at locations with and without sea otters. We also quantified modern mussel size distributions from eight locations on the Central Coast of British Columbia, Canada, varying in sea otter occupation time. Comparisons of mussel size spectra revealed that ancient mussel size distributions are consistently more similar to modern size distributions at locations with a prolonged absence of sea otters. This indicates that late Holocene sea otters were maintained well below carrying capacity near human settlements as a result of human intervention. These findings illuminate the conditions under which sea otters and humans persisted over millennia prior to the Pacific maritime fur trade and raise important questions about contemporary conservation objectives for an iconic marine mammal and the social-ecological system in which it is embedded.
Landscape Controls on Nutrient Stoichiometry Regulate Lake Primary Production at the Margin of the Greenland Ice Sheet
Authors: Prater Clay , Bullard Joanna E. , Osburn Christopher L. , Martin Sarah L. , Watts Michael J. , Anderson N. John 
Published: August 2021

AbstractGlobal change is reshaping the physical environment and altering nutrient dynamics across the Arctic. These changes can affect the structure and function of biological communities and influence important climate-related feedbacks (for example, carbon (C) sequestration) in biogeochemical processing hot spots such as lakes. To understand how these ecosystems will respond in the future, this study examined recent (< 10 y) and long-term (1000 y) shifts in autotrophic production across paraglacial environmental gradients in SW Greenland. Contemporary lake temperatures and light levels increased with distance from the ice sheet, along with dissolved organic C (DOC) concentrations and total nitrogen:total phosphorus (TN:TP) ratios. Diatom production measured as biogenic silica accumulation rates (BSiARs) and diatom contribution to microbial communities declined across these gradients, while total production estimated using C accumulation rates and δ13C increased, indicating that autochthonous production and C burial are controlled by microbial competition and competitive displacement across physiochemical gradients in the region. Diatom production was generally low across lakes prior to the 1800’s AD but has risen 1.5–3× above background levels starting between 1750 and 1880 AD. These increases predate contemporary regional warming by 115–250 years, and temperature stimulation of primary production was inconsistent with paleorecords for ~ 90% of the last millennium. Instead, primary production appeared to be more strongly related to N and P availability, which differs considerably across the region due to lake landscape position, glacial activity and degree of atmospheric nutrient deposition. These results suggest that biological responses to enhanced nutrient supply could serve as important negative feedbacks to global change.
Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models
Authors: Mondelli Marco , Thrampoulidis Christos , Venkataramanan Ramji 
Published: August 2021

AbstractWe study the problem of recovering an unknown signal $${\varvec{x}}$$

x

given measurements obtained from a generalized linear model with a Gaussian sensing matrix. Two popular solutions are based on a linear estimator $$\hat{\varvec{x}}^\mathrm{L}$$

x

^

L

and a spectral estimator $$\hat{\varvec{x}}^\mathrm{s}$$

x

^

s

. The former is a data-dependent linear combination of the columns of the measurement matrix, and its analysis is quite simple. The latter is the principal eigenvector of a data-dependent matrix, and a recent line of work has studied its performance. In this paper, we show how to optimally combine $$\hat{\varvec{x}}^\mathrm{L}$$

x

^

L

and $$\hat{\varvec{x}}^\mathrm{s}$$

x

^

s

. At the heart of our analysis is the exact characterization of the empirical joint distribution of $$({\varvec{x}}, \hat{\varvec{x}}^\mathrm{L}, \hat{\varvec{x}}^\mathrm{s})$$

(

x

,

x

^

L

,

x

^

s

)

in the high-dimensional limit. This allows us to compute the Bayes-optimal combination of $$\hat{\varvec{x}}^\mathrm{L}$$

x

^

L

and $$\hat{\varvec{x}}^\mathrm{s}$$

x

^

s

, given the limiting distribution of the signal $${\varvec{x}}$$

x

. When the distribution of the signal is Gaussian, then the Bayes-optimal combination has the form $$\theta \hat{\varvec{x}}^\mathrm{L}+\hat{\varvec{x}}^\mathrm{s}$$

θ

x

^

L

+

x

^

s

and we derive the optimal combination coefficient. In order to establish the limiting distribution of $$({\varvec{x}}, \hat{\varvec{x}}^\mathrm{L}, \hat{\varvec{x}}^\mathrm{s})$$

(

x

,

x

^

L

,

x

^

s

)

, we design and analyze an approximate message passing algorithm whose iterates give $$\hat{\varvec{x}}^\mathrm{L}$$

x

^

L

and approach $$\hat{\varvec{x}}^\mathrm{s}$$

x

^

s

. Numerical simulations demonstrate the improvement of the proposed combination with respect to the two methods considered separately.
Convergence Rates of First- and Higher-Order Dynamics for Solving Linear Ill-Posed Problems
Authors: Boţ Radu , Dong Guozhi , Elbau Peter , Scherzer Otmar 
Published: August 2021

AbstractRecently, there has been a great interest in analysing dynamical flows, where the stationary limit is the minimiser of a convex energy. Particular flows of great interest have been continuous limits of Nesterov’s algorithm and the fast iterative shrinkage-thresholding algorithm, respectively. In this paper, we approach the solutions of linear ill-posed problems by dynamical flows. Because the squared norm of the residual of a linear operator equation is a convex functional, the theoretical results from convex analysis for energy minimising flows are applicable. However, in the restricted situation of this paper they can often be significantly improved. Moreover, since we show that the proposed flows for minimising the norm of the residual of a linear operator equation are optimal regularisation methods and that they provide optimal convergence rates for the regularised solutions, the given rates can be considered the benchmarks for further studies in convex analysis.
A DICOM Framework for Machine Learning and Processing Pipelines Against Real-time Radiology Images
Authors: Kathiravelu Pradeeban , Sharma Puneet , Sharma Ashish , Banerjee Imon , Trivedi Hari , Purkayastha Saptarshi , Sinha Priyanshu , Cadrin-Chenevert Alexandre , Safdar Nabile , Gichoya Judy Wawira 
Published: August 2021

AbstractReal-time execution of machine learning (ML) pipelines on radiology images is difficult due to limited computing resources in clinical environments, whereas running them in research clusters requires efficient data transfer capabilities. We developed Niffler, an open-source Digital Imaging and Communications in Medicine (DICOM) framework that enables ML and processing pipelines in research clusters by efficiently retrieving images from the hospitals’ PACS and extracting the metadata from the images. We deployed Niffler at our institution (Emory Healthcare, the largest healthcare network in the state of Georgia) and retrieved data from 715 scanners spanning 12 sites, up to 350 GB/day continuously in real-time as a DICOM data stream over the past 2 years. We also used Niffler to retrieve images bulk on-demand based on user-provided filters to facilitate several research projects. This paper presents the architecture and three such use cases of Niffler. First, we executed an IVC filter detection and segmentation pipeline on abdominal radiographs in real-time, which was able to classify 989 test images with an accuracy of 96.0%. Second, we applied the Niffler Metadata Extractor to understand the operational efficiency of individual MRI systems based on calculated metrics. We benchmarked the accuracy of the calculated exam time windows by comparing Niffler against the Clinical Data Warehouse (CDW). Niffler accurately identified the scanners’ examination timeframes and idling times, whereas CDW falsely depicted several exam overlaps due to human errors. Third, with metadata extracted from the images by Niffler, we identified scanners with misconfigured time and reconfigured five scanners. Our evaluations highlight how Niffler enables real-time ML and processing pipelines in a research cluster.
HIV Transmission Potential and Sex Partner Concurrency: Evidence for Racial Disparities in HIV Risk Among Gay and Bisexual Men (MSM)
Authors: Tilchin Carla , Wagner Jessica , Schumacher Christina M. , Ghanem Khalil G. , Hamill Matthew M. , Rompalo Anne , Fields Errol , Latkin Carl A. , Greenbaum Adena , Jennings Jacky M. 
Published: August 2021

AbstractWe determined whether racial disparities in HIV infection among gay and bisexual men (MSM) may be partially explained by racial differences in the HIV transmission potential (i.e. mixing of people living with HIV and people not living with HIV or of unknown HIV serostatus) and density (i.e. sex partner concurrency) of sexual networks. Data included a behavioral survey, testing for HIV, and an egocentric sexual network survey. Mixed effects logistic regressions were used for hypothesis testing. Black (vs. non-Black) MSM were more likely to not know their partner’s HIV serostatus (21.8% vs. 9.6%). Similar proportions reported sex partner concurrency (67.1% vs. 68.0%). In adjusted analyses, among Black MSM, sex partner concurrency significantly increased the odds of an HIV transmission potential partnership (TPP), and this association was not significant among non-Black indexes. The association between an HIV TPP and sex partner concurrency may help explain persistent racial disparities in HIV prevalence.
Preliminary finding of a randomized, double-blind, placebo-controlled, crossover study to evaluate the safety and efficacy of 5-hydroxytryptophan on REM sleep behavior disorder in Parkinson’s disease
Authors: Meloni Mario , Figorilli Michela , Carta Manolo , Tamburrino Ludovica , Cannas Antonino , Sanna Fabrizio , Defazio Giovanni , Puligheddu Monica 
Published: August 2021

Abstract
Purpose
Altered serotonergic neurotransmission may contribute to the non-motor features commonly associated with Parkinson’s disease (PD) such as sleep disorders. The 5-hydroxytryptophan (5-HTP) is the intermediate metabolite of l-tryptophan in the production of serotonin and melatonin. The purpose of this study was to compare the effects of 5-HTP to placebo on REM sleep behavior disorder (RBD) status in patients with PD.

Methods
A single-center, randomized, double-blind placebo-controlled crossover trial was performed in a selected population of 18 patients with PD and RBD. The patients received a placebo and 50 mg of 5-HTP daily in a crossover design over a period of 4 weeks.

Results
5-HTP produced an increase in the total percentage of stage REM sleep without a related increase of RBD episodes, as well as a marginal, non-significant reduction in both arousal index and wake after sleep onset. The self-reported RBD frequency and clinical global impression (CGI) were improved during 5-HTP and placebo treatment in comparison to baseline. 5-HTP significantly improved our patients’ motor experiences of daily living as rated by the Unified Parkinson’s Disease Rating Scale (UPDRS) part II.

Conclusions
This study provides evidence that 5-HTP is safe and effective in improving sleep stability in PD, contributing to ameliorate patients’ global sleep quality. Larger studies with higher doses and longer treatment duration are needed to corroborate these preliminary findings.
Creating a Composite Index to Target Recruitment of UK Students from Areas of Low Participation in Higher Education
Authors: Bell Douglas , Burns Luke 
Published: August 2021

AbstractThis research presents a framework through which a new Higher Education Access and Deprivation (HEAD) composite index was created to assist UK universities in efficiently recruiting and supporting students from areas with traditionally low engagement rates in higher education. The index was designed to be easily adaptable by university staff to suit their own work priorities and/or an institution’s strategic requirements by utilising open socio-demographic data and construction techniques that require minimal technical statistical skills. Although Cornwall was used as the study area in this research, this index has been designed such that it can be readily applied elsewhere. Two differently weighted models were created using the framework – one with equal weights and the other based on the frequency the constituent indicators appeared in the reviewed academic literature. Both models were mapped across Cornwall, identifying areas of deprivation at a finer resolution than under the current widely used Participation of Local Areas (POLAR) methodology. The weighted model performed marginally better than both the equal weighted model and the current POLAR methodology when validated against external data, and additionally it worked well in both rural and urban environments leading to it being selected as the new HEAD index. The HEAD index maps smaller scale areas of deprivation than previously available, and by enabling users to investigate the underlying socio-demographic characteristics of an area, it also allows universities to create interventions, support, and policies that best targets the students they aim to recruit and teach.
A High Throughput Method for Generating Dihaploids from Tetraploid Potato
Authors: Busse James S. , Jansky Shelley H. , Agha Husain I. , Schmitz Carley Cari A. , Shannon Laura M. , Bethke Paul C. 
Published: August 2021

AbstractThere is a worldwide effort to increase the efficiency of potato (Solanum tuberosum L.) cultivar development by using inbred diploid breeding lines. This activity is impeded by the cost and effort required to produce dihaploids from cultivated tetraploid potatoes. We developed a high throughput dihaploid production method based on the 60-year-old method of Peloquin and Hougas. Red Norland inflorescences from commercial fields were transferred to greenhouses. As buds developed, pollen from the dihaploid inducer IVP 101 was applied systematically to thousands of stigmas per trial. Berries were harvested 21 days after pollination. Seeds of putative dihaploids lacking a seed spot marker were retained and ploidy was confirmed using flow cytometry. We recovered 23 dihaploids from 21,651 pollinations. This is a promising method for systematically carrying out thousands of pollinations since the cost of field-grown flowers is dramatically less than that of greenhouse-grown flowers.