bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Anatomy of the Temporal and Zygomatic Branches of the Facial Nerve: Application to Crow's Feet Wrinkles
Authors: Ye Pin , Feng Xiao-Liang , Yang Zhi-Hong , Li Guo-Ping , Sun Jun , Wu Hong-Xiang , Chen Shao-Chun 
Published: October 2020

Background:
Advances in the understanding of wrinkling crow's feet while improving the safety and efficacy of botulinum toxin type A injection has pointed to drug dispersion in the lateral orbital wrinkles as a cause of adverse events of botulinum toxin type A injection. The purpose of this study is to identify the distribution of temporal and zygomatic branches of facial nerve in the orbicularis oculi muscles.

Methods:
Anatomical dissection of cadavers was performed in 31 cadavers, 13 females and 18 males, with ages ranging from 20 to 60 years, which of all had been embalmed by 10% formalin solution. The facial nerve was identified within subcutaneous tissue close periorbital region and both traced proximal and distal. Its temporal branch, zygomatic branch, facial and muscular entrance were located and accurately measured relative to established surface landmarks.

Results:
Dissection of the facial nerve revealed 2 to 6 entrances of the temporal branch into the orbicularis oculi and 1 to 5 entrances of the zygomatic branch into the orbicularis oculi. Concerning the measurements of neural entering points, distance and angle from orbicularis oculi muscle to lateral ocular angle, a distribution map of its muscular entrance and their patterns of distribution were constructed. According to the dense area of the coordinate map, there were 3 points determined as the muscular entrance points to established surface landmarks.

Conclusions:
An anatomical dissection of cadavers was performed to identify the distribution of temporal and zygomatic branches of the facial nerve in the orbicularis oculi. According to the dense area of the coordinate map, the surface landmarks of 3 points were established as the muscular entrance of the facial nerve (MEF).
Anesthetic Exposure in Staged Versus Single-Stage Cleft Lip and Palate Repair: Can We Reduce Risk of Anesthesia-Induced Developmental Neurotoxicity?
Authors: Davila Armando A. , Holzmer Stephanie W. , Kubiak Jeremy , Martin Mark C. 
Published: October 2020

Abstract
Cleft lip and palate (CLP) repair is typically performed in a staged fashion, which requires multiple instances of anesthetic exposure during a critical period of infant neurodevelopment. One solution to this concern includes the implementation of a single-stage CLP repair performed between 6 and 12 months of age. This study aimed to compare total anesthetic exposure between single-stage and staged CLP repairs. A retrospective review of unilateral CLP repairs between 2013 and 2018 conducted at a single institution was performed. Patients underwent either traditional, staged lip and palate repair, or single-stage complete cleft repair, where palate, lip, alveolus, and nasal repair was performed simultaneously. Primary endpoints included: total surgical time and total anesthetic exposure. Secondary endpoints included: excess anesthesia time, recovery room time, length of stay, and type of anesthetic administered. Two hundred twenty-five (n = 225) unilateral CLP repairs were conducted at the Loma Linda University. Detailed anesthetic data for eighty-six (n = 86) single-stage and twenty-eight (n = 28) staged operations were available. There was a statistically significant decrease in anesthetic exposure in single-stage versus staged repairs (316 minutes versus 345 minutes, P = 0.017), despite similar procedure times (260 minutes versus 246 minutes, P = 0.224). This resulted in near double excess anesthetic exposure time in the staged group (98 minutes versus 56 minutes, P < 0.001), primarily occurring during induction. This analysis suggests that single-stage CLP repair can reduce wasted time under general anesthesia and potentially reduce harmful neuronal toxicity in the developmental period in this at-risk population.
Aesthetic Restoration of Severe Hemifacial Atrophy With Free Adipofacial Antero Lateral Thigh Flap Followed by Autologous Fat Grafting; Optimizing Result and Long-Term Outcome
Authors: Ouf Mohamed Osama , Zayid Tarek , Elbatawy Amr , Zidan Serag M. , Ismail Hany , Hamdy Abdelnaser , Sholkamy Khallad , Dahshan Hazem , Ayad Wael 
Published: October 2020

Background:
Hemifacial atrophy (Romberg disease) is characterized by progressive soft tissue and bone atrophy on 1 side of the face. The process of atrophy usually starts in the late first or early second decade of life. Romberg Patients usually require soft tissue augmentation for the correction of their defect. There are many reconstructive tools available to correct such facial asymmetry. In this study, we evaluate the outcome of the free adipofacial flap followed by autologous fat grafting in the treatment of Romberg disease, regarding aesthetics and longevity of the treatment.

Patients and Methods:
A retrospective review of 12 patients with moderate to severe hemifacial atrophy from April 2016 till March 2019. All patients received soft tissue augmentation with free adipofascial anterolateral thigh flaps, followed by autologous fat grafting 6 to 12 months later for correction of residual deformity. The average follow-up period was 18 months (range, 6–30).

Results:
There were 9 females and 3 males in this study. All flaps were survived, and the effect is long-lasting during follow-up. Patients were satisfied with the result especially after refinement of the result of free tissue transfer. The donor sites were closed directly and with no apparent morbidities nor dysfunctions.

Conclusions:
Microsurgical free tissue transfer is considered a gold standard tool in the management of moderate and severe form of hemifacial atrophy. Among different flaps available, free adipofacial anterolateral thigh flap (ALT) works as a workhorse flap in the correction of a severe form of the disease. Autologous fat grafting is a versatile and reliable option to correct residual deformities. We believed that such a combination is a superb approach to optimize the outcome of the severe form of the progressive hemifacial atrophy.
Co-Expression Networks in the Green AlgaChlamydomonas reinhardtiiEmpower Gene Discovery and Functional Exploration
Authors: Salomé Patrice A. , Merchant Sabeeha S. 
Published: October 2020

ABSTRACTThe unicellular green algaChlamydomonas reinhardtiiis a choice reference system for the study of photosynthesis, cilium assembly and function, lipid and starch metabolism and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R packagecorrplot, to easily assess co-expression and anti-correlation between genes from manually-curated and community-generated gene lists. We extracted 400 high-confidence cilia-related genes at the intersection of multiple co-expressed lists, illustrating the power of our simple method. Surprisingly, Chlamydomonas experiments did not cluster according to an obvious pattern, suggesting an underappreciated variable during sample collection. One possible source of variation may stem from the strong clustering of nuclear genes as a function of their diurnal phase, even in samples collected in constant conditions, indicating substantial residual synchronization in batch cultures. We provide a step-by-step guide into the analysis of co-expression across Chlamydomonas transcriptome datasets to help foster gene function discovery.One-sentence summarywe reveal co-expression potential between Chlamydomonas genes and describe strong synchronization of cells grown in batch cultures as a possible source of underappreciated variation.
Psychiatric morbidity and protracted symptoms in recovered COVID-19 patients
Authors: Poyraz Burç Çağrı , Poyraz Cana Aksoy , Olğun Yeşim , Gürel Özge , Alkan Sena , Özdemir Yusuf Emre , İnanç Balkan İlker , Karaali Rıdvan 
Published: October 2020

AbstractWe investigated the psychiatric symptomatology and the protracted symptoms in recently recovered COVID-19 patients. This cross-sectional study assessed 284 patients recruited from a tertiary hospital. Patients completed a web-based survey on socio-demographic data, past medical/psychiatric history, and additional information relevant to the outbreak conditions. The psychiatric status was assessed using the Impact of Events Scale-Revised (IES-R), Hospital Anxiety and Depression Scale (HADS), Pittsburgh Sleep Quality Index (PSQI), and MINI suicidality scale. Patients completed a checklist for the acute symptom burden and protracted symptoms that were experienced after the acute infection. After a mean of 50 days following the diagnosis of COVID-19, 98 patients (34.5%) reported clinically significant PTSD, anxiety, and/or depression, with PTSD being the most common condition reported (25.4%). One hundred and eighteen patients (44.3%) reported one or more protracted symptom(s), with fatigue, muscle aches, alteration of smell/taste, headache and difficulty in concentration, being the most common symptoms reported. Predictors of PTSD symptom severity were the female gender, past traumatic events, protracted symptoms, perceived stigmatization, and a negative view on the seriousness of the COVID-19 pandemic. Binary logistic regression analysis showed that PTSD symptom severity was the sole independent predictor of the presence of protracted symptoms. Our results suggest that COVID-19 patients may be prone to substantial psychological distress in the first months after the infection. The protracted symptoms were also frequent in this period, and these were related to the posttraumatic psychiatric morbidity. Both the psychiatric morbidity and the protracted symptoms were independent of the initial infection severity. Further research on the neurobiological commonalities between the protracted symptoms and PTSD in COVID-19 patients is warranted.
Gene network modeling via TopNet reveals robust epistatic interactions between functionally diverse tumor critical mediator genes
Authors: McMurray Helene R. , Ambeskovic Aslihan , Newman Laurel A. , Aldersley Jordan , Balakrishnan Vijaya , Smith Bradley , Stern Harry A. , Land Hartmut , McCall Matthew N. 
Published: October 2020

AbstractMalignant cell transformation and the underlying genomic scale reprogramming of gene expression require cooperation of multiple oncogenic mutations. Notably, this cooperation is reflected in the synergistic regulation of downstream genes, so-called cooperation response genes (CRGs). CRGs impact diverse hallmark features of cancer cells and are not known to be functionally connected. Yet, they act as critical mediators of the cancer phenotype at an unexpectedly high frequency of >50%, as indicated by genetic perturbations. Here we demonstrate that CRGs function within a network of strong genetic interdependencies that are critical to the robustness of the malignant state. Our approach, termed TopNet, utilizes attractor-based ternary network modeling that takes the novel approach of incorporating uncertainty in the underlying gene perturbation data and is capable of identifying non-linear gene interactions. TopNet reveals topological gene network architecture that effectively predicts previously unknown, functionally relevant epistatic gene interactions, and thus, among a broad range of applications, has utility for identification of non-mutant targets for cancer intervention.
RAL GTPases mediate EGFR-driven intestinal stem cell hyperproliferation and tumourigenesis
Authors: Nászai Máté , Bellec Karen , Yu Yachuan , Román-Fernández Álvaro , Sandilands Emma , Johansson Joel , Campbell Andrew D , Norman Jim C , Sansom Owen J , Bryant David M , Cordero Julia B 
Published: October 2020

SummaryRAS-like (RAL) GTPases function in Wnt signalling-dependent intestinal stem cell proliferation and regeneration. Whether RAL proteins work as canonical RAS effectors in the intestine, and the mechanisms of how they contribute to tumourigenesis remain unclear. Here, we show that RAL GTPases are necessary and sufficient to activate EGFR/MAPK signalling in the intestine, via induction of EGFR internalisation. Knocking downDrosophila RalAfrom intestinal stem and progenitor cells leads to increased levels of plasma membrane-associated EGFR and decreased MAPK pathway activation. Importantly, in addition to impacting stem cell proliferation during damage-induced intestinal regeneration, this role of RAL GTPases impacts on EGFR-dependent tumorigenic growth in the intestine and in human mammary epithelium. However, the effect of oncogenic RAS in the intestine is independent from RAL function. Altogether, our results reveal previously unrecognised cellular and molecular contexts where RAL GTPases become essential mediators of adult tissue homeostasis and malignant transformation.
Electrophysiological investigation of reward anticipation and outcome evaluation during slot machine play
Authors: Fryer SL , Roach BJ , Holroyd CB , Paulus MP , Sargent K , Boos A , Ford JM , Mathalon DH 
Published: October 2020

ABSTRACTSlot machines are a popular form of gambling, offering a tractable way to experimentally model reward processes. This study used a 3-reel slot paradigm to assess psychologically distinct phases of reward processing, reflecting anticipation, and early and late-stage outcome processing. EEG measures of winning, nearly missing (a losing outcome revealed at the final, third reel), and “totally” missing (a losing outcome revealed earlier, at the second reel) were collected from healthy adults (n=54). Condition effects were evaluated in: i) event-related potential (ERP) components reflecting anticipatory attention (stimulus preceding negativity, SPN) and outcome processing (reward positivity, RewP and late-positive potential, LPP) and ii) total power and phase synchrony of theta and delta band oscillations. Behaviorally, trial initiation was fastest after a near miss outcome and slowest after a winning outcome. As expected, a significant SPN was observed for possible wins (AA) vs. total misses (AB), consistent with reward anticipation. In addition, significantly larger win (AAA) vs. near miss (AAB) amplitudes were observed for the RewP and LPP to wins and LPP to near misses (vs. total misses) reflecting early and late-stage outcome processing effects. There was an effect of reel position on the RewP, with larger effects in the final reel (AAA-AAB) relative to the 2nd-reel locked difference waves (AA-AB). Across all outcomes, near misses elicited the largest and most phase-synchronized theta responses, while wins elicited larger and more phase-synchronized delta responses than total misses, with near misses not differing from wins or total misses. Phase locking measures contrasting win vs. near miss delta and theta synchronization, within time windows corresponding to ERP measurements, covaried with RewP, but not SPN or LPP, amplitude. Lastly, EEG measures showed differential relationships with age and self-reported consummatory pleasure. In the context of slot machine play, where reward anticipation and attainment place minimal demands on effort and skill, ERP and time-frequency methods capture distinct neurophysiological signatures of reward anticipation and outcome processing.
An agent-based model of adaptation of holobionts with different microbial symbiont transmission modes
Authors: Ye Siao , Liu Zhu , Siemann Evan 
Published: October 2020

ABSTRACTThe hologenome theory suggests that holobionts (host plus symbiont) with hosts that are only able to adapt slowly may be able to persist in deteriorating environmental conditions via rapid adaptation of their microbial symbionts. The effectiveness of such symbiont adaptation may vary depending on whether symbionts are passed directly to offspring (vertical transmission) or acquired from the environment (horizontal transmission). However, it has been suggested that holobionts with horizontal transmission cannot pass down their symbionts faithfully, preventing adaptation at the holobiont level because of host-symbiont disassociation between generations. Here we used an agent-based model to investigate whether holobionts with horizontal microbial symbiont transmission can adapt to increasing stress solely through symbiont adaptation and compared their adaptation to holobionts with vertical transmission. We found that holobionts with either transmission mode were able to adapt to increasing abiotic stress solely via symbiont adaptation. Moreover, those with horizontal transmission were more competitive than those with vertical transmission when hosts were able to selectively associate with the most suitable symbionts. However, those with horizontal transmission were less competitive than those with vertical transmission when symbiont establishment was random. Our results support the hologenome theory and demonstrate that holobionts with horizontal microbial symbiont transmission could adapt to increasing abiotic stress via their symbionts. We also showed that whether holobionts with horizontal or vertical symbiont transmission are favored in increasingly stressful conditions depends on the ability of hosts to recognize and foster microbial symbionts that confer stress tolerance.IMPORTANCESymbiotic organisms such as reef building corals are sensitive to environmental perturbations due to anthropogenic disturbances or climate change, and it is critical to understand whether they are able to adapt to previously unfavorable conditions. To date, studies have focused on the impacts of existing microbial symbiont variation on holobiont stress tolerance but here we use agent-based models to explore holobiont adaptation via symbiont adaptation. We studied both deterministic and stochastic processes in holobiont adaptation by investigating the following four factors: holobiont transmission modes, a host’s ability to recognize tolerance-conferring symbionts, a symbiont’s mutational variance, and rate of stress increase. Our simulation provides a comprehensive understanding of holobiont adaptation under stress, which not only has implications for future endangered symbiotic species management, but also provides fresh insight into species evolution as proposed by the hologenome theory.
The Extracellular Loops of OmpA Control the Slow Rate ofIn VitroFolding
Authors: Franklin Meghan W. , Stevens Jacqueline J. , Krise Joanna , Slusky Joanna S.G. 
Published: October 2020

ABSTRACTOuter membrane proteins are all beta barrels and these barrels have a variety of well-documented loop conformations. Here we test the effect of three different loop types on outer membrane protein A (OmpA) folding. We designed twelve 5-residue loops and experimentally tested the effect of replacing the long loops of outer membrane protein OmpA with the designed loops. Our studies succeeded in creating the smallest known outer membrane barrel. We find that significant changes in OmpA loops do not have a strong overall effect on OmpA folding. However, when decomposing folding into a fast rate and a slow rate we find that changes in loops strongly affect the slow rate of OmpA folding. Extracellular loop types with higher levels of hydrogen bonds had more instances of increasing the slow folding rate and extracellular loop types with low levels of hydrogen bonds had more instances of decreasing the slow folding rate. Having the slow rate affected by loop composition is consistent with the slow rate being associated with the insertion step of outer membrane protein folding.
Transcriptional landscape of PTEN loss in primary prostate cancer
Authors: Imada Eddie Luidy , Sanchez Diego Fernando , Dinalankara Wikum , Vidotto Thiago , Ebot Ericka M , Tyekucheva Svitlana , Franco Gloria Regina , Mucci Lorelei , Loda Massimo , Schaeffer Edward M , Lotan Tamara , Marchionni Luigi 
Published: October 2020

ABSTRACTPTEN is the most frequently lost tumor suppressor in primary prostate cancer (PCa) and its loss is associated with aggressive disease. However, the transcriptional changes associated with PTEN loss in PCa have not been described in detail. Here, we applied a meta-analysis approach, leveraging two large PCa cohorts with experimentally validated PTEN and ERG status, to derive a transcriptomic signature ofPTENloss, while also accounting for potential confounders due toERGrearrangements. Strikingly, the signature indicates a strong activation of both innate and adaptive immune systems uponPTENloss, as well as an expected activation of cell-cycle genes. Moreover, we made use of our recently developed FC-R2 expression atlas to expand this signature to include many non-coding RNAs recently annotated by the FANTOM consortium. With this resource, we analyzed the TCGA-PRAD cohort, creating a comprehensive transcriptomic landscape ofPTENloss in PCa that comprises both the coding and an extensive non-coding counterpart.
Automated quality control and cell identification of droplet-based single-cell data using dropkick
Authors: Heiser Cody N. , Wang Victoria M. , Chen Bob , Hughey Jacob J. , Lau Ken S. 
Published: October 2020

AbstractA major challenge for droplet-based single-cell sequencing technologies is distinguishing true cells from uninformative barcodes in datasets with disparate library sizes confounded by high technical noise (i.e. batch-specific ambient RNA). We present dropkick, a fully automated software tool for quality control and filtering of single-cell RNA sequencing (scRNA-seq) data with a focus on excluding ambient barcodes and recovering real cells bordering the quality threshold. By automatically determining dataset-specific training labels based on predictive global heuristics, dropkick learns a gene-based representation of real cells and ambient noise, calculating a cell probability score for each barcode. Using simulated and real-world scRNA-seq data, we benchmarked dropkick against a conventional thresholding approach and EmptyDrops, a popular computational method, demonstrating greater recovery of rare cell types and exclusion of empty droplets and noisy, uninformative barcodes. We show for both low and high-background datasets that dropkick’s weakly supervised model reliably learns which genes are enriched in ambient barcodes and draws a multidimensional boundary that is more robust to dataset-specific variation than existing filtering approaches. dropkick provides a fast, automated tool for reproducible cell identification from scRNA-seq data that is critical to downstream analysis and compatible with popular single-cell analysis Python packages.