bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Image Fusion Technique for Cochlear Implant Imaging: A Study of its Application for Different Electrode Arrays
Authors: Sipari Sini , Iso-Mustajärvi Matti , Könönen Mervi , Löppönen Heikki , Dietz Aarno 
Published: December 2019

Objectives:
To investigate the benefits of the image fusion technique for precise postoperative assessment of intracochlear placement with six different electrode arrays.

Study Design:
Consecutive retrospective case study.

Settings:
Tertiary referral center.

Patients:
Analyses of imaging data of 30 patients implanted with six different electrode arrays.

Interventions:
Electrode reconstructions obtained from postoperative cone-beam computed tomography (CBCT) were overlaid onto preoperative magnetic resonance imaging (MRI) and/or high-resolution computed tomography (HRCT) registrations to create artefact-free images.

Main Outcome Measures:
Each electrode's intracochlear position was analyzed with the image fusion reconstructions and compared with the results obtained by CBCT alone. The electrode location was classified according to its position in relation to the basal membrane at four different insertion angles.

Results:
In 40 out of 151 measurements (26.5%), the location grading obtained by CBCT alone changed after the assessment with the image fusion reconstructions. A significant association was found between deep insertions (over 360 degrees) and the effectiveness of image fusion (p = 0.019). The difference between the impact of the fusion technique for the basal turn versus the apical part was highly significant (p = 0.001). There was no significant difference between the effectiveness of the image fusion and the different electrodes.

Conclusions:
By utilizing an image fusion technique, a more accurate assessment of electrode placement could be achieved for all types of electrodes. Image fusion was especially beneficial for insertions beyond 360 degrees.
Transplantation in older individuals: is it really better than dialysis?
Authors: Hellemans Rachel , Jager Kitty J. , Abramowicz Daniel 
Published: December 2019

Purpose of review
The kidney transplantation landscape has changed dramatically over the last 2 decades. First, transplantation is performed in patients previously considered ineligible for transplantation, including older patients and patients with multiple comorbidities. Second, organ shortages have increased the use of less-than-optimal donor kidneys, like organs from expanded criteria donors or donors after cardiac death. Third, improvements in managing chronic kidney disease and dialysis have improved survival on dialysis. Therefore, the question arises: does transplantation currently benefit older transplant candidates?

Recent findings
The current review describes important changes in transplantation over the last 20 years. We review recent data on survival with dialysis versus transplantation in older individuals. Finally, we consider methodological issues that might influence conclusions drawn in current studies.

Summary
Limited data are available to assess the potential survival benefit of kidney transplantations in older individuals. The available evidence suggests that transplantation might provide survival benefit in older individuals, even with aged kidney donors, but risks vary widely with donor quality and recipient health status. More research is needed to make adequate predictions of which donor kidneys might lead to good outcomes and which patient characteristics might define a good transplant candidate.
Genetic analysis of functional rare germline variants across 9 cancer types from the DiscovEHR study
Authors: Shivakumar Manu , Miller Jason E. , Dasari Venkata Ramesh , Carey David , Gogoi Radhika , Kim Dokyoon 
Published: December 2019

AbstractRare variants play an essential role in the etiology of cancer and characterizing rare germline variants that impact the risk of cancer is an ongoing challenge. We performed a genome-wide rare variant analysis using germline whole exome sequencing (WES) data derived from the Geisinger MyCode initiative to discover cancer predisposition variants. The case-control association analysis was conducted by binning pathogenic and likely pathogenic variants in 5,538 cancer patients and 7,286 matched controls in a discovery set and 1,991 cancer patients and 2,504 matched controls in a validation set across nine cancer types. We discovered 87 genes and 106 pathways significantly associated with cancer (Bonferroni-corrected P< 0.05) out of which seven genes and 26 pathways replicated from the validation set (suggestive threshold P< 0.05). Further, four genes and 21 pathways were discovered to be associated with multiple cancers (Bonferroni-corrected P< 0.05). Additionally, we identified 13 genes and two pathways associated with survival outcome across seven cancers (Bonferroni-corrected P< 0.05), where two genes,PCDHB8andDCHS2, were also associated with survival outcome in TCGA data. In summary, we conducted one of the largest pan-cancer association studies using germline data derived from a single hospital system to find novel predisposition genes and pathways associated with nine cancers. Our results can inform future guidelines for germline genetic testing in cancer, which will be helpful in screening for cancer high-risk patients. This work adds to the knowledge base and progress being made in precision medicine.
The genetic basis of sex determination in grapevines (Vitis spp.)
Authors: Massonnet Mélanie , Cochetel Noé , Minio Andrea , Vondras Amanda M. , Muyle Aline , Lin Jerry , Garcia Jadran F. , Zhou Yongfeng , Delledonne Massimo , Riaz Summaira , Figueroa-Balderas Rosa , Gaut Brandon S. , Cantu Dario 
Published: December 2019

AbstractSex determination in grapevine evolved through a complex succession of switches in sexual systems. Phased genomes built with single molecule real-time sequencing reads were assembled for eleven accessions of cultivated hermaphrodite grapevines and dioecious males and females, including the ancestor of domesticated grapevine and other related wild species. By comparing the phased sex haplotypes, we defined the sex locus of theVitisgenus and identified polymorphisms spanning regulatory and coding sequences that are in perfect association with each sex-type throughout the genus. These findings identified a novel male-fertility candidate gene,INP1, and significantly refined the model of sex determination inVitisand its evolution.
Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential
Authors: Rabanus-Wallace M. Timothy , Hackauf Bernd , Mascher Martin , Lux Thomas , Wicker Thomas , Gundlach Heidrun , Báez Mariana , Houben Andreas , Mayer Klaus F.X. , Guo Liangliang , Poland Jesse , Pozniak Curtis J. , Walkowiak Sean , Melonek Joanna , Praz Coraline , Schreiber Mona , Budak Hikmet , Heuberger Matthias , Steuernagel Burkhard , Wulff Brande , Börner Andreas , Byrns Brook , Čížková Jana , Fowler D. Brian , Fritz Allan , Himmelbach Axel , Kaithakottil Gemy , Keilwagen Jens , Keller Beat , Konkin David , Larsen Jamie , Li Qiang , Myśków Beata , Padmarasu Sudharsan , Rawat Nidhi , Sesiz Uğur , Sezgi Biyiklioglu , Sharpe Andy , Šimková Hana , Small Ian , Swarbreck David , Toegelová Helena , Tsvetkova Natalia , Voylokov Anatoly V. , Vrána Jan , Bauer Eva , Bolibok-Bragoszewska Hanna , Doležel Jaroslav , Hall Anthony , Jia Jizeng , Korzun Viktor , Laroche André , Ma Xue-Feng , Ordon Frank , Özkan Hakan , Rakoczy-Trojanowska Monika , Scholz Uwe , Schulman Alan H. , Siekmann Dörthe , Stojałowski Stefan , Tiwari Vijay , Spannagl Manuel , Stein Nils 
Published: December 2019

AbstractWe present a chromosome-scale annotated assembly of the rye (Secale cerealeL. inbred line ‘Lo7’) genome, which we use to explore Triticeae genomic evolution, and rye’s superior disease and stress tolerance. The rye genome shares chromosome-level organization with other Triticeae cereals, but exhibits unique retrotransposon dynamics and structural features. Crop improvement in rye, as well as in wheat and triticale, will profit from investigations of rye gene families implicated in pathogen resistance, low temperature tolerance, and fertility control systems for hybrid breeding. We show that rye introgressions in wheat breeding panels can be characterised in high-throughput to predict the yield effects and trade-offs of rye chromatin.
Targeting the Long Non-Coding RNA LINC00599-205 splicing by novel candidate drug ABX464 to produce the anti-inflammatory microRNA miR-124
Authors: Manchon Laurent , Vautrin Audrey , Tazi Jamal , Garcel Aude , Campos Noelie 
Published: December 2019

AbstractMany nascent long non-coding RNAs have received considerable attention in recent years because of their major regulatory roles in gene expression and signaling pathways at various levels. Indeed long non-coding RNAs undergo the same maturation steps as pre-mRNAs of proteincoding genes, but they are less efficiently spliced and polyadenylated in comparison to them. Here we focus on a specific human long non-coding RNA and we show the activity of a new candidate drug that potentially affect its splicing and generate an anti-HIV and anti-inflammatory effects driven by upregulation of microRNA biogenesis. To investigate this activity we combine the use of capture sequencing technology and anab initiotranscript assembly on cells from six healthy individuals. The sequencing depth of capture sequencing permitted us to assemble transcripts exhibiting a complex array of splicing patterns. In essence, we revealed that splicing of the long non-coding RNA is activated by the drug whereas this splicing was not present in untreated samples.
Early sexual dimorphism in the developing gut microbiome of northern elephant seals
Authors: Stoffel M.A. , Acevedo-Whitehouse K. , Morales-Durán Nami , Grosser S. , Chakarov. N. , Krüger O. , Nichols H.J. , Elorriaga-Verplancken F.R. , Hoffman J.I. 
Published: December 2019

AbstractThe gut microbiome is an integral part of a species’ ecology, but we know little about how host characteristics impact its development in wild populations. Here, we explored the role of such intrinsic factors in shaping the gut microbiome of northern elephant seals during a critical developmental window of six weeks after weaning, when the pups stay ashore without feeding. We show that the early-life gut microbiome is already substantially different in male and female pups, even though males and females cannot yet be distinguished morphologically. Sex and age both explain around 15% of the variation in gut microbial beta diversity, while microbial communities sampled from the same individual show high levels of similarity across time, explaining another 40% of the variation. Only a small proportion of the variation in beta diversity is explained by health status, but healthy individuals have a greater microbial alpha diversity than their non-healthy peers. Across the post-weaning period, the elephant seal gut microbiome is highly dynamic. We found evidence for several colonisation and extinction events as well as a decline inBacteriodesand an increase inPrevotella, a pattern that has previously been associated with the transition from nursing to solid food. Lastly, we show that genetic relatedness is correlated with gut microbiome similarity in males but not females, again reflecting substantial early sex-differences. Our study represents a naturally diet-controlled and longitudinal investigation of how intrinsic factors shape the early gut microbiome in a species with extreme sex differences in morphology and life history.
Predicting Geographic Location from Genetic Variation with Deep Neural Networks
Authors: Battey C.J. , Ralph Peter L. , Kern Andrew D. 
Published: December 2019

AbstractMost organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of known geographic origin. Here we describe a deep learning method, which we callLocator, to accomplish this task faster and more accurately than existing approaches. In simulations,Locatorinfers sample location to within 4.1 generations of dispersal and runs at least an order of magnitude faster than a recent model-based approach. We leverageLocator’s computational efficiency to predict locations separately in windows across the genome, which allows us to both quantify uncertainty and describe the mosaic ancestry and patterns of geographic mixing that characterize many populations. Applied to whole-genome sequence data fromPlasmodiumparasites,Anophelesmosquitoes, and global human populations, this approach yields median test errors of 16.9km, 5.7km, and 85km, respectively.
Tracking attention in a visual active paradigm for the diagnosis of disorders of consciousness
Authors: Lesenfants Damien , Chatelle Camille , Laureys Steven , Noirhomme Quentin 
Published: December 2019

AbstractBackgroundClinical assessment of patients with disorders of consciousness (DOC) relies on the clinician’s ability to detect a behavioral response to an instruction (e.g., “squeeze my hand”). However, recent studies have shown that some of these patients can produce volitional brain responses to command while no behavioral response is present. This highlights the importance of developing motor-independent diagnostic tool for this population, complementing standardized behavioral evaluation. We here evaluate the ability of a novel gaze-independent attention-based EEG paradigm to detect volitional attentional processes in patients with disorders of consciousness.MethodsThirty patients with DOC were included in the study: 12 with an unresponsive wakefulness syndrome, 16 in a minimally conscious state (MCS), two who emerged from a MCS. Patients were randomly instructed to either concentrate on a task or rest while brain activity was recorded using EEG during a gaze-independent paradigm.ResultsOne of two EMCS, one of 16 MCS and one of 12 UWS patients showed a response to command using the attention task. Interestingly, this method could detect a brain-based response to command in one MCS patient who did not present a behavioral response to command at the bedside the day of the assessment.ConclusionThis study show that task-related variation of attention during an active task could help to objectively detect response to command in patients with DOC.
Reward value revealed by auction in rhesus monkeys
Authors: Al-Mohammad Alaa , Schultz Wolfram 
Published: December 2019

AbstractEconomic choice is thought to involve the elicitation of the subjective values of the choice options. Thus far, value estimation in animals has relied upon stochastic choices between multiple options presented in repeated trials and expressed from averages of dozens of trials. However, subjective reward valuations are made moment-to-moment and do not always require alternative options; their consequences are usually felt immediately. Here we describe a Becker-DeGroot-Marschak (BDM) auction-like mechanism that provides more direct and simple valuations with immediate consequences. The BDM encourages agents to truthfully reveal their true subjective value in individual choices (’incentive compatibility’). Monkeys reliably placed well-ranked BDM bids for up to five juice volumes while paying from a water budget. The bids closely approximated the average subjective values estimated with conventional binary choices, thus demonstrating procedural invariance and aligning with the wealth of knowledge acquired with these less direct estimation methods. The feasibility of BDM bidding in monkeys paves the way for an analysis of subjective neuronal value signals in single trials rather than from averages; the feasibility also bridges the gap to the increasingly used BDM method in human neuroeconomics.SignificanceThe subjective economic value of rewards cannot be measured directly but must be inferred from observable behavior. Until now, the estimation method in animals was rather complex and required comparison between several choice options during repeated choices; thus, such methods did not respect the imminence of the outcome from individual choices. However, human economic research has developed a simple auction-like procedure that can reveal in a direct and immediate manner the true subjective value in individual choices (Becker-DeGroot-Marschak, BDM, mechanism). The current study implemented this mechanism in rhesus monkeys and demonstrates its usefulness for eliciting meaningful value estimates of liquid rewards. The mechanism allows future neurophysiological assessment of subjective reward value signals in single trials of controlled animal tasks.
Combined salinity and acidity stressors alterDaphnia magnapopulation growth and structure under severe absence of photoperiod
Authors: Khudr Mouhammad Shadi , Purkiss Samuel Alexander , Hager Reinmar 
Published: December 2019

AbstractAlthough natural and anthropogenic influences affect freshwater ecosystems globally at unprecedented levels, the effects of co-occurring physico-chemical stress on zooplankton phenotypic plasticity under extreme conditions remain understudied.We exposed a laboratory-raised clonal population ofDaphnia magnato different stress levels of acidity and salinity undergoing complete constant light over 30 days. Overall, population size and age structure at day 10 considerably differed between specific stress contexts. All populations expanded compared to the starting population on day 1. On day 30, overall, population size increased but showed significant differences between treatment groups. Surprisingly,Daphniaperformed better under combined stress of salinity and acidity than under acidity alone as the extra salinity in the medium may have counterbalanced sodium loss caused by lower pH. Our results reveal a considerable degree of differential reproductive and ontogenetic plasticity in response to combined stressors under disrupted photoperiod. Exposure to constant light led to increased population size, which may be a result of supercharged ion regulation that enables zooplankton to survive better under specific levels of extreme environmental change and adverse chemical stress. Our findings merit further molecular investigation of phenotypic plasticity of the congeners across severe combined stress conditions.
The effect of left fronto-parietal resections on hand selection: a lesion-tractography study
Authors: Howells Henrietta , Puglisi Guglielmo , Leonetti Antonella , Vigano Luca , Fornia Luca , Simone Luciano , Forkel Stephanie J. , Rossi Marco , Riva Marco , Cerri Gabriella , Bello Lorenzo 
Published: December 2019

AbstractStrong right-hand preference on the population level is a uniquely human feature, although the neural basis for this is still not clearly defined. Recent behavioural and neuroimaging literature suggests that hand preference may be related to the orchestrated function and size of fronto-parietal white matter tracts bilaterally. Lesions to these tracts induced during tumour resection may provide an opportunity to test this hypothesis. In the present study, a cohort of seventeen neurosurgical patients with left hemisphere brain tumours were recruited to investigate whether resection of certain white matter tracts affects the choice of hand selected for the execution of a goal-directed task (assembly of jigsaw puzzles). Patients performed the puzzles, but also tests for basic motor ability, selective attention and visuo-constructional ability, preoperatively and one month after surgery. Diffusion tractography of fronto-parietal tracts (the superior longitudinal fasciculus) and the corticospinal tract were performed, to evaluate whether resection of tracts was significantly associated with changes in hand selection. A complementary atlas-based disconnectome analysis was also conducted. Results showed a shift in hand selection despite the absence of any motor or cognitive deficits, which was significantly associated with patients with frontal and parietal resections, compared with those with resections in other lobes. In particular, this effect was significantly associated with the resection of dorsal fronto-parietal white matter connections, but not with the ventral fronto-parietal tract. Dorsal white matter pathways contribute bilaterally, with specific lateralised competencies, to control of goal-directed hand movements. We show that unilateral lesions, by unbalancing the cooperation of the two hemispheres, can alter the choice of hand selected to accomplish movements.
Lactobacillus reuteri: direct passage from ingested yogurts to urine microbiota
Authors: Lagier Jean-Christophe , Mekhalif Fatima , Merhej Vicky , Chaudet Hervé , Delerce Jérémy , Levasseur Anthony , Raoult Didier 
Published: December 2019

AbstractBackgroundSerendipitously, it was observed that fecal transplantation made forClostridium difficilemay cure chronic urinary tract infections. This led us to evaluate the passage in the urine of probiotics contained in yoghurt, which have been claimed to prevent urinary infections.ResultsA commercial yogurt that contained 3 probiotics (Bifidobacterium animalis, Lactobacillus delbrueckiiiandLactobacillus reuteri) was consumed by 28 healthy subjects. We performed by culturomics, urine analysis before and after feeding these yogurts. Genome sequencing of the bacterial strains absent before yogurt consumption and present after consumption was performed. Testing more than 40,000 colonies by MALDI-TOF, we observed in two men and one woman (11% of subjects included), the urine colonization of the sameLactobacillus reuteripresent in yogurts, with the same genome with 50 genes never identified in other lactobacilli.ConclusionThis confirms that, as ingested,Lactobacillus salivariuspasses into the milk of lactating women, some bacteria, particularlyLactobacilluscan colonize body fluids previously considered sterile after ingestion via the digestive route. Although the consequences of this passage remain unknown, we prove for the first time that there is a digestive passage in the urine after consumption of probiotics, including fermented products sold commercially.
Helping those who help others for indirect fitness benefits not indirect reciprocity
Authors: Roberts Gilbert 
Published: December 2019

AbstractHelping those who help others appears to be a widespread phenomenon. It is typically framed as indirect reciprocity in which individuals who are seen to help later receive returns from third parties. However, indirect reciprocity only works when individuals condition their help not just on how their recipient has behaved in the past but also on whether their recipient was justified in behaving that way. It also requires sufficient repeated interactions of this type among other individuals for a benefit to be reciprocated. These factors limit the scope of indirect reciprocity to explain cases where people do help those who help others. Here, I propose instead that helping can be explained by the indirect fitness benefits (or ‘relatedness’) that result from helping other helpers in groups. This means that when individuals help other helpers, they may not make any returns via indirect reciprocity, but rather they may be helping a strategy of helping those who help. In this way, the helping strategy can spread even when helping has no net benefit to the individual helper. This is a form of relatedness in which individuals help their kin that are recognized by their helping behaviour. As such, conditional helping is likely to be found where population structure promotes relatedness through non-random association. The analysis suggests indirect reciprocity may not have played the decisive role in the evolution of human cooperation that is often thought, but paradoxically that the use of image scores deserves renewed attention as a strategy of helping those with the same behaviour.