bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biphenotypic Differentiation of Pancreatic Cancer in 3-Dimensional Culture
Authors: Matsushita Yoshihisa , Smith Barbara , Delannoy Michael , Trujillo Maria A. , Chianchiano Peter , McMillan Ross , Kamiyama Hirohiko , Liang Hong , Thompson Elizabeth D. , Hruban Ralph H. , Matsui William , Wood Laura D. , Roberts Nicholas J. , Eshleman James R. 
Published: October 2019

Objective
Pancreatic ductal adenocarcinoma (PDAC) is the third most common cause of cancer death in the United States. Improved characterized models of PDAC are needed for drug screening.

Methods
We grew 4 established pancreatic cancer cell lines in hanging drop cultures to produce spheroids. We also grew organoids from explanted xenografted PDAC and surgically resected primary PDAC. We performed transmission and scanning electron microscopy and compared findings with those of the normal pancreatic duct. We also performed single-cell cloning to determine the potential options for differentiation.

Results
Spheroids contained tight junctions and desmosomes but lacked zymogen granules, as expected. The former features were present in normal pancreatic duct but absent from PDAC cell lines grown in standard 2-dimensional culture. Spheroids functionally excluded macromolecules in whole mounts. Cells on the surface of PDAC spheroids were carpeted by microvilli except for rare cells with prominent stereocilia. Carpets of microvilli were also seen in low passage organoids produced from xenografts and surgically resected human PDAC, in addition to normal human pancreatic duct. We performed single-cell cloning and resulting spheroids produced both cell phenotypes at the same approximate ratios as those from bulk cultures.

Conclusions
Pancreatic cancer spheroids/organoids are capable of biphenotypic differentiation.
Case Series: Slight Intraocular Lens Malpositioning as a Potential Cause of Vision Loss
Authors: Rong Xianfang , Miao Ao , Yu Jifeng , Du Yu , He Wenwen , Lu Yi , Zhu Xiangjia 
Published: October 2019

SIGNIFICANCE
The cases illustrate an insidious cause of decreased visual acuity after cataract surgery.

PURPOSE
The purpose of this study was to identify cases of postoperative vision loss caused by slight intraocular lens (IOL) malpositioning after cataract surgery.

CASE REPORTS
Three patients presented with visual acuity decreased after cataract surgery. Silt-lamp examination before mydriasis revealed no abnormalities in two of the patients; mild IOL inferonasal decentration was found by the trifocal IOL diffraction ring in the third patient. Manifest refraction of these patients showed remarkable astigmatism with low corneal astigmatism. After pupil dilation, slight IOL decentration and tilt were observed in all patients, which were further confirmed using the Scheimpflug imaging system. Wavefront aberrometry showed a high level of ocular higher-order aberrations, most of which were derived from intraocular aberrations.

CONCLUSIONS
Inconspicuous IOL malpositioning is one of the reasons responsible for decreased vision acuity after cataract surgery, which may not be easily identified by slit-lamp examination. High astigmatism and ocular higher-order aberrations derived from malpositioned IOL can be important clues.
Does a Hand Strength–Focused Exercise Program Improve Grip Strength in Older Patients With Wrist Fractures Managed Nonoperatively?
Authors: Nguyen Antony , Vather Mehr , Bal Gobind , Meaney Donna , White Megan , Kwa Myles , Sungaran Jai 
Published: October 2019

Objective
Distal radius fractures in the older population significantly impair grip strength. The aim of the study was to investigate whether a hand strength focused exercise program during the period of immobilization for nonoperatively managed distal radius fractures in this population improved grip strength and quality of life.

Design
This is a single-center randomized controlled trial with concealed allocation, assessor blinding, and intention-to-treat analysis. Fifty-two patients older than 60 yrs who experienced distal radius fractures managed nonoperatively with cast immobilization. The intervention group (n = 26) received a home hand strength–focused exercise program from 2 and 6 wks after injury while immobilized in a full short arm cast. The control group (n = 26) performed finger range of motion exercises as per protocol. Primary outcome was grip strength ratio of injured arm compared with uninjured arm. Secondary outcome included functional scores of the 11-item shortened version of the Disabilities of the Arm, Shoulder and Hand. Outcomes were measured at 2, 6, and 12 wks after injury.

Results
The intervention group significantly improved grip strength ratio at both 6 and 12 wks (6 wks: 40% vs 25%, P = 0.0044, and 12 wks: 81% vs 51%, P = 0.0035). The intervention group improved the 11-item Disabilities of the Arm, Shoulder and Hand score at 12 wks; however, this was not statistically significant (25 vs 40, P = 0.066).

Conclusions
A hand strength–focused exercise program for elderly patients with distal radius fractures while immobilized significantly improved grip strength.
Arm Subscore of Motricity Index to Predict Recovery of Upper Limb Dexterity in Patients With Acute Ischemic Stroke
Authors: Malmut Laura , Lin Chen , Srdanovic Nina , Kocherginsky Masha , Harvey Richard L. , Prabhakaran Shyam 
Published: October 2019

Objective
The aim of this study was to determine whether the arm subscore of the Motricity Index 1 wk after stroke can predict recovery of upper limb function according to the Action Research Arm Test before inpatient rehabilitation facility discharge and at 3-mo outpatient follow-up.

Design
This was a prospective cohort study of patients with acute ischemic stroke admitted to a single acute care hospital and affiliated inpatient rehabilitation facility between 2016 and 2018. Upper limb dexterity of the impaired limb was assessed using the arm subscore of the Motricity Index and Action Research Arm Test. Receiver operating characteristic curve analysis was used to determine optimal cutoffs of the initial arm subscore of the Motricity Index for a good functional outcome defined as Action Research Arm Test score of 45 or higher.

Results
Ninety-five patients were evaluated at median 6, 26, and 98.5 days after stroke. The median (interquartile range) arm subscore of the Motricity Index at 1 wk was 77 (20.3–93). The median (interquartile range) Action Research Arm Test scores before inpatient rehabilitation facility discharge and at 3-mo outpatient follow-up were 33 (3.5–52) and 52 (34–55.8), respectively. The optimal arm subscore of the Motricity Index to predict Action Research Arm Test score of 45 or higher before inpatient rehabilitation facility discharge and at 3-mo outpatient follow-up were 71 and 58, respectively.

Conclusions
Early arm subscore of the Motricity Index at 1 wk predicts upper limb functional capacity before inpatient rehabilitation facility discharge and at 3-mo outpatient follow-up.
Comparison of Hamra's and Mendelson's Models of Midface Lift
Authors: Choi Jeongho , Hwang Kun 
Published: October 2019

Abstract
The aim of this study was to compare Hamra's and Mendelson's models of midface lift.
The terms “Hamra ST” and “Mendelson BC” were used to search PubMed, yielding 35 and 48 papers, respectively. Of the 83 abstracts, 55 were excluded and 28 full papers discussing midface lift were reviewed. Among those 28 papers, 13 were excluded because they did not have sufficient content. Among the 15 full texts, 5 mined papers were added. Thereafter, 20 papers were analyzed.
Hamra's description of his surgical technique changed twice. In 1990 (The Deep-Plane Rhytidectomy), he wrote that he performed Skoog-type subsuperficial muscular aponeurotic system (SMAS) dissection to the nasolabial fold. In 1992 (Composite Rhytidectomy), however, he cited a paper insisting that the SMAS does not exist in the cheek area. He wrote that his deep-plane rhytidectomy was not a sub-SMAS procedure, stating that he dissected the cheek fat that is attached to the zygomaticus major, then repositioned the skin. This was a substantially different explanation of the dissection plane. In 1997, he stated that instead of dividing the orbicularis oculi muscle from the zygomaticus major and minor, he elevated them together in a flap. Thus, his method returned to the sub-SMAS plane. Mendelson introduced the concepts of the prezygomatic space, orbicularis-retaining ligament, and zygomatic-retaining ligament, and proposed an anatomical model.
If the authors explain Hamra's zygorbicular dissection using Mendelson's model, the dissection starts just beneath the roof of the prezygomatic space, traverses the floor, and then releases the zygomatic ligament (lower boundary of the space). The authors should consider the necessity and riskiness of this release.
Integrative modelling of the full-length human dehydrodolichyl diphosphate synthase using a hybrid computational and experimental approach
Authors: Barel Michal Lisnyansky , Lee Su Youn , Ki Ah Young , Kapelushnik Noa , Loewenstein Anat , Chung Ka Young , Schneidman-Duhovny Dina , Giladi Moshe , Newman Hadas , Haitin Yoni 
Published: October 2019

AbstractDehydrodolichyl diphosphate synthase (DHDDS) and Nogo-B receptor (NgBR) form the heteromeric human cis-prenyltransferase complex, synthesizing the precursor for the glycosyl carrier involved in N-linked protein glycosylation. In line with the important role of N-glycosylation in protein biogenesis, mutations in DHDDS, the catalytic subunit of the complex, were shown to result in human diseases. Importantly, well-characterized DHDDS homologs function as homodimers and not as heteromeric complexes. Moreover, DHDDS encompasses a C-terminal region, which does not converge with any known conserved domains. Therefore, despite the clinical importance of DHDDS, our understating of its structure-function relations remains poor. Here, we provide a structural model for the full-length human DHDDS using a multidisciplinary experimental and computational approach. Our model suggests that the C-terminal domain of DHDDS forms a helix-loop-helix motif, tightly packed against the core catalytic cis-prenyltransferase domain. This model is consistent with small-angle X-ray scattering data, indicating that the full-length DHDDS maintains a similar conformation in solution. Moreover, hydrogen-deuterium exchange mass-spectrometry experiments show time-dependent deuterium uptake in the C-terminal domain, consistent with its overall folded state. Finally, we provide a model for the DHDDS-NgBR heterodimer, offering a structural framework for future structural and functional studies of the human cis-prenyltransferase complex.
MetaSanity: An integrated, customizable microbial genome evaluation and annotation pipeline
Authors: Neely Christopher J , Graham Elaina D , Tully Benjamin J 
Published: October 2019

AbstractSummaryAs the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g., marine, built, host-associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity incorporates analyses from eleven existing and widely used genome evaluation and annotation suites into a single, distributable workflow, thereby decreasing the workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. MetaSanity has been designed to provide separate, reproducible workflows, that (1) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (2) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function and putative extracellular localization of peptidases and carbohydrate-active enzymes. Importantly, this software provides built-in optimization for “big data” analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research.Availability and implementationMetaSanity is provided under the GNU General Public License v.3.0 and is available for download at https://github.com/cjneely10/MetaSanity. This application is distributed as a Docker image. MetaSanity is implemented in Python3/Cython and C++.Supplementary informationSupplementary data are available below.
Epigenetic contributions to hemisphere asymmetry in healthy brain, aging, and Parkinson’s disease
Authors: Li Peipei , Ensink Elizabeth , Lang Sean , Marshall Lee , Schilthuis Meghan , Lamp Jared , Vega Irving , Labrie Viviane 
Published: October 2019

AbstractHemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson’s disease (PD), but its molecular determinants are unknown. Here, we determine epigenetic differences involved in hemispheric asymmetry in the healthy and the PD brain. Neurons of the healthy brain exhibit numerous hemispheric differences in DNA methylation, which affect genes implicated in neurodegenerative diseases. In PD patients, hemispheric asymmetry in DNA methylation is even greater and involves many PD risk genes. The lateralization of clinical PD symptoms involves epigenetic, transcriptional, and proteomic differences across hemispheres that affect neurodevelopment, immune activation, and synaptic transmission. During aging, healthy neurons show a progressive loss of hemispheric asymmetry in the epigenome, which is amplified in PD. For PD patients, a long disease course is associated with greater hemispheric asymmetry in neuronal epigenomes than a short disease course. Hemispheric differences in epigenetic gene regulation are prevalent in neurons and may affect the progression and symptoms of PD.
Scalable empirical mixture models that account for across-site compositional heterogeneity
Authors: Schrempf Dominik , Lartillot Nicolas , Szöllősi Gergely 
Published: October 2019

AbstractBiochemical demands constrain the range of amino acids acceptable at specific sites resulting in across-site compositional heterogeneity of the amino acid replacement process. Phylogenetic models that disregard this heterogeneity are prone to systematic errors, which can lead to severe long branch attraction artifacts. State-of-the-art models accounting for across-site compositional heterogeneity include the CAT model, which is computationally expensive, and empirical distribution mixture models estimated via maximum likelihood (C10 to C60 models). Here, we present a new, scalable method EDCluster for finding empirical distribution mixture models involving a simple cluster analysis. The cluster analysis utilizes specific coordinate transformations which allow the detection of specialized amino acid distributions either from curated databases, or from the alignment at hand. We apply EDCluster to the HOGENOM and HSSP databases in order to provide universal distribution mixture (UDM) models comprising up to 4096 components. Detailed analyses of the UDM models demonstrate the removal of various long branch attraction artifacts and improved performance compared to the C10 to C60 models. Ready-to-use implementations of the UDM models are provided for three established software packages (IQ-TREE, Phylobayes, and RevBayes).
Relationship between neural phase-locked responses to speech and perception of speech in noise in young and older adults
Authors: Mai Guangting , Howell Peter 
Published: October 2019

AbstractAuditory phase-locked responses are affected by aging and it has been proposed that this increases the challenges experienced during speech perception in noise (SPiN). However, this proposal lacks direct support. This issue was addressed by measuring speech-evoked phase-locked responses at subcortical (frequency-following responses, FFRs) and cortical (theta-band phase-locking, θ-PLV) levels, and studying the relationship between these phase-locked responses and SPiN (word report accuracies of sentences listened to in noise) in adults across a wide age-range (19-75 years old). It was found that: (1) FFR magnitudes declined with age after hearing loss was controlled for; (2) θ-PLV increased with age, suggesting cortical hyperexcitability in audition; (3) SPiN correlated positively with FFR magnitudes obtained in quiet and with θ-PLV obtained in noise, suggesting that impacts of aging (smaller FFR magnitudes and greater θ-PLV) on SPiN differ at subcortical and cortical levels. Thus, the current study provided evidence for different mechanisms at subcortical and cortical levels through which age affects speech-evoked phase-locked activities and SPiN.
Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l
Authors: Morales-Briones Diego F. , Kadereit Gudrun , Tefarikis Delphine T. , Moore Michael J. , Smith Stephen A. , Brockington Samuel F. , Timoneda Alfonso , Yim Won C. , Cushman John C. , Yang Ya 
Published: October 2019

AbstractGene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The dataset included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.
Evolution of the DAN gene family in vertebrates
Authors: Opazo Juan C. , Hoffmann Federico G. , Zavala Kattina , Edwards Scott V. 
Published: October 2019

AbstractThe DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the monophyly of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our phylogenetic results revealed the presence of two new DAN gene lineages; one is only retained in cephalochordates, whereas the other one (GREM3) was only identified in cartilaginous fish, holostean fish, and coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.
Genotype Concordance and Polygenic Risk Score Estimation across Consumer Genetic Testing Data
Authors: Batra Prag , Huang Kuan-lin 
Published: October 2019

AbstractThe consumer genomics industry is steadily growing and delivering genetic information to over 10 million individuals. Yet, the implications of using data from different services remain unclear. We investigated the genotyped sites, concordance, and genetic risk estimation using data from three major consumer services. We found low overlap among reported genotyped sites (2.7% across all three). While there was a high concordance between overlapping sites of the two SNP-array services (99.6%), there was a lower concordance between them and a low-pass whole-genome service (73.0%). Finally, we demonstrated that the discrepancy resulted in distinct APOE genotypes and genetic risk scores of Alzheimer’s disease determined using these data. Our results demonstrate genotype results across consumer genomics platforms may lead to different genetic risk estimates, highlighting the need for careful quality control and interpretation.
From cognitive control to creativity: The conflict resolution of surrealistic imagery
Authors: Ruzzoli Manuela , McGuinness Aoife , Morís Fernández Luis , Soto-Faraco Salvador 
Published: October 2019

AbstractSurrealistic imagery juxtaposes common visual elements to create un-ordinary associations with semantically conflicting representations. We hypothesize that these images engage the conflict processing network that has been described in cognitive neuroscience theories, and probed with laboratory protocols such as the Stroop or Flanker tasks. We addressed this hypothesis by measuring mid-frontal Theta power using EEG while participants watched surrealistic images through a social media-like interface. Surrealistic images, compared to controls, produced a significant Theta power increase, as predicted from cognitive conflict theory. We also found increased memory for surrealistic images one week after exposure, compared to the controls. These findings provide evidence for the surrealistic artistic strategy to effectively engage viewer’ s cognitive control and boost memorability. In these studies, we provide validation of cognitive theories in real-life scenarios and insights regarding the use of neural correlates as effectiveness metrics in creative communication, as well as the arts.