bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting long-range interactions between migrating cells
Authors: Metzner C. , Hörsch F. , Mark C. , Czerwinski T. , Winterl A. , Voskens C. , Fabry B. 
Published: July 2021

AbstractChemotaxis enables cells to systematically approach distant targets that emit a diffusible guiding substance. However, the visual observation of an encounter between a cell and a target does not necessarily indicate the presence of a chemotactic approach mechanism, as even a blindly migrating cell can come across a target by chance. To distinguish between the chemotactic approach and blind migration, we present an objective method that is based on the analysis of time-lapse recorded cell migration trajectories: For each movement step of a cell relative to the position of a potential target, we compute apvalue that quantifies the likelihood of the movement direction under the null-hypothesis of blind migration. The resulting distribution ofpvalues, pooled over all recorded cell trajectories, is then compared to an ensemble of reference distributions in which the positions of targets are randomized. First, we validate our method with simulated data, demonstrating that it reliably detects the presence or absence of remote cell-cell interactions. In a second step, we apply the method to data from three-dimensional collagen gels, interspersed with highly migratory natural killer (NK) cells that were derived from two different human donors. We find for one of the donors an attractive interaction between the NK cells, pointing to a cooperative behavior of these immune cells. When adding nearly stationary K562 tumor cells to the system, we find a repulsive interaction between K562 and NK cells for one of the donors. By contrast, we find attractive interactions between NK cells and an IL-15-secreting variant of K562 tumor cells. We therefore speculate that NK cells find wild-type tumor cells only by chance, but are programmed to leave a target quickly after a close encounter. We provide a freely available Python implementation of ourpvalue method that can serve as a general tool for detecting long-range interactions in collective systems of self-driven agents.
Modern and sub-fossil corals suggest reduced temperature variability in the eastern pole of the Indian Ocean Dipole during the medieval climate anomaly
Authors: Cahyarini Sri Yudawati , Pfeiffer Miriam , Reuning Lars , Liebetrau Volker , Dullo Wolf-Chr. , Takayanagi Hideko , Anwar Iwan Pramesti , Utami Dwi Amanda , Garbe-Schönberg Dieter , Hendrizan Marfasran , Eisenhauer Anton 
Published: July 2021

AbstractWe present two 40 year records of monthly coral Sr/Ca ratios from the eastern pole of the Indian Ocean Dipole. A modern coral covers the period from 1968 to 2007. A sub-fossil coral derives from the medieval climate anomaly (MCA) and spans 1100–1140 ad. The modern coral records SST variability in the eastern pole of the Indian Ocean Dipole. A strong correlation is also found between coral Sr/Ca and the IOD index. The correlation with ENSO is asymmetric: the coral shows a moderate correlation with El Niño and a weak correlation with La Niña. The modern coral shows large interannual variability. Extreme IOD events cause cooling > 3 °C (1994, 1997) or ~ 2 °C (2006). In total, the modern coral indicates 32 warm/cool events, with 16 cool and 16 warm events. The MCA coral shows 24 warm/cool events, with 14 cool and 10 warm events. Only one cool event could be comparable to the positive Indian Ocean Dipole in 2006. The seasonal cycle of the MCA coral is reduced (< 50% of to the modern) and the skewness of the Sr/Ca data is lower. This suggests a deeper thermocline in the eastern Indian Ocean associated with a La Niña-like mean state in the Indo-Pacific during the MCA.
Shoot-soil ecological stoichiometry of alfalfa under nitrogen and phosphorus fertilization in the Loess Plateau
Authors: Lu Jiaoyun , Tian Hong , Zhang Heshan , Xiong Junbo , Yang Huimin , Liu Yang 
Published: July 2021

AbstractPlants and soil interactions greatly affect ecosystems processes and properties. Ecological stoichiometry is an effective means to explore the C, N, P correlation between plants and soil and the relationship between plant growth and nutrient supply. Serious soil erosion on China’s Loess Plateau has further barrenness the soil. Fertilization solves the problem of ecosystem degradation by improving soil fertility and regulating the ecological stoichiometric between soil and plants. No fertilization (CK), nitrogen fertilization (N), phosphorus fertilization (P) and N and P combined fertilization (NP) treatments were set in an alfalfa grassland. Organic carbon (C), nitrogen (N) and phosphorus (P) nutrients and their stoichiometry were measured in shoot and soil. P and NP fertilization increased shoot C concentration (3.12%, 0.91%), and all fertilization decreased shoot N concentration (6.96%). The variation of shoot C and N concentrations resulted in a greater increase in shoot C:N under the fertilization treatment than that under CK (8.24%). Most fertilization treatments increased shoot P concentration (4.63%) at each cut, which induced a decrease of shoot C:P. Shoot N:P of most treatments were greater than 23, but it was lower under N and NP fertilization than that under CK. Fertilization only increased soil C in 2014, but had no effect on soil N. Soil P content was significantly higher under P fertilization in 2014 (34.53%), and all fertilization in the second cut of 2015 (124.32%). Shoot and soil C:P and N:P having the opposite changes to shoot and soil P, respectively. Our results suggest that the change of P after fertilization largely drove the changes of stoichiometric. The growth of alfalfa in the Loess Plateau was severely restricted by P. It is an effective method to increase the biomass of alfalfa by increasing the addition of N or NP fertilizer to alleviate P limitation.
Identification of prognostic alternative splicing events in sarcoma
Authors: Li Hongshuai , Yang Jie , Yang Guohui , Ren Jia , Meng Yu , Qi Peiyi , Wang Nan 
Published: July 2021

AbstractSarcoma is a rare malignancy with unfavorable prognoses. Accumulating evidence indicates that aberrant alternative splicing (AS) events are generally involved in cancer pathogenesis. The aim of this study was to identify the prognostic value of AS-related survival genes as potential biomarkers, and highlight the functional roles of AS events in sarcoma. RNA-sequencing and AS-event datasets were downloaded from The Cancer Genome Atlas (TCGA) sarcoma cohort and TCGA SpliceSeq, respectively. Survival-related AS events were further assessed using a univariate analysis. A multivariate Cox regression analysis was also performed to establish a survival-gene signature to predict patient survival, and the area-under-the-curve method was used to evaluate prognostic reliability. KOBAS 3.0 and Cytoscape were used to functionally annotate AS-related genes and to assess their network interactions. We detected 9674 AS events in 40,184 genes from 236 sarcoma samples, and the 15 most significant genes were then used to construct a survival regression model. We further validated the involvement of ten potential survival-related genes (TUBB3, TRIM69, ZNFX1, VAV1, KCNN2, VGLL3, AK7, ARMC4, LRRC1, and CRIP1) in the occurrence and development of sarcoma. Multivariate survival model analyses were also performed, and validated that a model using these ten genes provided good classifications for predicting patient outcomes. The present study has increased our understanding of AS events in sarcoma, and the gene-based model using AS-related events may serve as a potential predictor to determine the survival of sarcoma patients.
Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe
Authors: Rohrlach Adam B. , Papac Luka , Childebayeva Ainash , Rivollat Maïté , Villalba-Mouco Vanessa , Neumann Gunnar U. , Penske Sandra , Skourtanioti Eirini , van de Loosdrecht Marieke , Akar Murat , Boyadzhiev Kamen , Boyadzhiev Yavor , Deguilloux Marie-France , Dobeš Miroslav , Erdal Yilmaz S. , Ernée Michal , Frangipane Marcella , Furmanek Mirosław , Friederich Susanne , Ghesquière Emmanuel , Hałuszko Agata , Hansen Svend , Küßner Mario , Mannino Marcello , Özbal Rana , Reinhold Sabine , Rottier Stéphane , Salazar-García Domingo Carlos , Diaz Jorge Soler , Stockhammer Philipp W. , de Togores Muñoz Consuelo Roca , Yener K. Aslihan , Posth Cosimo , Krause Johannes , Herbig Alexander , Haak Wolfgang 
Published: July 2021

AbstractUniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.
Variations in the oral microbiome are associated with depression in young adults
Authors: Wingfield Benjamin , Lapsley Coral , McDowell Andrew , Miliotis Georgios , McLafferty Margaret , O’Neill Siobhan M. , Coleman Sonya , McGinnity T. Martin , Bjourson Anthony J. , Murray Elaine K. 
Published: July 2021

AbstractA growing body of evidence supports an important role for alterations in the brain-gut-microbiome axis in the aetiology of depression and other psychiatric disorders. The potential role of the oral microbiome in mental health has received little attention, even though it is one of the most diverse microbiomes in the body and oral dysbiosis has been linked to systemic diseases with an underlying inflammatory aetiology. This study examines the structure and composition of the salivary microbiome for the first time in young adults who met the DSM-IV criteria for depression (n = 40) and matched controls (n = 43) using 16S rRNA gene-based next generation sequencing. Subtle but significant differences in alpha and beta diversity of the salivary microbiome were observed, with clear separation of depressed and healthy control cohorts into distinct clusters. A total of 21 bacterial taxa were found to be differentially abundant in the depressed cohort, including increasedNeisseriaspp. andPrevotella nigrescens, while 19 taxa had a decreased abundance. In this preliminary study we have shown that the composition of the oral microbiome is associated with depression in young adults. Further studies are now warranted, particuarly investigations into whether such shifts play any role in the underling aetiology of depression.
Lycopene suppresses palmitic acid-induced brain oxidative stress, hyperactivity of some neuro-signalling enzymes, and inflammation in female Wistar rat
Authors: Ugbaja Regina Ngozi , James Adewale Segun , Ugwor Emmanuel Ifeanyichukwu , Akamo Adio Jamiu , Thomas Funmilola Clara , Kosoko Ayokulehin Muse 
Published: July 2021

AbstractNeuroinflammation can be triggered by certain high caloric nutrients such as palmitic acid (PA). The effect of lycopene against PA-induced neuroinflammation in female rats has not been as explored. In the present study, thirty rats (weighing 150–200) g were randomly allotted into six groups (n = 5) comprising normal control, PA control, PA + lycopene (0.24 mg/kg), PA + lycopene (0.48 mg/kg), lycopene (0.24 mg/kg), and lycopene (0.48 mg/kg), respectively. After seven weeks of PA challenge (5 mM) including two weeks of lycopene treatment, the brain was excised for analyses. Palmitic acid overload caused significant (p < 0.05) increases in adenosine deaminase, monoamine oxidase-A, nucleotides tri-phosphatase, 5′-nucleotidase, acetylcholine esterase, and myeloperoxidase activities, and malondialdehyde (MDA) levels which were reduced significantly in the lycopene-treated groups. Conversely, catalase and glutathione peroxidase activities, and reduced glutathione levels concentration decreased by 43%, 34%, and 12%, respectively in the PA control groups compared with the Control. Also, PA triggered a decrease in the brain phospholipids (11.43%) and cholesterol (11.11%), but increased triacylglycerol level (50%). Furthermore, upregulated expressions of Interleukin-1β, Interleukin-6, and NF-ĸB-p65 in the PA control were attenuated, while decreased Interleukine-10 expression was upregulated due to lycopene treatment. Severe brain vacuolation observed in the histology of the PA control rats was normalized by lycopene. This study concludes that lycopene ameliorated PA-induced neuroinflammation, probably via attenuation of oxidative stress, and downregulation of TLR4/ NF-κB -p65 axis.
Movement kinematics and cortical activation in children with and without autism spectrum disorder during sway synchrony tasks: an fNIRS study
Authors: Su Wan-Chun , Culotta McKenzie , Tsuzuki Daisuke , Bhat Anjana 
Published: July 2021

AbstractChildren with Autism Spectrum Disorder (ASD) have difficulties with socially embedded movements such as imitation and interpersonal synchrony (IPS); however, related movement characteristics and underlying neural mechanisms are not well understood. This study compared the movement characteristics and cortical activation patterns of children with and without ASD during a whole-body, sway synchrony task when different levels of social information were provided. Thirty children with and without ASD (mean age: 12.6 years, SE: 0.6 years) participated. Movement kinematics and fNIRS-based cortical activation were recorded when the child observed an adult tester sway side to side, when they swayed solo, or when they swayed face to face with the tester with or without fingertips touching (i.e., IPS). Children with ASD showed reduced synchrony and smaller sway amplitude compared to typically developing children without ASD. They showed reduced cortical activation over the inferior frontal gyrus and superior temporal sulcus during IPS and did not show significant increase in cortical activation when more social information was provided. The cortical activation findings were significantly associated with IPS behaviors and social communication performance. The ASD-related neurobiomarkers identified in our study could be used as objective measures to evaluate intervention effects in children with ASD.
Data-driven modelling approach to circadian temperature rhythm profiles in free-living conditions
Authors: Lipsanen Jari , Kuula Liisa , Elovainio Marko , Partonen Timo , Pesonen Anu-Katriina 
Published: July 2021

AbstractThe individual variation in the circadian rhythms at the physiological level is not well understood. Albeit self-reported circadian preference profiles have been consolidated, their premises are grounded on human experience, not on physiology. We used data-driven, unsupervised time series modelling to characterize distinct profiles of the circadian rhythm measured from skin surface temperature in free-living conditions. We demonstrate the existence of three distinct clusters of individuals which differed in their circadian temperature profiles. The cluster with the highest temperature amplitude and the lowest midline estimating statistic of rhythm, or rhythm-adjusted mean, had the most regular and early-timed sleep–wake rhythm, and was the least probable for those with a concurrent delayed sleep phase, or eveningness chronotype. While the clusters associated with the observed sleep and circadian preference patterns, the entirely unsupervised modelling of physiological data provides a novel basis for modelling and understanding the human circadian functions in free-living conditions.
Prognostic impact of pre-transplant chromosomal aberrations in peripheral blood of patients undergoing unrelated donor hematopoietic cell transplant for acute myeloid leukemia
Authors: Wang Youjin , Zhou Weiyin , McReynolds Lisa J. , Katki Hormuzd A. , Griffiths Elizabeth A. , Thota Swapna , Machiela Mitchell J. , Yeager Meredith , McCarthy Philip , Pasquini Marcelo , Wang Junke , Karaesmen Ezgi , Rizvi Abbas , Preus Leah , Tang Hancong , Wang Yiwen , Pooler Loreall , Sheng Xin , Haiman Christopher A. , Van Den Berg David , Spellman Stephen R. , Wang Tao , Kuxhausen Michelle , Chanock Stephen J. , Lee Stephanie J. , Hahn Theresa E. , Sucheston-Campbell Lara E. , Gadalla Shahinaz M. 
Published: July 2021

AbstractTo improve risk stratification and treatment decisions for patients with acute myeloid leukemia (AML) undergoing hematopoietic cell transplantation (HCT). We used SNP-array data from the DISCOVeRY-BMT study to detect chromosomal aberrations in pre-HCT peripheral blood (collected 2–4 weeks before the administration of conditioning regimen) from 1974 AML patients who received HCT between 2000 and 2011. All aberrations detected in ≥ 10 patients were tested for their association with overall survival (OS), separately by remission status, using the Kaplan–Meier estimator. Cox regression models were used for multivariable analyses. Follow-up was through January 2019. We identified 701 unique chromosomal aberrations in 285 patients (7% of 1438 in complete remission (CR) and 36% of 536 not in CR). Copy-neutral loss-of-heterozygosity (CNLOH) in chr17p in CR patients (3-year OS = 20% vs. 50%, with and without chr17p CNLOH, p = 0.0002), and chr13q in patients not in CR (3-year OS = 4% vs. 26%, with and without chr13q CNLOH, p < 0.0001) are risk factors for poor survival. Models adjusted for clinical factors showed approximately three-fold excess risk of post-HCT mortality with chr17p CNLOH in CR patients (hazard ratio, HR = 3.39, 95% confidence interval CI 1.74–6.60, p = 0.0003), or chr13q CNLOH in patients not in CR (HR = 2.68, 95% CI 1.75–4.09, p < 0.0001). The observed mortality was mostly driven by post-HCT relapse (HR = 2.47, 95% CI 1.01–6.02, p = 0.047 for chr17p CNLOH in CR patients, and HR = 2.58, 95% CI 1.63–4.08, p < 0.0001 for chr13q CNLOH in patients not in CR. Pre-transplant CNLOH in chr13q or chr17p predicts risk of poor outcomes after unrelated donor HCT in AML patients. A large prospective study is warranted to validate the results and evaluate novel strategies to improve survival in those patients.
Olfactory shifts linked to postpartum depression
Authors: Peng Mei , Potterton Hazel , Chu Joanna Ting Wai , Glue Paul 
Published: July 2021

AbstractPostpartum Depression (PPD) is the most common non-obstetric complications associated with childbearing, but currently has poor diagnostic regimes. Sensory symptoms of PPD are understudied, particularly with regard to the sense of olfaction. The present study addresses this research gap by assessing differences in olfactory abilities between 39 depressed mothers, who were within the perinatal period (i.e., during pregnancy and up to 1-year post pregnancy) and assessed with Edinburgh Postnatal Depression Scale, and their case-matched healthy volunteers. The assessments include two olfactory testing sessions conducted 4-weeks apart, each comprising a standard odour detection threshold test (i.e., Snap & Sniff Olfactory Test System), and intensity and valence ratings for 3 “pleasant” and 3 “unpleasant” odorants. The results revealed no difference between patients (M = 5.6; SE = 0.3) and control group (M = 5.7; SE = 0.4) in terms of olfactory detection threshold. However, the patients group perceived the 3 “unpleasant” odours as significantly less pleasant (p < 0.05), and 2 odorants (1 “pleasant” and 1 “unpleasant”) as less intense. Additionally, these results did not appear to be significantly interacted with the individual’s perinatal stage. The present study is the first to evaluate associations between olfactory function and PPD. Findings from the study suggest that, while PPD has little effect on the early stages of olfactory processing, these conditions may have stronger influence on higher-order olfactory perception, including both hedonic and intensity perception. These novel findings add knowledge to sensory symptoms of PPD.
Ocular surface cooling rate associated with tear film characteristics and the maximum interblink period
Authors: Ding Jennifer E. , Kim Young Hyun , Yi Sarah M. , Graham Andrew D. , Li Wing , Lin Meng C. 
Published: July 2021

AbstractThe surface of the human eye is covered with a protective tear film that refreshes with each blink. Natural blinking occurs involuntarily, but one can also voluntarily blink or refrain from blinking. The maximum time one can refrain from blinking until the onset of discomfort is the maximum interblink period (MIBP). During the interblink period the tear film evaporates and thins from the ocular surface. Infrared thermography provides a non-invasive measure of the ocular surface temperature (OST). Due to evaporation, ocular surface cooling (OSC) generally occurs when the eyes are open and exposed to the environment. The purpose of our study was to investigate the effect of OSC rate on the MIBP, and to investigate the association of the MIBP with tear film characteristics in subjects who do and do not exhibit OSC. The MIBP was measured simultaneously with OST over time. Non-invasive tear breakup time, tear meniscus height, tear lipid layer thickness, and Schirmer I test strip wetted lengths were measured on a day prior to the thermography visit. Subjects were divided into cooling and non-cooling groups based on OSC rate, and demographic and tear film characteristics were tested for inter-group differences. A faster OSC rate was associated with an exponentially shorter duration of the MIBP overall and within the cooling group alone. Faster non-invasive tear breakup time was significantly associated with a shorter MIBP in both groups. These results suggest that tear film evaporation initiates a pathway that results in the onset of ocular discomfort and the stimulus to blinking. The presence of a subset of subjects with no or minimal OSC who nevertheless have a short MIBP indicates that evaporative cooling is not the only mechanism responsible for the onset of ocular discomfort.