bluuebunny/crossref_metadata_2025_split huggingface dataset:
PATIENT DOSES IN WHOLE-BODY PET/CT EXAMINATIONS IN THE LARGEST TERTIARY HOSPITAL IN GREECE
Authors: Tzampazidou E , Fotina A A , Chatonidis V , Tsalafoutas I A , Datseris I E , Samartzis A 
Published: November 2021

Abstract
The purpose of this study was to determine the patient radiation dose in combined whole-body positron emission tomography/computed tomography (PET/CT) examinations performed in the largest tertiary hospital in Greece. Computed tomography dose index (CTDIvol), dose length product (DLP), weight, height and administered activity of 2-[18F] fluoro-2-deoxy-D-glucose values for PET/CT examinations were recorded in a sample of 1014 randomly selected patients. The mean (±standard deviation) and median (interquartile) CTDIvol values were equal to 5.5 ± 2.4 and 4.8 (2.5) mGy, respectively. The respective DLP values were 483.3 ± 212.4 and 426 (234.6) mGy·cm. For the administered activity, mean and median were equal to 363.9 ± 68.3 and 361.6 (85.6) MBq. The mean administered activity per body weight was 4.8 ± 0.6 and the median 4.8 (0.6) MBq/kg. The results of this survey are within the range of values reported in the literature and can be used as a standard of reference until national diagnostic reference levels are established for whole-body PET/CT procedures.
Maternal dopamine encodes affective signals of human infants
Authors: Zeevi Lior , Irani Merav , Catana Ciprian , Feldman Barrett Lisa , Atzil Shir 
Published: November 2021

Abstract
Mothers are highly responsive to their offspring. In non-human mammals, mothers secrete dopamine in the nucleus accumbens (NAcc) in response to their pups. Yet, it is still unknown which aspect of the offspring behavior elicits dopaminergic responses in mothers. Here, we tested whether infants’ affective signals elicit dopaminergic responses in the NAcc of human mothers. First, we conducted a behavioral analysis on videos of infants’ free play and quantified the affective signals infants spontaneously communicated. Then, we presented the same videos to mothers during a magnetic resonance-positron emission tomography scan. We traced the binding of [11C]raclopride to free D2/3-type receptors to assess maternal dopaminergic responses during the infant videos. When mothers observed videos with many infant signals during the scan, they had less [11C]raclopride binding in the right NAcc. Less [11C]raclopride binding indicates that less D2/3 receptors were free, possibly due to increased endogenous dopamine responses to infants’ affective signals. We conclude that NAcc D2/3 receptors are involved in maternal responsiveness to affective signals of human infants. D2/3 receptors have been associated with maternal responsiveness in nonhuman animals. This evidence supports a similar mechanism in humans and specifies infant-behaviors that activate the maternal dopaminergic system, with implications for social neuroscience, development and psychopathology.
Splitting of RNA-dependent RNA polymerase is common in Narnaviridae: Identification of a type II divided RdRp from deep-sea fungal isolates
Authors: Chiba Yuto , Oiki Sayoko , Zhao Yanjie , Nagano Yuriko , Urayama Syun-ichi , Hagiwara Daisuke 
Published: November 2021

Abstract
Until recently, it was accepted that RNA-dependent RNA polymerase (RdRp) is the only essential gene for non-retro RNA viruses and is encoded by a single open reading frame (ORF) in their genomes. However, divided RdRps that are coded by two ORFs were discovered in fungal RNA viruses in a few independent reports. This discovery showed higher plasticity of viral RdRp than was expected. Among these divided RdRps, the division site was common; specifically, the first part of the RdRp contains motifs F, A, and B, whereas the latter part possesses motifs C and D. These RdRps are designated as type I divided RdRp and have been limited to viruses in a specific clade of Narnaviridae. In this study, to further understand the plasticity of RdRp, we explored viruses from deep sea–derived fungal strains as an untapped resource with a focus on Aspergillus section Versicolores. Seven strains were found to be infected by a total of 13 viruses, and the viral RNA genomes were determined by fragmented and primer-ligated double-stranded RNA sequencing technology. Among them, six strains belong to Narnaviridae. One of the strains, Aspergillus tennesseensis narnavirus 1, which infects an Aspergillus tennesseensis, has a divided RdRp with a new division site (referred to as type II divided RdRp). A couple of sequences for possible type II divided RdRps were also detected in public metagenomic data sets. Our findings reveal that different types of divisions in RdRp are present in the virosphere, and two types of RdRp splitting occurred independently within Narnaviridae.
Bursaphelenchus xylophilus: An Important Pathogenic Factor of Pine Wilt Disease and Its Relationship with Bursaphelenchus mucronatus
Authors: Li Yu-Long , Fan Chang-Ji , Jiang Xiao-Hui , Tian Xing-Yi , Han Zheng-Min 
Published: November 2021

Pine wilt disease is the most devastating pine disease caused by Bursaphelenchus xylophilus. Bursaphelenchus mucronatus is morphologically similar to B. xylophilus and geographically overlaps in its distribution. Although interspecific hybridization of the two nematodes has been performed in vitro, the dynamic regularity of hybrid formation and its risk in forests has not been well evaluated. In this study, a hybrid of B. xylophilus and Bursaphelenchus mucronatus mucronatus was identified in the laboratory and fields by molecular markers. The heterozygosity of ITS-5.8S loci for identification was unstable in the hybrid population, and the allele inherited from B. m. mucronatus was lost over several generations. We also provided evidence that hybrids existed in some new epidemic areas, while old epidemic areas were usually dominated by B. xylophilus. Hybrids could be generated when B. m. mucronatus was invaded by B. xylophilus, and the pathogenicity of the hybrids was similar to that of B. xylophilus. These findings may improve the understanding of the natural hybridization between B. xylophilus and B. m. mucronatus and pathogenic variation in pine wilt disease, providing new insights for future studies on disease detection, transmission, and quarantine.
Development of a Novel Tear Lipid Test Strip
Authors: Li Qian , Jiao Shu-Jie , Wang Yue-Qi , Xie Hua-Tao , Zhang Ming-Chang 
Published: November 2021

Purpose:
The unifying characteristic of dry eye is the loss of tear film homeostasis, and the tear lipid layer is a key component for maintaining film stability. The detection of tear lipid is of great significance for the diagnosis of dry eye. In this study, we explored a new test strip for the detection of tear lipid.

Methods:
The tear lipid test strip was prepared by coating the strip material with hydrophobic nano-silica. We tested its physical properties with iodine vapor chromogenic and cobalt chloride test methods. Its biosafety was evaluated by an ocular irritation test in rabbits. Finally, we established a rabbit meibomian gland dysfunction model and measured both eyes with the tear lipid test strip at the first, third, seventh, 14th, 16th, and 21st day after surgery.

Results:
The tear lipid test strip had fine lipophilicity and hydrophobicity. It can extract lipid from tear, and the tear lipid can be quantified by measuring the length of lipid infiltration. In the ocular irritation test, the test strip had no obvious eye irritation. The length of lipid infiltration between experimental and control rabbit eyes began to show statistical difference since the third day after surgery.

Conclusions:
The novel tear lipid test strip has great lipophilicity, hydrophobicity, and biological safety. It might be effectively applied in diagnosis of dry eye.
Outcomes of Descemet Membrane Endothelial Keratoplasty Using Cornea From Elderly Donors Aged 80 Years and Older: In the Aftermath of Current Donor Shortage
Authors: Basak Samar K. , Basak Soham , Gajendragadkar Nidhi 
Published: November 2021

Purpose:
The purpose of this study was to report the outcomes of Descemet membrane endothelial keratoplasty (DMEK) using corneas from elderly donors aged 80 years and older.

Methods:
Eighty eyes of 78 patients who underwent DMEK-only or DMEK combined with cataract extraction (triple-DMEK) with surgeon-prepared graft between April 2016 and March 2020 were reviewed. Corrected distance visual acuity, endothelial cell density (ECD), and endothelial cell loss after 6 months, 1 year, and 2 years were analyzed.

Results:
The mean donor age was 83.6 ± 3.7 years (range: 80–100 years), and the mean donor ECD was 2889 ± 177 cells/mm2 (range: 2604–3460 cells/mm2). The mean recipient age was 67.2 ± 6.9 years (range: 60–89 years), and the mean follow-up was 21 ± 11 months (range: 6–52 months). The mean corrected distance visual acuity improved from a preoperative value of 1.36 ± 0.67 logarithm of the minimum angle of resolution to 0.22 ± 0.18 at 6 months (n = 75), 0.21 ± 0.2 at 1 year (n = 64), and 0.23 ± 0.3 logarithm of the minimum angle of resolution at 2 years (n = 41), respectively (P < 0.001). In 72 eyes (96%), the graft remained transparent until the last follow-up visit. The mean postoperative ECD was 2073 ±336 (n = 75), 1951 ± 379 (n = 65), and 1807 ± 431 cells/mm2 (n = 41) at 6 months, 1 year, and 2 years, respectively. Five eyes (6.7%) had donor detachments of which 4 required rebubbling. Two grafts failed after 1 year, and 2 eyes (2.6%) had graft rejection, of which 1 eye was reverted successfully by medical management.

Conclusions:
Cornea from elderly donors aged 80 years and older with good selection criteria may be considered for DMEK with successful outcomes. For India and other countries with unmet tissue needs, every best single cornea counts.
PACK Cross-Linking as Adjuvant Therapy Improves Clinical Outcomes in Culture-Confirmed Bacterial Keratitis
Authors: Achiron Asaf , Elhaddad Omar , Regev Tamir , Krakauer Yonit , Tsumi Erez , Hafezi Farhad , Knyazer Boris 
Published: November 2021

Purpose:
We recently showed the positive clinical effects of combining accelerated corneal cross-linking (PACK-CXL) with antibiotic treatment in patients with presumed bacterial keratitis. In this study, we compare the impacts of a combined PACK-CXL/standard antibiotic treatment (PACK-ABX group) with standard antibiotic treatment alone (ABX group) in patients with culture-confirmed bacterial keratitis.

Methods:
We reviewed patients with moderate and severe bacterial keratitis and confirmed bacterial cultures. Clinical outcomes were compared for standard antibiotic treatment alone, before the initiation of PACK-CXL, and after adjuvant use of PACK-CXL.

Results:
A total of 47 eyes of 47 patients were included: 26 eyes in the PACK-ABX group and 21 eyes in the ABX group. Pathogens, baseline demographics (besides age), and clinical parameters were similar between the 2 groups. The PACK-ABX patients had better final uncorrected visual acuity [mean difference 0.57 Logarithm of the Minimum Angle of Resolution, 95% Confidence Interval (CI): 0.16–0.99, P = 0.07] and best-corrected visual acuity (mean difference 0.70 Logarithm of the Minimum Angle of Resolution, 95% CI: 0.23–1.16, P = 0.04), shorter reepithelialization time (mean difference 9.63 days, 95% CI: 3.14–16.12, P = 0.004), and reduced number of clinic visits (mean difference 4.8 meetings, 95% CI: 1.4–8.2, P = 0.007) and need for tectonic grafts (0 vs. 33.3%, P = 0.002). A multivariate analysis controlling for age, sex, ulcer size, and Gram stain showed that PACK-ABX treatment remained significantly associated with reepithelialization time (β = 14.5, P = 0.001).

Conclusions:
In our study, PACK-CXLs addition to the standard of care in cases of culture-proven bacterial keratitis had a positive effect on the final visual acuity and time to resolution, compared with the standard-of-care treatment.
Construction and Validation of a Predictive Nomogram Based on Ultrasound for Lymph Node Metastasis of Papillary Thyroid Carcinoma in the Cervical Central Region
Authors: Shen Haolin , Lv Guorong , Li Tingting , Wang Yuegui , Chen Keyue , Wang Kangjian , Li Ling , Zheng Xiaoyun , Yang Shuping 
Published: November 2021

Abstract
To establish and validate a nomogram for predicting lymph node metastasis (LNM) of papillary thyroid carcinoma (PTC) in the cervical central region. This retrospective study included 287 PTC patients with 309 nodules treated from December 2018 to May 2020 at our hospital. The cohort was divided randomly into a training set and a testing set according to a 7:3 ratio. The training set contained 216 nodules, and the testing set contained 93 nodules. The nomogram was developed using the training set, and the data of the testing set were used to validate the performance of nomogram. The predictive accuracy and discriminative ability of the nomogram were determined by concordance index (C-index) and calibration curve. The study showed multifocality, thyroid lesion size, and American College of Radiology Thyroid Imaging, Reporting and Data System (TI-RADS) score were significantly independently associated with LNM in the cervical central region. In the testing set, the calibration curve showed that the nomogram had good discrimination with a C-index of 0.775 (95% confidence interval, 0.680–0.869) and adequate calibration (P = 0.808). By decision curve analysis and clinical impact curve analysis, the nomogram was shown to have a satisfactory net benefit between thresholds of 0.40 and 0.75. The nomogram can be used for predicting LNM of PTC in the cervical central region and may provide valuable guidance for planning the surgical treatment of PTC patients.
CXCL13 Is an Indicator of Germinal Center Activity and Alloantibody Formation Following Transplantation
Authors: Crichton Emma S. , Zeng Shan , La Muraglia G. Michael , Badell I. Raul 
Published: November 2021

Background.
Donor-specific antibodies (DSA) are a recognized cause of allograft injury, yet biomarkers that indicate their development posttransplant or guide management are not available. CXCL13 (chemokine [C-X-C motif] ligand 1) is a chemoattractant produced within secondary lymphoid organs necessary for germinal center (GC) and alloantibody formation. Perturbations in serum CXCL13 levels have been associated with humoral immune activity. Therefore, CXCL13 may correlate with the formation of HLA antibodies following transplantation.

Methods.
A murine skin graft model was utilized to define the production and kinetics of CXCL13 in response to alloantigen. Human Tfh:B-cell in vitro cocultures were performed to evaluate CXCL13 production by human lymphocytes, and serum from healthy controls and human transplant recipients with and without de novo DSA was tested for CXCL13.

Results.
CXCL13 was detectable in the blood of allografted mice and correlated with Tfh and GC B-cell responses. Greater CXCL13 expression was observed in the draining lymph nodes of allografted mice as compared with naïve or syngeneic graft recipients, and serum levels preceded the detection of DSA posttransplant. Similarly, productive human Tfh:B-cell interactions that led to plasmablast differentiation and IgG formation also exhibited CXCL13 expression. CXCL13 levels in human transplant recipients with de novo DSA were greater than in healthy controls and stable transplant patients and also correlated with the development of alloantibodies in a small cohort of serially monitored recipients.

Conclusions.
CXCL13 indicates GC alloreactivity and alloantibody formation and correlated with DSA formation in kidney transplant recipients, thereby introducing CXCL13 as a potential biomarker for HLA antibodies.
Modern perspectives on near-equilibrium analysis of Turing systems
Authors: Krause Andrew L. , Gaffney Eamonn A. , Maini Philip K. , Klika Václav 
Published: November 2021

In the nearly seven decades since the publication of Alan Turing’s work on morphogenesis, enormous progress has been made in understanding both the mathematical and biological aspects of his proposed reaction–diffusion theory. Some of these developments were nascent in Turing’s paper, and others have been due to new insights from modern mathematical techniques, advances in numerical simulations and extensive biological experiments. Despite such progress, there are still important gaps between theory and experiment, with many examples of biological patterning where the underlying mechanisms are still unclear. Here, we review modern developments in the mathematical theory pioneered by Turing, showing how his approach has been generalized to a range of settings beyond the classical two-species reaction–diffusion framework, including evolving and complex manifolds, systems heterogeneous in space and time, and more general reaction-transport equations. While substantial progress has been made in understanding these more complicated models, there are many remaining challenges that we highlight throughout. We focus on the mathematical theory, and in particular linear stability analysis of ‘trivial’ base states. We emphasize important open questions in developing this theory further, and discuss obstacles in using these techniques to understand biological reality.This article is part of the theme issue ‘Recent progress and open frontiers in Turing’s theory of morphogenesis’.
Healthcare professionals’ knowledge and practices towards hospital infections in surgical clinics
Authors: Galanis Petros , Kokkoliou Katerina , Vraka Irene , Konstantakopoulou Olympia , Siskou Olga , Bilali Angeliki , Kaitelidou Daphne 
Published: November 2021

AbstractBackgroundHospital-acquired infections are a major public health problem, as they increase hospitalization, cost, morbidity, mortality and antibiotic resistance.AimTo assess the level of knowledge and practices of health professionals about hospital infections in surgical clinics and investigate possible determinants that affects their compliance with international protocols for prevention and control of hospital infections.MethodsA cross-sectional study with a convenience sample was conducted. Study population included 106 health professionals from medical and nursing staff in surgical clinics of a general hospital in Attica. Data collection was conducted during October and December 2019. We used the Healthcare-Associated Infections questionnaire to measure knowledge and practices of health professionals about hospital infections.ResultsThe mean overall knowledge score for hospital infections was 59.4, indicating a moderate level of knowledge. The highest level of knowledge was about the safety of healthcare professionals, while the lowest level was about the source of hospital infections. The results of the multivariate linear regression showed that participants who were aware of the infection control program at their hospital and knew they had to wash their hands following the six steps of the hand hygiene protocol had a higher level of knowledge score regarding hospital infections. In contrast, participants who felt that their hospital was following a good infection control and prevention strategy had a lower level of knowledge. In addition, healthcare professionals who washed their hands before and after examining patients, after using medical equipment for patient care, throughout and after the end of the shift, and after removing disposable gloves had a higher level of knowledge for hospital infections.ConclusionsThe findings of the present study are consistent with the international literature on the existence of a moderate level of knowledge regarding international prevention guidelines. Compliance of healthcare professionals is essential to achieve universal, quality and safe healthcare and a safe working environment.
The effects of chronic consumption of lipid-rich and delipidated bovine dairy milk on brown adipose tissue volume in wild-type mice
Authors: D’Alonzo Zachary , Mamo John , Graneri Liam , Takechi Ryu , Lam Virginie 
Published: November 2021

AbstractBrown adipose tissue (BAT) activation is associated with increased energy expenditure by inducing non-shivering thermogenesis. Ingestion of a milk fat globule membrane (MFGM) supplement and a high calorie diet are reported gateways into BAT activation. However, little is known about the effect of MFGM and high calorie diets on BAT volume. To gain insight into this, mice were maintained on a high fat (HF) or low-fat (LF) diet in conjunction with either full-cream (FC) or skim bovine dairy milk (BDM). After being maintained on their respective diets for 13 weeks, body composition, including BAT volume, was measured using X-ray microtomography. A high calorie diet resulted in an increase in BAT volume and mice consuming a HF diet in conjunction with FC BDM had significantly greater BAT volume than all other groups. Conversely, mice consuming a HF diet in addition to skim milk had lower BAT volume compared to the HF control. The data presented suggests that consumption of a high calorie diet in conjunction with FC BDM increases BAT volume in wild-type mice. This study may provide valuable insight into future studies investigating BAT volume and BAT activity in relation to environmental factors including diet.
Spacemake: processing and analysis of large-scale spatial transcriptomics data
Authors: Sztanka-Toth Tamas Ryszard , Jens Marvin , Karaiskos Nikos , Rajewsky Nikolaus 
Published: November 2021

AbstractSpatial sequencing methods increasingly gain popularity within RNA biology studies. State-of-the-art techniques can read mRNA expression levels from tissue sections and at the same time register information about the original locations of the molecules in the tissue. The resulting datasets are processed and analyzed by accompanying software which, however, is incompatible across inputs from different technologies. Here, we present spacemake, a modular, robust and scalable spatial transcriptomics pipeline built in snakemake and python. Spacemake is designed to handle all major spatial transcriptomics datasets and can be readily configured to run on other technologies. It can process and analyze several samples in parallel, even if they stem from different experimental methods. Spacemake’s unified framework enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports. Moreover, spacemake is built with a modular design and offers additional functionality such as sample merging, saturation analysis and analysis of long-reads as separate modules. Moreover, spacemake employs novoSpaRc to integrate spatial and single-cell transcriptomics data, resulting in increased gene counts for the spatial dataset. Spacemake is open-source, extendable and can be readily integrated with existing computational workflows.
A combinatorial indexing strategy for epigenomic profiling of plant single cells
Authors: Tu Xiaoyu , Marand Alexandre P. , Schmitz Robert J. , Zhong Silin 
Published: November 2021

ABSTRACTUnderstanding how cis-regulatory elements facilitate gene expression is a key question in biology. Recent advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs. However, the high equipment and reagent costs of commercial systems limit their applications for many laboratories. In this study, we profiled the Arabidopsis root single-cell epigenome using a combinatorial index and dual PCR barcode strategy without the need of any specialized equipment. We generated chromatin accessibility profiles for 13,576 Arabidopsis thaliana root nuclei with an average of 12,784 unique Tn5 integrations per cell and 85% of the Tn5 insertions localizing to discrete accessible chromatin regions. Comparison with data generated from a commercial microfluidic platform revealed that our method is capable of unbiased identification of cell type-specific chromatin accessibility with improved throughput, quality, and efficiency. We anticipate that by removing cost, instrument, and other technical obstacles, this combinatorial indexing method will be a valuable tool for routine investigation of single-cell epigenomes and usher new insight into plant growth, development and their interactions with the environment.