bluuebunny/crossref_metadata_2025_split huggingface dataset:
A full-dimensional ab initio potential energy and dipole moment surfaces for (NH3)2
Authors: Yang Shuo , Zhang Zhaojun , Zhang Dong H. 
Published: October 2021

A full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) for the ammonia dimer (NH3)2 are reported. The database of the PES consists of 27 736 ab initio energy points and all of these points were calculated at the UCCSD(T)-F12a/AVTZ level. The PES was fitted by using the fundamental invariant neural network (FI-NN) method that satisfies the permutational symmetry of identical atoms, and the root mean square fitting error for the PES is very small as low as 0.562 meV. The geometries for the (NH3)2 DMS are the same as those used for the PES and are calculated at the XYG3/AVTZ level. This PES can describe a variety of internal floppy motions, including all kinds of vibrational modes no matter intermolecular or intramolecular. The CCSD(T)-PES can dissociate correctly to two NH3 monomers, with De = 1135.55 cm−1 (13.58 kJ/mol) which agrees accurately with the 13.5 ± 0.3 kJ/mol predicted by previous work.
Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling
Authors: Tower Robert J. , Li Zhu , Cheng Yu-Hao , Wang Xue-Wei , Rajbhandari Labchan , Zhang Qian , Negri Stefano , Uytingco Cedric R. , Venkatesan Arun , Zhou Feng-Quan , Cahan Patrick , James Aaron W. , Clemens Thomas L. 
Published: October 2021

Significance
Sensory nerves innervate bone and are required for normal skeletal development, but the molecular mechanisms through which nerves exert these essential functions have remained obscure. Here, we validate a spatial transcriptomics platform, which allowed us to map changes in the molecular landscape across the developing cranium of mice in which sensory nerve innervation is genetically blocked. We show that sensory, nerve-derived signals, including follistatin-like 1, coordinate cranial bone patterning by regulating the proliferation and differentiation of bone precursor cells within the suture mesenchyme.
A specialized spinal circuit for command amplification and directionality during escape behavior
Authors: Guan Na N. , Xu Lulu , Zhang Tianrui , Huang Chun-Xiao , Wang Zhen , Dahlberg Elin , Wang Haoyu , Wang Fangfang , Pallucchi Irene , Hua Yunfeng , El Manira Abdeljabbar , Song Jianren 
Published: October 2021

Significance
We are constantly faced with a choice moving to the left or right; understanding how the brain solves the selection of action direction is of tremendous interest both from biological and clinical perspectives. In vertebrates, action selection is often considered to be the realm of higher cognitive processing. However, by combining electrophysiology, serial block-face electron microscopy, and behavioral analyses in zebrafish, we have revealed a pivotal role, as well as the full functional connectome of a specialized spinal circuit relying on strong axo-axonic synaptic connections. This includes identifying a class of cholinergic V2a interneurons and establishing that they act as a segmentally repeating hub that receives and amplifies escape commands from the brain to ensure the appropriate escape directionality.
The mesoscale order of nacreous pearls
Authors: Gim Jiseok , Koch Alden , Otter Laura M. , Savitzky Benjamin H. , Erland Sveinung , Estroff Lara A. , Jacob Dorrit E. , Hovden Robert 
Published: October 2021

Significance
Despite a century of scientific fascination with nacre’s periodic mesostructure, there remains a fundamental question of whether long-range order exists. In this work, the stochastic growth that leads to mesoscale order in the nacreous pearl is revealed by quantifying its structural coherence across entire pearl specimens. We find that mollusks strike a balance between preserving translational symmetry and minimizing thickness variation of layers by creating a paracrystal with medium-range order. Self-correcting growth processes allow pearls to quickly attenuate disorder, accommodate topological defects in tablet structure, and maintain order throughout a fluctuating external environment. These observations were made possible by characterizing the entire structure of Akoya “keshi” pearls (∼3 mm) at high resolution (<∼3 nm).
Berlesiella nigerrima
. [Descriptions of Fungi and Bacteria].
Authors: Cannon P. F. , Minter D. W. 
Published: October 2021

Abstract

A description is provided for
Berlesiella nigerrima
, parasitic on stromata of
Cryptosphaeria lignyota
growing on rotten twig of
Salix capre
. Some information on its morphological characteristics, associated organisms and substrata, dispersal and transmission, habitats and conservation status is given, along with details of its geographical distribution (Asia (India, Madhya Pradesh, Maharashtra, Taiwan), Europe (Austria, Belgium, Denmark, France, Germany, Hungary, Lithuania, Luxembourg, Netherlands, Norway, Romania, Russia, Spain, Sweden, Ukraine, UK), North America (Canada, Ontario, USA, California, Florida, Georgia, Oregon, Tennessee), South America (Argentina)).
Capronia sexdecimspora
. [Descriptions of Fungi and Bacteria].
Authors: Cannon P. F. , Minter D. W. 
Published: October 2021

Abstract

A description is provided for
Capronia sexdecimspora
, which is very poorly known, and this constitutes the first comprehensive description of the species. Some information on its associated organisms and substrata, dispersal and transmission, habitats and conservation status is given, along with details of its geographical distribution (Europe (Iceland, UK)).
Deep learning-based advances and applications for single-cell RNA-sequencing data analysis
Authors: Bao Siqi , Li Ke , Yan Congcong , Zhang Zicheng , Qu Jia , Zhou Meng 
Published: October 2021

AbstractThe rapid development of single-cell RNA-sequencing (scRNA-seq) technology has raised significant computational and analytical challenges. The application of deep learning to scRNA-seq data analysis is rapidly evolving and can overcome the unique challenges in upstream (quality control and normalization) and downstream (cell-, gene- and pathway-level) analysis of scRNA-seq data. In the present study, recent advances and applications of deep learning-based methods, together with specific tools for scRNA-seq data analysis, were summarized. Moreover, the future perspectives and challenges of deep-learning techniques regarding the appropriate analysis and interpretation of scRNA-seq data were investigated. The present study aimed to provide evidence supporting the biomedical application of deep learning-based tools and may aid biologists and bioinformaticians in navigating this exciting and fast-moving area.
Metrics for evaluating differentially methylated region sets predicted from BS-seq data
Authors: Peng Xiaoqing , Luo Hongze , Kong Xiangyan , Wang Jianxin 
Published: October 2021

AbstractInvestigating differentially methylated regions (DMRs) presented in different tissues or cell types can help to reveal the mechanisms behind the tissue-specific gene expression. The identified tissue-/disease-specific DMRs also can be used as feature markers for spotting the tissues-of-origins of cell-free DNA (cfDNA) in noninvasive diagnosis. In recent years, many methods have been proposed to detect DMRs. However, due to the lack of benchmark DMRs, it is difficult for researchers to choose proper methods and select desirable DMR sets for downstream studies. The application of DMRs, used as feature markers, can be benefited by the longer length of DMRs containing more CpG sites when a threshold is given for the methylation differences of DMRs. According to this, two metrics ($Qn$ and $Ql$), in which the CpG numbers and lengths of DMRs with different methylation differences are weighted differently, are proposed in this paper to evaluate the DMR sets predicted by different methods on BS-seq data. DMR sets predicted by eight methods on both simulated datasets and real BS-seq datasets are evaluated by the proposed metrics, the benchmark-based metrics, and the enrichment analysis of biological data, including genomic features, transcription factors and histones. The rank correlation analysis shows that the $Qn$ and $Ql$ are highly correlated to the benchmark metrics for simulated datasets and the biological data enrichment analysis for real BS-seq data. Therefore, with no need for additional biological data, the proposed metrics can help researchers selecting a more suitable DMR set on a certain BS-seq dataset.
Acoustic clue: bringing echolocation call data into the distribution dilemma of Pteronotus (Chiroptera: Mormoopidae) complexes in Central America
Authors: Arias-Aguilar Adriana , Ramos Pereira Maria João 
Published: October 2021

Abstract
In Central America, the distributional limits and the contact zones of some Pteronotus species, such as the naked-backed bats and the lesser mustached bats, are unclear. To elucidate the distributional dilemma of the species groups Pteronotus fulvus + Pteronotus davyi and Pteronotus psilotis + Pteronotus personatus in Central America, we studied the acoustic variation of their echolocation calls along the range of possible contact zones and the existence of distinct phonic groups. We performed hierarchical k-means clustering on principal components (HCPC) using acoustic samples from Mexico, Honduras, El Salvador, Nicaragua and Costa Rica to describe the global acoustic diversity, possibly overlooking differences between species groups. We assessed whether those acoustic differences were related to the geographical distance and geographical location. We found evidence of sympatry for three phonic groups within each species complex, without a clear correspondence to the known distribution of species. The changes in frequency of their echolocation calls seem to follow a similar pattern to the geographical variation in body size of the species. Future studies in Central America should include an integrative sampling of individually captured, tagged and recorded bats to help in resolution of the distribution dilemma raised here.
Evidence that pubertal status impacts kisspeptin/neurokinin B/dynorphin neurons in the gilt
Authors: Harlow KaLynn , Renwick Allison N , Shuping Sydney L , Sommer Jeffrey R , Lents Clay A , Knauer Mark T , Nestor Casey C 
Published: October 2021

Abstract
Puberty onset is a complex physiological process, which enables the capacity for reproduction through increased gonadotropin-releasing hormone and subsequently luteinizing hormone secretion. While cells that coexpress kisspeptin, neurokinin B (NKB), and dynorphin in the hypothalamic arcuate nucleus are believed to govern the timing of puberty, the degree to which kisspeptin/NKB/dynorphin (KNDy) neurons exist and are regulated by pubertal status remains to be determined in the gilt. Hypothalamic tissue from prepubertal and postpubertal, early follicular phase gilts was used to determine the expression of kisspeptin, NKB, and dynorphin within the arcuate nucleus. Fluorescent in situ hybridization revealed that the majority (&gt;74%) of arcuate nucleus neurons that express mRNA for kisspeptin coexpressed mRNA for NKB and dynorphin. There were fewer arcuate nucleus cells that expressed mRNA for dynorphin in postpubertal gilts compared to prepubertal gilts (P &lt; 0.05), but the number of arcuate nucleus cells expressing mRNA for kisspeptin or NKB was not different between groups. Within KNDy neurons, mRNA abundance for kisspeptin, NKB, and dynorphin of postpubertal gilts was the same as, less than, and greater than, respectively, prepubertal gilts. Immunostaining for kisspeptin did not differ between prepubertal and postpubertal gilts, but there were fewer NKB immunoreactive fibers in postpubertal gilts compared to prepubertal gilts (P &lt; 0.05). Together, these data reveal novel information about KNDy neurons in gilts and support the idea that NKB and dynorphin play a role in puberty onset in the female pig.
Joint frailty modeling of time-to-event data to elicit the evolution pathway of events: a generalized linear mixed model approach
Authors: Ng Shu Kay , Tawiah Richard , Mclachlan Geoffrey J , Gopalan Vinod 
Published: October 2021

SummaryMultimorbidity constitutes a serious challenge on the healthcare systems in the world, due to its association with poorer health-related outcomes, more complex clinical management, increases in health service utilization and costs, but a decrease in productivity. However, to date, most evidence on multimorbidity is derived from cross-sectional studies that have limited capacity to understand the pathway of multimorbid conditions. In this article, we present an innovative perspective on analyzing longitudinal data within a statistical framework of survival analysis of time-to-event recurrent data. The proposed methodology is based on a joint frailty modeling approach with multivariate random effects to account for the heterogeneous risk of failure and the presence of informative censoring due to a terminal event. We develop a generalized linear mixed model method for the efficient estimation of parameters. We demonstrate the capacity of our approach using a real cancer registry data set on the multimorbidity of melanoma patients and document the relative performance of the proposed joint frailty model to the natural competitor of a standard frailty model via extensive simulation studies. Our new approach is timely to advance evidence-based knowledge to address increasingly complex needs related to multimorbidity and develop interventions that are most effective and viable to better help a large number of individuals with multiple conditions.
141 New Guidelines to Reduce Unnecessary Blood Tests, Delayed Discharge and Costs Following Robot Assisted Radical Prostatectomy
Authors: Nathan A , Hanna N , Rashid A , Patel S , Phuah Y , Flora K , Fricker M , Cleaveland P , Kasivisvanathan V , Williams N , Miah S , Shah N , Hines J , Collins J , Sridhar A , Kelkar A , Briggs T , Kelly J , Shaw G , Sooriakumaran P , Rajan P , Lamb B , Nathan S 
Published: October 2021

Abstract

Objectives
Routine postoperative blood tests (POBT) following robot assisted radical prostatectomy (RARP) are used to evaluate the impact of surgery on pre-existing co-morbidities and to detect early complications. This practice dates back to an era of open surgery, when blood loss and complication rates were higher. We propose new guidelines to improve the specificity of POBT.

Method
The cases of 1040 consecutive patients who underwent a primary or salvage RARP at two large tertiary urology centres in the United Kingdom were retrospectively reviewed to form new guidelines. The new guidelines were prospectively validated in a sample of 300 patients.

Results
Derivation Dataset: 3% and 5% had intra- and post-operative Clavien-Dindo complications, respectively. 15% had clinical concerns postoperatively. 0.9% required perioperative transfusion. 78% had routine blood tests without clinical concerns, none of whom developed a complication. 98% of complications were suspected by clinical judgement. 6% of patients had a discharge delay of ≥ 1 day due to delayed or incomplete blood tests. Validation Dataset: No significant difference existed in complication, clinical concern or transfusion rates between the derivation and validation datasets. Number of POBT requested reduced by 73% (p &lt; 0.001). The new guidelines improved POBT sensitivity for complications from 98% to 100% and specificity from 0% to 74%. Discharge delays reduced from 6% to 0% (p = 0.008). Cost savings were £178 per patient.

Conclusions
Postoperative complications and transfusion following RARP are rare. Routine POBT without clinical indication are unnecessary and inefficient. A guideline-based approach to POBT can reduce costs and optimise discharge without compromising patient safety or care.
1557 Readmission Rates Are Not A Surrogate for Poor Practice – An Audit of Readmissions to An Emergency Surgical Unit [Emsu]- The Devil Lies in The Detail!
Authors: Kakos C , Clements J S , Clements B W D 
Published: October 2021

Abstract

Aim
Readmission rates are considered an indicator of poor performance resulting in financial penalty to healthcare trusts. The national peer review figure for monthly readmission varies considerably (1.71%-7.53%). This metric can be misleading and requires detailed analysis. The aim of this audit was to critically review the readmissions to the EMSU.

Method
A 1-month review of all patients presenting to the EMSU via a prospectively maintained electronic database was interrogated. (October 2020). The primary outcome was “true” readmission rate (i.e., inclusion criteria - readmission within 30 days of discharge). Secondary outcomes were to assess the appropriateness of readmission and consequent morbidity.

Results
331 patients were admitted with 39 readmissions (11.8%). 22 patients failed to meet the inclusion criteria. The true readmission rate was 17 (5.1%). 7/17 had a post-operative complication. The remainder had a miscellaneous minor upper and lower gastrointestinal complaints. 6/10 required cross-sectional imaging and blood work. There were no mortalities.

Conclusions
The readmission rate reported by Trust coding was erroneously high due to inaccurate recording of data. The accurate readmission rate was 5.1%. The majority of those readmitted could have been managed successfully in a Surgical Ambulatory Service [SAmS]. These data support the hypothesis that readmission rates can be misleading, and efforts should be directed not just in data recording and analysis but also in the utilization of SAmS.
1502 UK National Survey of Huber Needle Availability for Deflation of Gastric Band Balloon in The Acute Setting
Authors: Patel H R , Abdalazeez T , McDonald R , Williams R , Miller A 
Published: October 2021

Abstract

Introduction
The laparoscopic gastric band was popularised in the 1990’s. The procedure involves placement of an adjustable band around the proximal stomach, aiming to induce satiety and offering a surgical solution to morbid obesity. Complications such as band slippage and erosion, together with succession by sleeve gastrectomy and gastric bypass which offer more significant weight loss has meant the procedure has gone out of favour. However, their legacy continues with a stream of patients presenting annually with complications, many of whom have travelled abroad for the procedure. The aim of this study was to examine Huber needle availability in acute surgical units nationally.

Method
All acute general surgical admission units across the UK were identified from the National Emergency Laparotomy Audit database. The senior nurse managing each unit was contacted by telephone and asked three questions; whether their hospital has an elective bariatric service on site, whether they review acute bariatric emergencies and whether the unit stocks Huber needles.

Results
151 acute general surgical units were identified across the UK, of which 60% responded. 30/90(33%) have an elective bariatric service on site and 65/90(72%) reviewed acute bariatric patients. 8/90(8.9%) stock Huber needles for the acute deflation of gastric bands.

Conclusions
Patients presenting acutely with gastric band complications typically need urgent deflation of the gastric band. The Huber needle is a non-coring needle used for gastric band adjustment, preventing damage to the port. The Huber needle is a low-cost item and should be stocked by all acute general surgical units.
114 The Use of Magnetic Resonance Imaging in Patients with A Post-Operative Diagnosis of Invasive Lobular Carcinoma, A Retrospective Analysis
Authors: Marks B , Jalini L 
Published: October 2021

Abstract

Aim
Magnetic Resonance Imaging (MRI) is recommended pre-operatively for some patients with invasive breast carcinomas, particularly mammographically occult cancers and when tumour size may affect surgical management. Research has shown a higher incidence of both multifocal (32.7%) and bilateral (7%) cancers in invasive lobular carcinoma (ILC), affecting the surgical management of 27% of cases. The study aim was to identify whether MRI is indicated post-operatively when the pre-operative diagnosis is invasive ductal carcinoma (IDC) but post-operative diagnosis is ILC.

Method
Retrospective analysis of the medical records of patients with dual coding of IDC and ILC over a five-year period (2014-2019) was conducted. Inclusion criteria included a pre-operative diagnosis of IDC but a post-operative diagnosis of ILC. 167 patients were identified.

Results
Twenty-nine patients (17%) fulfilled the inclusion criteria. Ten (34%) had MRI scans conducted. Six (21%) were performed pre-operatively, three (10%) post-operatively and one (3%) had both a pre-operative and post-operative scan. None of the post-operative MRI scans showed further disease. One pre-operative scan identified a secondary foci, however the patient still underwent breast conserving surgery. The other nineteen patients received annual mammographic follow-up as per multidisciplinary meeting documentation, with no recurrence to date.

Conclusions
MRI at our unit is carried out as per NICE guidelines pre-operatively. Our results did not identify any further disease in patients with a post-operative diagnosis of ILC, however the sample size was small. There are currently no guidelines on the use of MRI in these patients and further, larger studies are needed to clarify its role.
147 Association of Estrogen Receptor and Porgesteron Receptor Positivity with Nodal Involvement, Menopause Status and Stage of Primary Invasive Carcinoma of Breast Among Patients Presenting to Fauji Foundation Hospital, Islamabad
Authors: Bhatti D 
Published: October 2021

Abstract

Aim
To determine the percentage of estrogen and progesterone receptor positivity along with histological variants, stage, and menopausal status among carcinoma breast patients in our setup.

Method
This was a retrospective observational study. Data from records of patients with breast carcinoma presenting at Oncology Department Fauji Foundation Hospital, Islamabad was evaluated. H+E stained slides from 431 cases with carcinoma breast, patients over the age of 18 years, were reviewed and the presence of invasive carcinoma was confirmed in all cases. Patients with metastases were excluded. Paraffin blocks were assessed immunohistochemically for estrogen and progesterone receptor expression. Histological subtypes, stages of tumors, and nodal involvement were also noted. Data were analyzed using SPSS.

Results
Records of 431 patients were evaluated. The median age was 53 years. The most common histological variant was invasive ductal carcinoma. 4.6% of patients had stage I, 33.4% had stage II, 40% had Stage III and 22% had Stage IV disease. Overall, 62% had node-positive disease. Overall ER+, PR+, ER+/PR+, ER+/PR-, ER-/PR+ and ER-/PR- percentages were 52%, 54%, 42%, 11%, 12% and 35% respectively. 38% of patients were premenopausal, 59% were postmenopausal and 3% were perimenopausal. Patients with node positive diseases were 51% ER+,55% PR+, 43% ER+/PR+, 8% ER+/PR-, 12% ER-/PR+ and 37% ER-/PR-.

Conclusions
The percentage of ER/PR+ is the highest in our study. Pre-menopausal patients showed approximately equal positivity to post-menopausal patients. Node positive enrolments had increased positivity of ER/PR receptor.