bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unilateral Condylar Hyperplasia: A Comparison With Two Open-Source Softwares
Authors: Vellone Valentino , Costantini Ambra Maria , Ramieri Valerio , Alunni Fegatelli Danilo , Galluccio Gabriella , Cascone Piero 
Published: December 2019

Abstract
Unilateral condylar hyperplasia (UCH) is a condyle disorder that arises due to osteoblastic hyperactivity, resulting in facial asymmetry, malocclusion and dysfunction. Authors, in this retrospective study, compared “gold standard” manual-segmentation with a “semi-manual one” using 2 kinds of open-source software (Horos and ITK-SNAP; Penn Image Computing and Science Laboratory) to calculate volume of 80 UCH condyles (40 patients). Moreover, volumetric differences between affected condyle and unaffected 1, between males and females, ages, and classification type were also analyzed. Fifteen patients (37.5%) were male and 25 (62.5%) were female. The gender ratio was 5:2, not far from the ratio 2:1 shown in literature. The mean age was 24 (SD 8.6) years; 22.9 (SD 6.6) for males and 24.6 (SD 9.6) for females according with the mean age derived from the Raijmakers et al meta-analysis and the Nitzan et al study. Right side (60%, 24 patients) was more often affected than the left side (40%, 16 patients). The 67.5% (27 patients) were classified as trasversal type, 25% (10 patients) as vertical types and 7.5% (3 patients) as combined. Despite Horos and ITK-SNAP values presenting some differences, the data follows the same tendency. The relationship is stronger for healthy condyles than affected condyles.
The Effect of Concentrated Growth Factor on Calvarial Bone in Diabetic Healing
Authors: Kizilaslan Sema , Karabuda Zihni Cüneyt , Olgac Vakur 
Published: December 2019

Abstract
The aim of this study was to evaluate the effect of Concentrated Growth Factor (CGF) on bone healing in diabetic rat model. Experimental diabetes was induced in 24 male Sprague–Dawley rats by streptozotocin. Twenty-four animals served as healthy controls. The animals were divided into 4 subgroups; empty bone defect, grafting with xenogenous graft (Geno-os, OsteoBiol, Turin-Italy), CGF administration, and combined application of the CGF with the xenogenous graft in critical-sized defects in the calvaria of the rats. The diabetic group was given 4 units of Neutral Protamin Hagedorn per day. After 6 weeks, all animals were sacrificed and bone healing was histologically and histomorphometrically analyzed, and the evaluation revealed that the new bone formation in diabetic animals was significantly lower than in healthy group (P: 0.001, P: 0.023). In both groups, the highest rate of ossification was observed in the combined use of xenogenous graft and CGF. When the new bone formation was examined in the graft and CGF group, no significant difference was found between control and diabetic group (P = 0.562; P > 0.05). In conclusion, in patients with diabetes mellitus, combination therapy of CGF with graft is expected to contribute positively to the healing of bone defect.
One-year Outcome of Everolimus With Standard-dose Tacrolimus Immunosuppression in De Novo ABO-incompatible Living Donor Kidney Transplantation: A Retrospective, Single-center, Propensity Score Matching Comparison With Mycophenolate in 42 Transplants
Authors: Noguchi Hiroshi , Tsuchimoto Akihiro , Ueki Kenji , Kaku Keizo , Okabe Yasuhiro , Nakamura Masafumi 
Published: December 2019

Background.
Despite improvement in immunosuppressive therapy, long-term kidney allograft survival remains a major challenge. The outcomes of therapy with everolimus (EVR) and standard-dose tacrolimus (Tac) have not been compared with those of mycophenolate mofetil (MMF) and standard-dose Tac in recipients of de novo ABO-incompatible (ABOi) living donor kidney transplantation (LDKT).

Methods.
This retrospective, observational, single-center, propensity score matching (PSM) study compared the outcomes of EVR and standard-dose Tac with those of MMF and standard-dose Tac following de novo ABOi LDKT. In total, 153 recipients of ABOi LDKT between January 2008 and March 2018 were screened for inclusion in the study. The variables considered for PSM were: recipient age/sex, duration of dialysis, cytomegalovirus mismatch (seronegative recipient and seropositive donor), cause of kidney disease, donor age/sex, and numbers of mismatches (HLA-A, HLA-B, and HLA-DR). After PSM, there were 21 patients in each group (n = 42 overall).

Results.
Four patients in the EVR group and 1 patient in the MMF group were withdrawn because of adverse effects. There were no significant differences between the 2 groups in 1-year outcomes regarding patient death, graft loss, delayed graft function, biopsy-proven acute rejection, infection requiring hospital admission, or estimated glomerular filtration rate. The 1-year protocol biopsy showed that the severity of interstitial fibrosis/tubular atrophy was significantly milder in the EVR group than in the MMF group.

Conclusions.
The findings suggest that the renal efficacy and safety of EVR and standard-dose Tac in recipients of de novo ABOi LDKT are comparable with those of MMF and standard-dose Tac.
Neural basis of basic composition: what we have learned from the red–boat studies and their extensions
Authors: Pylkkänen Liina 
Published: December 2019

Language is our mind's most powerful generative system for the expression of meaning and thought. What are the neural mechanisms of our ability to compose complex meanings from simpler representations? This question is impossible to answer unless we decompose the notion of ‘meaning composition’ in some theoretically guided way and then begin to assess the extent to which brain activity tracks the posited subroutines. Here, I summarize results from a body of MEG research that has begun to address this question from the ground up, first focusing on simple combinations of two words. The work sets off with a hypothesis space offered by theoretical linguistics, positing syntactic and logico-semantic composition as the main combinatory routines, but then reveals that the most consistent and prominent reflection of composition, localized in the left anterior temporal cortex at 200–250 ms, cannot be described with this toolkit. Instead, this activity tracks a much more conceptually driven process, robustly sensitive to the density of the conceptual feature space of the composing items. I will describe our functional understanding of this activity and how it may operate within a broader ‘combinatory network.’This article is part of the theme issue ‘Towards mechanistic models of meaning composition’.
The acquisition of compositional meaning
Authors: Hendriks Petra 
Published: December 2019

How do people create meaning from a string of sounds or pattern of dots? Insights into this process can be obtained from the way children acquire sentence meanings. According to the well-known principle of compositionality, the meaning of an expression is a function of the meanings of its parts and the way they are syntactically combined. However, children frequently seem to ignore syntactic structure in their sentence interpretations, suggesting that syntax is merely one of the sources of information constraining meaning and does not have a special status. A fundamental assumption in the argument in favour of compositionality is that speakers and listeners generally agree upon the meanings of sentences. Remarkably, however, children as listeners do not always understand what they are able to produce as speakers, and vice versa. For example, children's production of word order appears to develop ahead of their comprehension of word order in the acquisition of languages like English and Dutch. Such production–comprehension asymmetries are not uncommon in child language and motivate a view of compositionality as a principle pertaining to the result of perspective taking, and of meaning composition as a process of speaker–listener coordination.This article is part of the theme issue ‘Towards mechanistic models of meaning composition’.
Altered cortical gyrification in adults who were born very preterm and its associations with cognition and mental health
Authors: Papini Chiara , Palaniyappan Lena , Kroll Jasmin , Froudist-Walsh Sean , Murray Robin M , Nosarti Chiara 
Published: December 2019

AbstractBackgroundThe last trimester of pregnancy is a critical period for the establishment of cortical gyrification and altered folding patterns have been reported following very preterm birth (< 33 weeks of gestation) in childhood and adolescence. However, research is scant on the persistence of such alterations in adulthood and their associations with cognitive and psychiatric outcomes.MethodsWe studied 79 very-preterm adults and 81 age-matched full-term controls. T1-weighted images were used to measure local gyrification index (LGI), indicating the degree of folding across multiple vertices of the reconstructed cortical surface. Group and group-sex LGI differences were assessed using per-vertex adjustment for cortical thickness and overall intracranial volume. Within-group correlations were also computed between LGI and functional outcomes, including general intelligence (IQ) and psychopathology.ResultsVery preterm adults had significantly reduced LGI in extensive cortical regions encompassing the frontal, anterior temporal and occipito-parietal lobes. Alterations in lateral fronto-temporal-parietal and medial occipito-parietal regions were present in both males and females, although males reported more extensive alterations. In both very preterm adults and controls, higher LGI was associated with higher IQ and lower psychopathology scores, with the spatial distribution of these associations substantially differing between the two groups.ConclusionsVery preterm adults’ brains are characterized by significant and widespread local hypogyria and these abnormalities might be implicated in cognitive and psychiatric outcomes. Gyrification reflects an early developmental process and provides a fingerprint for very preterm birth.
Global drivers of diversification in a marine species complex
Authors: Silva Catarina N.S. , Murphy Nicholas P. , Bell James J. , Green Bridget S. , Duhamel Guy , Cockcroft Andrew C. , Hernández Cristián E. , Strugnell Jan M. 
Published: December 2019

AbstractInvestigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence before speciation. The processes influencing species diversification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome-wide divergence, introgression patterns and inferred demographic history between species pairs of all extant rock lobster species (Jasusspp.), a complex with long larval duration, that has populated continental shelf and seamount habitats around the globe at approximately 40°S. Genetic differentiation patterns revealed the effects of the environment and geographic isolation. Species associated with the same habitat structure (either continental shelf or seamount/island) shared a common ancestry, even though the habitats were not adjacent. Differences in benthic temperature explained a significant proportion (41.3%) of the genetic differentiation. The Eastern Pacific species pair ofJ. caveorumandJ. frontalisretained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa and seamounts in the Indian and Atlantic oceans included events of introgression after secondary contact. Parameters estimated for time in isolation and gene flow were congruent with genetic differentiation metrics suggesting that the observed differentiation patterns are the product of migration and genetic drift. Our results reveal important effects of habitat and demographic processes on the divergence of species within the genusJasusproviding the first empirical study of genome-wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.
Forelimb movements evoked by optogenetic stimulation of the macaque motor cortex
Authors: Watanabe Hidenori , Sano Hiromi , Chiken Satomi , Kobayashi Kenta , Fukata Yuko , Fukata Masaki , Mushiake Hajime , Nambu Atsushi 
Published: December 2019

AbstractOptogenetics has become an indispensable tool for investigating brain functions. Although non-human primates are particularly useful models for understanding the functions and dysfunctions of the human brain, application of optogenetics to non-human primates is still limited. In the present study, we generated an effective adeno-associated viral vector serotype DJ to express channelrhodopsin-2 (ChR2) under the control of a strong ubiquitous CAG promoter and injected into the somatotopically identified forelimb region of the primary motor cortex in macaque monkeys. ChR2 was strongly expressed around the injection sites, and optogenetic intracortical microstimulation (oICMS) through a homemade optrode induced prominent cortical activity: Even single-pulse, short duration oICMS evoked long-lasting repetitive firings of cortical neurons. In addition, oICMS elicited distinct forelimb movements and muscle activity, which were comparable to those elicited by conventional electrical ICMS. The present study removed obstacles to optogenetic manipulation of neuronal activity and behaviors in non-human primates.
Growth rate alterations of human colorectal cancer cells by 157 gut bacteria
Authors: Taddese Rahwa , Garza Daniel R. , Ruiter Lilian N. , de Jonge Marien I. , Belzer Clara , Aalvink Steven , Nagtegaal Iris D. , Dutilh Bas E. , Boleij Annemarie 
Published: December 2019

ABSTRACTSeveral bacteria in the human gut microbiome have been associated with colorectal cancer (CRC) by high-throughput screens. In some cases, molecular mechanisms have been elucidated that drive tumorigenesis, including bacterial membrane proteins or secreted molecules that interact with the human cancer cells. For most gut bacteria, however, it remains unknown if they enhance or inhibit cancer cell growth. Here, we screened bacteria-free supernatants (secretomes) and inactivated cells of over 150 cultured bacterial strains for their effect on CRC cell growth. We observed family-level and strain-level effects that often differed between bacterial cells and secretomes, suggesting that different molecular mechanisms are at play. Secretomes ofBacteroidaceae,Enterobacteriaceae,andErysipelotrichaceaebacteria enhanced CRC cell growth, while mostFusobacteriaceaecells and secretomes inhibited growth, contrasting prior findings. In some bacteria, the presence of specific functional genes was associated with CRC cell growth rates, including the virulence genes TcdA inClostridialesand FadA inFusobacteriaceae, which both inhibited growth.Bacteroidaceaecells that enhanced growth were enriched for genes of the cobalamin synthesis pathway, whileFusobacteriaceaecells that inhibit growth were enriched for genes of the ethanolamine utilization pathway. Together, our results reveal how different gut bacteria have wide-ranging effects on cancer cells, contribute a better understanding of the effects of the gut microbiome on the human host, and provide a valuable resource for identifying candidate target genes for potential microbiome-based diagnostics and treatment strategies.
Distinct transcriptomic cell types and neural circuits of the subiculum and prosubiculum along the dorsal-ventral axis
Authors: Ding Song-Lin , Yao Zizhen , Hirokawa Karla E. , Nguyen Thuc Nghi , Graybuck Lucas T. , Fong Olivia , Bohn Phillip , Ngo Kiet , Smith Kimberly A. , Koch Christof , Phillips John W. , Lein Ed S. , Harris Julie A. , Tasic Bosiljka , Zeng Hongkui 
Published: December 2019

SummarySubicular region plays important roles in spatial processing and many cognitive functions and these were mainly attributed to subiculum (Sub) rather than prosubiculum (PS). Using single-cell RNA-sequencing (scRNA-seq) technique we have identified up to 27 distinct transcriptomic clusters/cell types, which were registered to anatomical sub-domains in Sub and PS. Based on reliable molecular markers derived from transcriptomic clustering and in situ hybridization data, the precise boundaries of Sub and PS have been consistently defined along the dorsoventral (DV) axis. Using these borders to evaluate Cre-line specificity and tracer injections, we have found bona fide Sub projections topographically to structures important for spatial processing and navigation. In contrast, PS along DV axis sends its outputs to widespread brain regions crucial for motivation, emotion, reward, stress, anxiety and fear. Brain-wide cell-type specific projections of Sub and PS have also been revealed using specific Cre-lines. These results reveal two molecularly and anatomically distinct circuits centered in Sub and PS, respectively, providing a consistent explanation to historical data and a clearer foundation for future functional studies.Highlights27 transcriptomic cell types identified in and spatially registered to “subicular” regions.Anatomic borders of “subicular” regions reliably determined along dorsal-ventral axis.Distinct cell types and circuits of full-length subiculum (Sub) and prosubiculum (PS).Brain-wide cell-type specific projections of Sub and PS revealed with specific Cre-lines.In BriefDing et al. show that mouse subiculum and prosubiculum are two distinct regions with differential transcriptomic cell types, subtypes, neural circuits and functional correlation. The former has obvious topographic projections to its main targets while the latter exhibits widespread projections to many subcortical regions associated with reward, emotion, stress and motivation.
Separating overlapping bat calls with a bi-directional long short-term memory network
Authors: Zhang Kangkang , Liu Tong , Song Shengjing , Zhao Xin , Sun Shijun , Metzner Walter , Feng Jiang , Liu Ying 
Published: December 2019

AbstractAcquiring clear and usable audio recordings is critical for acoustic analysis of animal vocalizations. Bioacoustics studies commonly face the problem of overlapping signals, but the issue is often ignored, as there is currently no satisfactory solution. This study presents a bi-directional long short-term memory (BLSTM) network to separate overlapping bat calls and reconstruct waveform audio sounds. The separation quality was evaluated using seven temporal-spectrum parameters. The applicability of this method for bat calls was assessed using six different species. In addition, clustering analysis was conducted with separated echolocation calls from each population. Results showed that all syllables in the overlapping calls were separated with high robustness across species. A comparison between the seven temporal-spectrum parameters showed no significant difference and negligible deviation between the extracted and original calls, indicating high separation quality. Clustering analysis of the separated echolocation calls also produced an accuracy of 93.8%, suggesting the reconstructed waveform sounds could be reliably used. These results suggest the proposed technique is a convenient and automated approach for separating overlapping calls using a BLSTM network. This powerful deep neural network approach has the potential to solve complex problems in bioacoustics.Author summaryIn recent years, the development of recording techniques and devices in animal acoustic experiment and population monitoring has led to a sharp increase in the volume of sound data. However, the collected sound would be overlapped because of the existence of multiple individuals, which laid restrictions on taking full advantage of experiment data. Besides, more convenient and automatic methods are needed to cope with the large datasets in animal acoustics. The echolocation calls and communication calls of bats are variable and often overlapped with each other both in the recordings from field and laboratory, which provides an excellent template for research on animal sound separation. Here, we firstly solved the problem of overlapping calls in bats successfully based on deep neural network. We built a network to separate the overlapping calls of six bat species. All the syllables in overlapping calls were separated and we found no significant difference between the separated syllables with non-overlapping syllables. We also demonstrated an instance of applying our method on species classification. Our study provides a useful and efficient model for sound data processing in acoustic research and the proposed method has the potential to be generalized to other animal species.
The 9aaTAD activation domains in the four Yamanaka Oct4, Sox2, Myc, and Klf4 transcription factors essential during the stem cell development
Authors: Piskacek Martin , Jendruchova Kristina , Rezacova Martina , Havelka Marek , Gasparik Norbert , Hofrova Alena , Knight Andrea 
Published: December 2019

AbstractSomatic cells can be reprogrammed by the Yamanaka factors Oct4, Sox2, Myc and Klf4 activators into induced pluripotent stem cells. Throughout their genome, the Oct4, Sox2 and Klf4 cooperate with mediators of transcription, where the DNA binding sites serve as scaffolds for the phase-separated transcriptional condensates at distinct genome loci. In this study, we identified the 9aaTAD activation domains as the common interaction interface of the Yamanaka factors for transcription machinery. All four activation domains were identified by our online 9aaTAD prediction service and experimentally confirmed as strong activators of transcription. We considered the mediator interactions granted by 9aaTADs as part of the Yamanaka factors ability to reprogram cell fate.Graphical abstract
Optical activation of TrkB receptors
Authors: Huang Peiyuan , Liu Aofei , Song Yutong , Hope Jen M. , Cui Bianxiao , Duan Liting 
Published: December 2019

AbstractBrain-derived neurotrophic factor (BDNF), via activation of tropomyosin receptor kinase B (TrkB), plays a critical role in neuronal proliferation, differentiation, survival, and death. Dysregulation of TrkB signaling is implicated in neurodegenerative disorders and cancers. Precise activation of TrkB receptors with spatial and temporal resolution is greatly desired to study the dynamic nature of TrkB signaling and its role in related diseases. Here we develop different optogenetic approaches that use light to activate TrkB receptors. Utilizing the photosensitive proteinArabidopsis thalianacryptochrome 2 (CRY2), the light-inducible homo-interaction of the intracellular domain of TrkB (iTrkB) in the cytosol or on the plasma membrane is able to induce the activation of downstream MAPK/ERK and PI3K/Akt signaling as well as the neurite outgrowth of PC12 cells. Moreover, we prove that such strategies are generalizable to other optical homo-dimerizers by demonstrating the optical TrkB activation based on the light-oxygen-voltage domain of aureochrome 1 fromVaucheria frigida. The results open up new possibilities of many other optical platforms to activate TrkB receptors to fulfill customized needs. By comparing all the different strategies, we find that the CRY2-integrated approach to achieve light-induced cell membrane recruitment and homo-interaction of iTrkB is most efficient in activating TrkB receptors. The optogenetic strategies presented are promising tools to investigate BDNF/TrkB signaling with tight spatial and temporal control.