bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-time unmanned aerial vehicle flight path prediction using a bi-directional long short-term memory network with error compensation
Authors: Chen Sifan , Chen Baihe , Shu Peng , Wang Zhensheng , Chen Chengbin 
Published: November 2022

Abstract
In recent years, unmanned aerial vehicle (UAV) autonomous flight technology has been applied in many fields. However, in the process of autonomous operation, the UAV may deviate from the set flight path due to various disturbance factors, which results in mission failure. In order to find the abnormal situation in time and take corresponding measures, it is necessary to monitor the operation state of the UAV. Predicting the UAV flight path is the main monitoring method at present; however, the accuracy and real-time of the existing prediction methods are limited. Therefore, this paper proposes an error compensation Bessel bidirectional long short-term memory real-time path prediction model deployed in ground stations. First, because of inconsistency of the units in all directions of the original positioning information provided by global positioning system, the Bessel geodetic coordinate transformation is introduced to unify the units of three-dimensional coordinate data, so as to improve the prediction accuracy. Second, considering the problems of poor data quality and data missing in the operation process, the least square fitting method is used to supplement and correct the positioning coordinate data to obtain more reliable and accurate path observation values as the model input. Finally, a deep learning path prediction model based on bi-directional long short-term memory (BiLSTM) network is constructed, and the appropriate network parameters are determined with the prediction accuracy and time as evaluation indicators. In order to further improve the prediction accuracy, a compensator based on proportional integral differential error control theory is designed according to the output characteristics of the BiLSTM network, which is used for providing compensation values for the prediction results of the model. The training and testing results using the actual flight data of UAV operation show that, under the experimental environment built, the model proposed in this paper can complete the UAV flight path prediction with root mean square error &lt; 1 meter within 0.1 second, and has better performance and higher prediction accuracy than other neural network models.
Body mass index and molecular subtypes of colorectal cancer
Authors: Murphy Neil , Newton Christina C , Song Mingyang , Papadimitriou Nikos , Hoffmeister Michael , Phipps Amanda I , Harrison Tabitha A , Newcomb Polly A , Aglago Elom K , Berndt Sonja I , Brenner Hermann , Buchanan Daniel D , Cao Yin , Chan Andrew T , Chen Xuechen , Cheng Iona , Chang-Claude Jenny , Dimou Niki , Drew David , Farris Alton B , French Amy J , Gallinger Steven , Georgeson Peter , Giannakis Marios , Giles Graham G , Gruber Stephen B , Harlid Sophia , Hsu Li , Huang Wen-Yi , Jenkins Mark A , Laskar Ruhina S , Le Marchand Loic , Limburg Paul , Lin Yi , Mandic Marko , Nowak Johnathan A , Obón-Santacana Mereia , Ogino Shuji , Qu Conghui , Sakoda Lori C , Schoen Robert E , Southey Melissa C , Stadler Zsofia K , Steinfelder Robert S , Sun Wei , Thibodeau Stephen N , Toland Amanda E , Trinh Quang M , Tsilidis Kostas K , Ugai Tomotaka , Van Guelpen Bethany , Wang Xiaoliang , Woods Michael O , Zaidi Syed H , Gunter Marc J , Peters Ulrike , Campbell Peter T 
Published: November 2022

Abstract

Background
Obesity is an established risk factor for colorectal cancer (CRC), but the evidence for the association is inconsistent across molecular subtypes of the disease.

Methods
We pooled data on body mass index (BMI), tumor microsatellite instability status, CpG island methylator phenotype status, BRAF and KRAS mutations, and Jass classification types for 11 872 CRC cases and 11 013 controls from 11 observational studies. We used multinomial logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) adjusted for covariables.

Results
Higher BMI was associated with increased CRC risk (OR per 5 kg/m2 = 1.18, 95% CI = 1.15 to 1.22). The positive association was stronger for men than women but similar across tumor subtypes defined by individual molecular markers. In analyses by Jass type, higher BMI was associated with elevated CRC risk for types 1-4 cases but not for type 5 CRC cases (considered familial-like/Lynch syndrome microsatellite instability-H, CpG island methylator phenotype-low or negative, BRAF-wild type, KRAS-wild type, OR = 1.04, 95% CI = 0.90 to 1.20). This pattern of associations for BMI and Jass types was consistent by sex and design of contributing studies (cohort or case-control).

Conclusions
In contrast to previous reports with fewer study participants, we found limited evidence of heterogeneity for the association between BMI and CRC risk according to molecular subtype, suggesting that obesity influences nearly all major pathways involved in colorectal carcinogenesis. The null association observed for the Jass type 5 suggests that BMI is not a risk factor for the development of CRC for individuals with Lynch syndrome.
A novel genome sequence ofJasminum sambachelps uncover the molecular mechanism underlying the accumulation of jasmonates
Authors: Xu Min , Gao Qiang , Jiang Mengwei , Wang Wenling , Hu Juan , Chang Xiaojun , Liu Dinggao , Liang Yuwei , Jiang Yifan , Chen Fei , Li Chuhao , Huang Haoran , Chen Feng , Li Fan , Trigiano Robert N , Wang Jihua , Jiao Chen , Zhou Xiaofan , Zhang Liangsheng 
Published: November 2022

AbstractJasminum sambac is a well-known plant for its attractive and exceptional fragrance, the flowers of which are used to produce scented tea. Jasmonate (JA), an important plant hormone was first identified in Jasminum species. Jasmine plants contain abundant JA naturally, of which the molecular mechanisms of synthesis and accumulation are not clearly understood. Here, we report a telomere-to-telomere consensus assembly of a double-petal J. sambac genome along with two haplotype-resolved genomes. We found that gain-and-loss, positive selection, and allelic specific expression of aromatic volatile-related genes contributed to the stronger flower fragrance in double-petal J. sambac compared with single- and multi-petal jasmines. Through comprehensive comparative genomic, transcriptomic, and metabolomic analyses of double-petal J. sambac, we revealed the genetic basis of the production of aromatic volatiles and salicylic acid (SA), and the accumulation of JA under non-stress conditions. We identified several key genes associated with JA biosynthesis, and their non-stress related activities lead to extraordinarily high concentrations of JA in tissues. High JA synthesis coupled with low degradation in J. sambac results in accumulation of high JA under typical environmental conditions, similar to the accumulation mechanism of SA. This study offers important insights into the biology of J. sambac, and provides valuable genomic resources for further utilization of natural products.
Hyperbaric Oxygen Therapy for Veterans With Treatment-resistant PTSD: A Longitudinal Follow-up Study
Authors: Doenyas-Barak Keren , Kutz Ilan , Levi Gabriela , Lang Erez , Beberashvili Ilia , Efrati Shai 
Published: November 2022

ABSTRACT

Introduction
PTSD is common among veteran combatants. PTSD is characterized by brain changes, for which available treatments have shown limited effect. In a short-term study, we showed that hyperbaric oxygen therapy (HBOT) induced neuroplasticity and improved clinical symptoms of veterans with treatment-resistant PTSD. Here, we evaluated the long-term clinical symptoms of the participants of that study.

Materials and Methods
Veterans from our short-term study were recruited 1 or more years after completing HBOT. The Clinician-Administered PTSD Scale for DSM-5 (CAPS-5) and self-reported questionnaires were administered at a single site visit. Changes in clinical scores between long-term, short-term, and pretreatment evaluations were analyzed.

Results
Of the 28 participants who received HBOT during or following the short-term study, 22 agreed to participate in the current study. At a mean of 704 ± 230 days after completing the HBOT course, the mean CAPS-5 score (26.6 ± 14.4) was significantly better (lower) than at the pre-HBOT evaluation (47.5 ± 13.1, P &lt; .001) and not statistically different from the short-term evaluation (28.6 ± 16.7, P = .745). However, for the CAPS-5 subcategory D (cognition and mood symptoms), the mean score was significantly better (lower) at long-term than at short-term evaluation (7.6 ± 5.1 vs. 10.0 ± 6.0, P &lt; .001). At the long-term compared to the pretreatment evaluation, higher proportions of the participants were living with life partners (10 (46%) vs. 17 (77%), P = .011) and were working (9 (41%) vs. 16 (73%), P = .033). Decreases were observed between pretreatment and the long-term follow-up, in the number of benzodiazepine users (from 10 (46%) to 4 (18%), P = .07) and in the median (range) cannabis daily dose (from 40.0 g (0-50) to 22.5 g (0-30), P = .046).

Conclusions
The beneficial clinical effects of HBOT are persistent and were not attenuated at long-term follow-up of about 2 years after completion of HBOT. Additional long-term effects of the treatment were observed in social function and in decreased medication use.
Incidence and survival of primary central nervous system tumors diagnosed in 4 Canadian provinces from 2010 to 2015
Authors: Walker Emily V , Davis Faith G , Yasmin Farzana , Smith Trenton R , Yuan Yan 
Published: November 2022

AbstractBackgroundThe Brain Tumor Registry of Canada was established in 2016 to enhance infrastructure for surveillance and clinical research on Central Nervous System (CNS) tumors. We present information on primary CNS tumors diagnosed among residents of Canada from 2010 to 2015.MethodsData from 4 provincial cancer registries were analyzed representing approximately 67% of the Canadian population. Age-standardized incidence rates (ASIR) and 95% confidence intervals (CI) were calculated using the 2011 Canadian population age distribution. Net survival was estimated using the Pohar-Perme method.ResultsA total of 31 644 primary tumors were identified for an ASIR of 22.8 per 100 000 person-years. Nonmalignant tumors made up 47.1% of all classified tumors, with mixed behaviors present in over half of histology groupings. Unclassified were 19.5% of all tumors. The most common histological subtypes are meningiomas (ASIR = 5.5 per 100 000 person-years); followed by glioblastomas (ASIR 4.0 per 100 000 person-years). The overall 5-year net survival rate for CNS tumors was 65.5%; females 70.2% and males 60.4%. GBMs continue to be the most lethal CNS tumors for all sex and age groups.ConclusionsThe low annual frequency of most CNS tumor subtypes emphasizes the value of population-based data on all primary CNS tumors diagnosed among Canadians. The large number of histological categories including mixed behaviors and the proportion of unclassified tumors emphasizes the need for complete reporting. Variation in incidence and survival across histological groups by sex and age highlights the need for comprehensive and histology-specific reporting. These data can be used to better inform research and health system planning.
NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters
Authors: Leão Tiago F , Wang Mingxun , da Silva Ricardo , Gurevich Alexey , Bauermeister Anelize , Gomes Paulo Wender P , Brejnrod Asker , Glukhov Evgenia , Aron Allegra T , Louwen Joris J R , Kim Hyun Woo , Reher Raphael , Fiore Marli F , van der Hooft Justin J J , Gerwick Lena , Gerwick William H , Bandeira Nuno , Dorrestein Pieter C 
Published: November 2022

Abstract
Microbial specialized metabolites are an important source of and inspiration for many pharmaceuticals, biotechnological products and play key roles in ecological processes. Untargeted metabolomics using liquid chromatography coupled with tandem mass spectrometry is an efficient technique to access metabolites from fractions and even environmental crude extracts. Nevertheless, metabolomics is limited in predicting structures or bioactivities for cryptic metabolites. Efficiently linking the biosynthetic potential inferred from (meta)genomics to the specialized metabolome would accelerate drug discovery programs by allowing metabolomics to make use of genetic predictions. Here, we present a k-nearest neighbor classifier to systematically connect mass spectrometry fragmentation spectra to their corresponding biosynthetic gene clusters (independent of their chemical class). Our new pattern-based genome mining pipeline links biosynthetic genes to metabolites that they encode for, as detected via mass spectrometry from bacterial cultures or environmental microbiomes. Using paired datasets that include validated genes-mass spectral links from the Paired Omics Data Platform, we demonstrate this approach by automatically linking 18 previously known mass spectra (17 for which the biosynthesis gene clusters can be found at the MIBiG database plus palmyramide A) to their corresponding previously experimentally validated biosynthetic genes (e.g., via nuclear magnetic resonance or genetic engineering). We illustrated a computational example of how to use our Natural Products Mixed Omics (NPOmix) tool for siderophore mining that can be reproduced by the users. We conclude that NPOmix minimizes the need for culturing (it worked well on microbiomes) and facilitates specialized metabolite prioritization based on integrative omics mining.
Obesity in children with narcolepsy: metabolic and endocrine comorbidities
Authors: Arvis Laura , Doye Emilie , Perge Kevin , Zhang Min , Thieux Marine , Guyon Aurore , Franco Patricia , Villanueva Carine 
Published: November 2022

Abstract

Study Objectives
Narcolepsy with cataplexy is associated with obesity in children. We proposed to assess whether metabolic complications were linked to narcolepsy regardless of obesity. The second aim of the study was to compare endocrine comorbidities in obese children with narcolepsy and control patients.

Methods
We performed a case-control study in Pediatric Sleep Unit and Pediatric Endocrinology Unit of Woman Mother Child Hospital (Lyon, France) comparing 22 children with narcolepsy with 22 sex-, pubertal stage-, and BMI-matched non-syndromic obese patients. Clinical examination, biological measurements including an oral glucose tolerance test, and abdominal ultrasound were performed.

Results
No difference regarding glucidic, lipid profile, hepatic, respiratory, and cardiovascular parameters were found between narcoleptic and control participants. Insulin sensitivity did not differ between the two groups. Control patients had more first-degree family history of overweight or obesity than children with narcolepsy (83% vs. 50%, p = .05). Prevalence of precocious puberty in children with narcolepsy was not higher than in control participants, but all the cases of advanced puberty involved children with narcolepsy who were diagnosed before 11 years old. All cases of central hypothyroidism belong to the narcoleptic group, who presented lower thyroid-stimulating hormone and fTA values compared to control children (respectively p = .03 and p = .001).

Conclusions
No difference regarding metabolic complications was found between children with narcolepsy and control participants. Thus, metabolic disorders may be related to weight gain rather than a narcolepsy-specific risk. The presence of hypothyroidism and advanced puberty suggests a global involvement of hypothalamic structures in children with narcolepsy.
SARS-CoV-2 intra-host single-nucleotide variants associated with disease severity
Authors: Zhang Yi , Jiang Ning , Qi Weiqiang , Li Tao , Zhang Yumeng , Wu Jing , Zhang Haocheng , Zhou Mingzhe , Cui Peng , Yu Tong , Fu Zhangfan , Zhou Yang , Lin Ke , Wang Hongyu , Wei Tongqing , Zhu Zhaoqin , Ai Jingwen , Qiu Chao , Zhang Wenhong 
Published: November 2022

Abstract
Variants of severe acute respiratory syndrome coronavirus 2 frequently arise within infected individuals. Here, we explored the level and pattern of intra-host viral diversity in association with disease severity. Then, we analyzed information underlying these nucleotide changes to infer the impetus including mutational signatures and immune selection from neutralizing antibody or T-cell recognition. From 23 January to 31 March 2020, a set of cross-sectional samples were collected from individuals with homogeneous founder virus regardless of disease severity. Intra-host single-nucleotide variants (iSNVs) were enumerated using deep sequencing. Human leukocyte antigen (HLA) alleles were genotyped by Sanger sequencing. Medical records were collected and reviewed by attending physicians. A total of 836 iSNVs (3–106 per sample) were identified and distributed in a highly individualized pattern. The number of iSNVs paced with infection duration peaked within days and declined thereafter. These iSNVs did not stochastically arise due to a strong bias toward C &gt; U/G &gt; A and U &gt; C/A &gt; G substitutions in reciprocal proportion with escalating disease severity. Eight nonsynonymous iSNVs in the receptor-binding domain could escape from neutralization, and eighteen iSNVs were significantly associated with specific HLA alleles. The level and pattern of iSNVs reflect the in vivo viral–host interaction and the disease pathogenesis.
Coddiwomple
Authors: Frost Jody Shapiro 
Published: November 2022

Abstract:
This lectureship honors the legacy of Dr. Pauline Cerasoli who was a leader and pioneer in physical therapy education and who reimagined an innovative and bright future for the profession. This 2018 Lectureship titled “Coddiwomple” is divided into 3 mini talks. The first talk takes a 20-year look back on physical therapy education processes/inputs and products/outcomes to understand where we have been and how we arrived at this moment in physical therapy education. A second talk proposes that there are critical sea changes and forces at work seeking to transform physical therapy education as a result of external drivers, namely, disruptive innovation and technologies, big data analytics, and the transformation of health profession relationships. Given these changes, several critical course corrections are proposed for the future to include the implementation of collaborative shared leadership models, application of design thinking, and expanding partnerships for large scale population solutions. In conclusion, this lecture proposes that physical therapy education is cautioned not to default to “Coddiwomple” but rather to travel in a purposeful manner directed toward an intentional future given the many sea changes at work.
Mechanisms of ion selectivity and rotor coupling in the bacterial flagellar sodium-driven stator unit
Authors: Hu Haidai , Popp Philipp F. , Santiveri Mònica , Roa-Eguiara Aritz , Yan Yumeng , Liu Zheyi , Wadhwa Navish , Wang Yong , Erhardt Marc , Taylor Nicholas M. I. 
Published: November 2022

AbstractBacteria swim using a flagellar motor that is powered by stator units. These stator units are energized by an ionic gradient across the membrane, typically proton or sodium. The presumed monodirectional rotation of the stator units allows the bidirectional rotation of the flagellar motor. However, how ion selectivity is attained, how ion transport triggers the directional rotation of the stator unit, and how the stator unit is incorporated into the motor remain largely unclear. Here we have determined by cryo-electron microscopy the structure of the Na+-driven type stator unit PomAB from the gram-negative bacteriumVibrio alginolyticusin both lipidic and detergent environments, at a resolution up to 2.5 Å. The structure is in a plugged, auto-inhibited state consisting of five PomA subunits surrounding two PomB subunits. The electrostatic potential map uncovers sodium ion binding sites within the transmembrane domain, which together with functional experiments and explicit solvent molecular dynamics simulations, suggest a mechanism for ion translocation and selectivity. Resolved conformational isomers of bulky hydrophobic residues from PomA, in the vicinity of key determinant residues for sodium ion coupling of PomB, prime PomA for clockwise rotation. The rotation is tightly blocked by the trans-mode organization of the PomB plug motifs. The structure also reveals a conformationally dynamic helical motif at the C-terminus of PomA, which we propose regulates the distance between PomA subunit cytoplasmic domains and is involved in stator unit-rotor interaction, concomitant stator unit activation, and torque transmission. Together, our studies provide mechanistic insight for understanding flagellar stator unit ion selectivity and incorporation of the stator units into the motor.
Arabidopsistranscriptome responses to low water potential using high throughput plate assays
Authors: Gonzalez Stephen , Swift Joseph , Yaaran Adi , Xu Jiaying , Miller Charlotte , Illouz-Eliaz Natanella , Nery Joseph R. , Busch Wolfgang , Zait Yotam , Ecker Joseph R. 
Published: November 2022

AbstractSoil-free assays that induce water stress are routinely used to investigate drought responses in the plantArabidopsis thaliana. Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol and salt (NaCl) treatments to reduce the water potential of agar media, and thus induce drought conditions in the laboratory. However, while these types of stress can create phenotypes that resemble those of water deficit experienced by soil-grown plants, it remains unclear how these treatments compare at the transcriptional level. Here, we demonstrate that these different methods of lowering water potential elicit both shared and distinct transcriptional responses inArabidopsisshoot and root tissue. When we compared these transcriptional responses to those found inArabidopsisroots subject to vermiculite drying, we discovered many genes induced by vermiculite drying were repressed by low water potential treatments on agar plates (and vice versa). Additionally, we also tested another method for lowering water potential of agar media. By increasing the nutrient content and tensile strength of agar, we show the ‘hard agar’ (HA) treatment can be leveraged as a high-throughput assay to investigate natural variation inArabidopsisgrowth responses to low water potential.
Fear-Mouse Tracker (FMT): An open-source toolkit to track innate defensive behaviors with high precision
Authors: Garg Sanket , Pino Gabriela , Acuna Claudio 
Published: November 2022

ABSTRACTIn the past years, machine-learning-based approaches to track animal poses with high spatial and temporal resolution have become available, but toolkits to extract, integrate, and analyze coordinate datasets in a user-friendly manner have lagged behind. Here, we introduce Fear-Mouse Tracker (FMT), a simple and open-source MATLAB-based pipeline to extract and quantitatively analyze DeepLabCut-derived coordinates of mice presented with threatening stimuli that commonly trigger innate defensive responses. This framework allows for unbiased quantitative estimations of stretch-attend posture (SAP) observed during risk assessment behaviors, as well as for measurements of the timing and extent of freezing and escape responses that follow the presentation of threatening stimuli such as a predator odor, or sweeping and looming stimuli resembling predator approaches. FMT is specially designed for users not very experienced in using programming languages, thus making it more accessible to a broader audience.