bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration
Authors: Zheng Yuanting , Liu Yaqing , Yang Jingcheng , Dong Lianhua , Zhang Rui , Tian Sha , Yu Ying , Ren Luyao , Hou Wanwan , Zhu Feng , Mai Yuanbang , Han Jinxiong , Zhang Lijun , Jiang Hui , Lin Ling , Lou Jingwei , Li Ruiqiang , Lin Jingchao , Liu Huafen , Kong Ziqing , Wang Depeng , Dai Fangping , Bao Ding , Cao Zehui , Chen Qiaochu , Chen Qingwang , Chen Xingdong , Gao Yuechen , Jiang He , Li Bin , Li Bingying , Li Jingjing , Liu Ruimei , Qing Tao , Shang Erfei , Shang Jun , Sun Shanyue , Wang Haiyan , Wang Xiaolin , Zhang Naixin , Zhang Peipei , Zhang Ruolan , Zhu Sibo , Scherer Andreas , Wang Jiucun , Wang Jing , Xu Joshua , Hong Huixiao , Xiao Wenming , Liang Xiaozhen , Jin Li , Tong Weida , Ding Chen , Li Jinming , Fang Xiang , Shi Leming 
Published: November 2022

Abstract
Multiomics profiling is a powerful tool to characterize the same samples with complementary features orchestrating the genome, epigenome, transcriptome, proteome, and metabolome. However, the lack of ground truth hampers the objective assessment of and subsequent choice from a plethora of measurement and computational methods aiming to integrate diverse and often enigmatically incomparable omics datasets. Here we establish and characterize the first suites of publicly available multiomics reference materials of matched DNA, RNA, proteins, and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters, providing built-in truth defined by family relationship and the central dogma. We demonstrate that the "ratio"-based omics profiling data, i.e., by scaling the absolute feature values of a study sample relative to those of a concurrently measured universal reference sample, were inherently much more reproducible and comparable across batches, labs, platforms, and omics types, thus empower the horizontal (within-omics) and vertical (cross-omics) data integration in multiomics studies. Our study identifies "absolute" feature quantitation as the root cause of irreproducibility in multiomics measurement and data integration, and urges a paradigm shift from "absolute" to "ratio"-based multiomics profiling with universal reference materials.
External globus pallidus input to the dorsal striatum regulates habitual reward-seeking behavior
Authors: Baker Matthew , Kang Seungwoo , Hong Sa-Ik , Song Minryung , Yang Minsu Abel , Peyton Lee , Essa Hesham , Lee Sang Wan , Choi Doo-Sup 
Published: November 2022

Abstract
The external globus pallidus (GPe) coordinates action-selection through GABAergic projections throughout the basal ganglia. GPe arkypallidal (arky) neurons project exclusively to the dorsal striatum, which regulates goal-directed and habitual reward-seeking. However, the role of GPe arky neurons in reward-seeking remains unknown. Here, we identified that a majority of arky neurons target the dorsolateral striatum (DLS). Using fiber photometry, we found that arky activities were higher during random interval (RI; habit) compared to random ratio (RR; goal) operant reward-seeking. Support vector machine analysis demonstrated that arky neuron activities have sufficient information to distinguish between RR and RI behavior. Genetic ablation of this arkyGPe◊DLS circuit facilitated a shift from goal-directed to habitual behavior. Conversely, chemogenetic activation reduced habitual seeking-behaviors, which was blocked by systemic D1R agonism. Our findings reveal a novel role of this arkyGPe◊DLS circuit in constraining habitual reward-seeking, which is relevant to addictive behaviors and other compulsive disorders.
Perspectives on an enhanced ‘Improving Access to Psychological Therapies’ (IAPT) service addressing the wider determinants of mental health: a qualitative study.
Authors: Curtin Esther Louise , d'Apice Katrina , Porter Alice , Widnall Emily , Franklin Matthew , de Vocht Frank , Kidger Judi 
Published: November 2022

Abstract
Background

A new Health and Wellbeing pathway was introduced into the Improving Access to Psychological Therapies (IAPT) service in one geographical area of the UK in 2021 to address the wider determinants of mental health problems. It comprised assisted signposting to wider services and physical health promotion. This qualitative study aimed to understand stakeholders’ experiences of implementing and receiving this new support and the barriers and facilitators to its delivery.

Methods

Forty-seven interviews were conducted, with service developers (n = 6), service deliverers (n = 12), service users (n = 22) and community and clinical partners (n = 7), as part of a larger mixed-methods evaluation. Interviews were recorded, transcribed, and analysed using reflexive thematic analysis.

Results

Three themes spanned all participant groups, lending insight into potential service improvements. These included strengthening the quality of communication during referral and assessment to enhance ‘identifying suitability’, tailoring the support and delivery mode to provide a more ‘holistic service’, and increasing transparency around continued care to drive sustained benefits, reflected in the theme ‘moving forward’.

Limitations

Service users may have been selected due to their positive experiences of IAPT and were not demographically representative of the population, although participants’ experiences of the service did suggest variation in our sample.

Conclusions

The Health and Wellbeing pathway was perceived as having a positive impact on mental health and could reduce the burden on therapeutic services. However, service- and individual-level barriers need to be addressed to enhance statutory and community support links, manage service users’ expectations, and improve accessibility for certain groups.
High prevalence of mental disorder symptoms among medical and other health specialty residents during the COVID-19 pandemic
Authors: Silva Nayane Miranda , Pinho Rebeca da Nobrega Lucena , Costa Thais Ferreira , Areal Adriana Ferreira Barros , Salles André de Mattos , Oliveira Andrea Pedrosa Ribeiro Alves , Rassi Carlos Henrique Reis Esselin , Valero Caroline Elizabeth Brero , Gomes Ciro Martins , Silva Dayde Lane Mendonça da , de Oliveira Fernando Araujo Rodrigues , Jochims Isadora , Filho Ivan Henrique Ranulfo Vaz , Neves Juliana de Brito Seixas , Oliveira Lucas Alves de Brito , Dantas Maria Luisa Nogueira , Rosal Marta Alves , Soares Mayra Veloso Ayrimoraes , Kurizky Patrícia Shu , Peterle Viviane Cristina Uliana , Faro Yasmin Furtado , Gomides Ana Paula Monteiro , Mota Licia Maria Henrique da , de Albuquerque Cleandro Pires , Simaan Cezar Kozak , Amado Veronica Moreira 
Published: November 2022

Abstract
Background
The coronavirus epidemic was first identified in Wuhan, China, at the end of 2019. Because of the pandemic, health professionals, including residents in medicine and other health specialties, began working under intense physical and psychological pressure and were at a greater risk of developing mental disorders and psychological distress.
Methods
This study evaluated the prevalence of symptoms indicative of mental disorders such as depression, anxiety and stress among medical residents and other health specialties during the COVID-19 pandemic in Brazil. This study adopted a cross-sectional design that included postgraduate students in medical and other health residency programmes in Brazil. The recruitment extended from July 29 to September 5, 2020.
Results
In total, 1,313 resident medical and other health residents participated in the study. The Scale DASS-21 identified depression, anxiety and stress in 51.3%, 53.4% and 52.6% of the participants, respectively. Based on the Brief Resilient Coping Scale (BRCS), 61.9% of the participants had low resilience. A total of 60.9% of the residents had high scores on the Patient Health Questionnaire 9-item depression module (PHQ-9).
Conclusions
We found a high prevalence of symptoms of depression, anxiety and stress among medical and nonmedical residents during the COVID-19 pandemic in Brazil.
Tree dominance shapes soil and tree phyllosphere microbial communities in coniferous and broadleaf deciduous boreal forests
Authors: Rodríguez Juanita C. Rodríguez , Fenton Nicole J. , Bergeron Yves , Kembel Steven W. 
Published: November 2022

Abstract

Purpose:Natural and anthropogenic causes have produced changes in tree dominance from coniferous to broadleaf deciduous forests, generating shifts in litter inputs and plant understory composition. The impact of changes in canopy-associated factors on belowground microbial communities remain poorly understood. The objective of this study was to better understand how abiotic and biotic factors in black spruce and trembling aspen forests shape soil microbial community structure.Methods:With high throughput sequencing, we first analyzed differences in microbial communities between microhabitats (tree phyllosphere vs. soil microbiome) and forest types (black spruce vs. trembling aspen). Second, we analyzed how shifts in factors related to each forest type (litter deposition and understory vegetation) affected soil microbial community composition.Results:We found a high microhabitat specificity of bacterial communities interacting with forest type. Shifts in litter deposition and understory vegetation between forest types did not influence microbial community composition, but the legacy effects of each forest type defined soil bacterial and fungal communities. Fungal community composition was more strongly influenced by forest type compared with bacterial communities, and both were correlated with several soil physicochemical properties that differed among forest types.Conclusion:This study expands our knowledge of the microbial composition of tree phyllosphere and soil microbial communities in black spruce and trembling aspen forests and their correlation with abiotic and biotic factors in each forest type. Our study demonstrates the resistance of microorganisms to variation in canopy-related factors and the importance of legacy effects of forest type in defining soil microbial community composition.
Preferred Cataract Surgery Practices in Malaysia: A Survey Based Study
Authors: Wai Yong Zheng , Chong Yong Yuin , Lim Lik Thai , Chan Jan Bond , Chandrasekaran Sudhashini 
Published: November 2022

Abstract
Background:
To describe the preferred cataract surgery practices among Malaysian ophthalmologists and medical officers in comparison with the recommended practices.
Methods:
An online questionnaire was sent out in April 2021, to Malaysian Ophthalmologists and medical officers who perform cataract surgeries. The questions were focused on the preferred cataract surgery practices of the participants. All data obtained were collected, tabulated and analysed.
Results:
A total of 173 participants responded to the online questionnaire. 55% of the participants were within 31-40 years of age. 56.1% preferred peristaltic pump over venturi system. 91.3% of participants practised povidone iodine instillation to the conjunctival sac. With regards to the main wound incision, more than half of the surgeons (50.3%) preferred fixed superior incision and 72.3% of them preferred 2.75mm microkeratome blade. Most of the participants (63%) were inclined towards C-Loop clear intraocular lens (IOL) with a single-handed push preloaded system. 78.6% of the surgeons routinely use carbachol in their cataract surgery.
Conclusions:
This survey provides some insight into the current practices among Malaysian ophthalmologists. Most of the practices are in line with international guidelines for preventing postoperative endophthalmitis. This article could help trainees and ophthalmologists benchmark and observe the common cataract surgery practices among their seniors and peers in Malaysia.
Comparison between double J stent and double J stent combined with pyelostomy in pediatric laparoscopic pyeloplasty:a 5-year clinical experience in a single center
Authors: Chen Zhiqiang , Wang Yunjin , Wu Changwei , Chen Hong , Cui XU , Zhou Chaoming 
Published: November 2022

Abstract
Objective：To compare the outcome of using a double J(DJ) stent combined with pyelostomy with a DJ stent alone in Laparoscopic Pyeloplasty (LP) for pediatric ureteropelvic junction obstruction (UPJO).
Methods: We conducted a retrospective review of all patients with UPJO treated with LP between January 2017 and November 2021 in our center. According to different postoperative drainage methods patients were divided into a DJ stent group (52 cases) and a DJ stent combined with pyelostomy group (combination group, 41 cases). Operative time, bleeding volume, perirenal drainage stent removal time, and postoperative hospital stay, postoperative complications, and renal function recovery were compared between the two groups. Renal ultrasound and diuretic renogram (DR) were used for preoperative and postoperative follow-up.
Results: A total of 52 patients were in the DJ stent group and 41 patients in the combination group. The mean hospital stay was 6.46±2.66 days in the DJ stent group and 5.22±1.63 days in the combination group (p<0.05). Postoperative complications developed in 14 out of 52 patients in the DJ stent group(26.9%), while complications developed in 8 out of 41 patients in the combination group (19.5%) (p>0.05). Non-catheter-related complications developed in 10/52 patients in the DJ stent group (19.2%) and only 1/41 patients in the combination group (2.4%) (p<0.05). The renal function and renal cortex thickness in both groups were improved.
Conclusion:A DJ stent combined with pyelostomy can reduced non-catheter related complications,which is conducive to patient recovery after pyeloplastyand,and the hospital stay was significantly shorter than the DJ stent. However, it is necessary to pay attention to the nursing treatment of the pyelostomy tube and guard against the occurrence of pyelostomy tube shedding.
Comparative analysis of wild and domestic carnivore animal hairs.
Authors: Patle Sangeeta , Singh K. P. , Bagchi Divya 
Published: November 2022

Abstract
The present study was conducted to find out the microscopic characteristics and keratin protein pattern of hair of wild and domestic carnivores animals with the objective of species identification. Hairs have ability to remain unchanged chemically and histologically for years. For this study the shredded hair sample of Panther (Panthera pardus), Tiger (Panthera tigris), cat (felis catus), dog (Canis familiaris) were collected from school of wildlife forensic and health NDVSU, Jabalpur, (MP). Medullary pattern and cuticular characters were observed by binocular compound microscope under 40x – 100x magnification. The specific variations were observed in this study among hair color, texture, scale margin, scale distance, and scale pattern and variation in medullary pattern. These parameters of hair analysis play important role species identification.On the basis of microscopic characteristics species identification was done and further confirmed by extraction of keratin protein found between 40-60kDa by SDS-PAGE. The study emphasized that both the microscopic and SDS- PAGE analyses of guard hairs would be useful for recognition of an individual species particularly in forensic uses.
Impact of changing temperature combinations on the biology and life table parameters of Nilaparvata lugens (Stål) (Hemiptera: Delphacidae)
Authors: GURJOT Gurjot kaur , Preetinder Preetinder Singh Sarao , Naveen Naveen Aggarwal 
Published: November 2022

AbstractNilaparvata lugens(Stål) (Hemiptera: Delphacidae) is one of the major insect pests of paddy crop which significantly reduces the quality and quantity of yield. The biology and life table parameters of this pest were studied at five set of controlled temperature combinations as 23:9, 27:12, 33:19, 36:23 and 39:27°C with 75 ± 5 per cent humidity and 14 h photoperiod under laboratory conditions. Different biological parameters like number of days for development, nymph survival, oviposition rate, adult longevity and reproductive parameters ofN. lugenswere influenced at different temperature combinations. Optimum temperature range lies between 27:12°C and 33:19°C as fecundity (102 ± 8.50, 112 ± 3.75), per cent egg hatchability (86.86 ± 1.21, 87.14 ± 1.99) and viability of fifth nymphal instar (57.4 ± 4.02, 58.20 ± 3.76) (mean ± standard error) respectively, were recorded higher than other temperature combinations. Various life table parameters like net reproductive rate, true generation time, true intrinsic rate of increase, finite rate of increase, doubling time and weekly multiplication rate of the pest also varied significantly among population at different temperature combinations. The net reproductive rate (163.49) and intrinsic rate of increase (0.1993 females female− 1day− 1) were maximum at 33:19°C. Generation time decreases significantly with increase in temperature. The finite rate of increase was 1.1522, 1.2004, 1.2227, 1.1321 and 1.1300 females female-1day-1at with multiplication rate of 2.8201, 3.5926, 4.2501, 2.3833 and 2.3821, respectively, at 23:9, 27:12, 33:19, 36:23 and 39:27°C temperature combinations. The relatively high values of population growth parameters suggest thatN. lugensthrive well at 33:19°C followed by 27:12°C temperature combinations. In the field conditions when the weather conditions tend to move towards this range of temperature combinations during the crop season, the farmers should be more cautious and frequently monitor the paddy crop to assess economic threshold level of BPH for timely remedial measures.
The Inhibitory Effect of Resina draconis on the Proliferation of MCF-7 Breast Cancer Cells, and its Mechanism: An Investigation Using Network Pharmacology-Based Analysis
Authors: Lv Yana , Mou Yan , Su Jing , Liu Shifang , Ding Xuan , Yuan Yin , Li Ge , Li Guang 
Published: November 2022

Abstract
Resina draconis(RD), is known as the "holy medicine for promoting blood circulation", which is shown to possess anti-tumor properties in various types of cancer include Breast cancer(BC), however, the underlying mechanism is not well understood. To explore the potential mechanism of RD against BC using network pharmacology and experimental validation. Data on bioactive compounds, potential targets of RD, related genes of BC, were obtained from multiple public databases. Gene ontology (GO) and KEGG pathway analysis were performed via the DAVID database. The protein interaction was download from STRING database. The mRNA, protein expression levels and survival analysis of the hub targets were analyzed using UALCAN, HPA, Kaplan-Meier Mapper, and cBioPortal databases. Subsequently, molecular docking was used to verify the selected key ingredients and hub targets. Finally, the predicted results of network pharmacology methods were verified by cells experiments. In total, 160 active ingredients were obtained, 148 RD target genes for the treatment of BC were identified. KEGG pathway analysis indicated that RD could exert its therapeutic effects on BC by regulating multiple pathways. Of these, the PI3K-AKT pathway could play an important role. In addition, RD could treat BC by regulating hub targets that were determined with the PPI interaction network. The validation in different databases showed that may AKT1, ESR1, HSP90AA1, CASP3, SRC and MDM2 be involved in the carcinogenesis and progression of BC, as well as ESR1, IGF1 and HSP90AA1 were correlated to worse overall survival (OS) in BC. Molecular docking results showed that flavonoids compounds have good binding activity with the hub targets. Therefore, the sanguis draconis flavones (SDF) were selected for subsequent cell experiments. The experimental results showed that SDF significantly inhibits the cell cycle and cell proliferation through the PI3K-AKT pathway and that it can induce apoptosis of MCF-7 cells. The study has preliminarily discussed the active ingredients, potential targets, and molecular mechanism of RD against BC; and RD could exert its therapeutic effects on BC by regulating PI3K/AKT pathway and related gene targets. Importantly, our work could provide a theoretical basis for further study on its complex anti-BC mechanism.
Influence of expeditionary liqueur on the formation of foam properties of sparkling wines
Authors: Taranenko V. , Оseledtseva I. , Strukova V. 
Published: November 2022

AbstractWhen determining the quality of sparkling wines, first of all, we thought to focus on the assessment of processes of formation of sparkling and frothy properties, as the process of cavitation reveals the relationship with the chemical components, which affects organoleptic indicators. The effect of expeditionary liquor on frothy properties was investigated and it was found that expeditionary liquor directly affects the concentration of dissolved carbon dioxide. The control samples were made according to the classical technology of sparkling wine production, including "prise de mousse", due to which the carbon dioxide molecules were promoted and dissolved, increasing the degree of diffusion in the liquid. Such a sparkling wine is characterized by a fine foam and a high pressure index. Foam formation is associated with proteins, as they exhibit the ability to adsorb and unfold at the gas-liquid interface, and foam stability is provided by amino acids due to strong bonds that increase wine viscosity. When expeditionary liqueur was added, the pressure dropped from 7 atmospheres to 4 atmospheres, which allowed the sparkling wine to calm down and stabilize bubble formation, and this is the result of the subtle interaction between dissolved carbon dioxide molecules and tensioactive wine components.
Whole Genome CRISPR Screening Strategy for Identification of Host Genes Contributing to Envelope Mediated Entry of SARS-CoV-2 Spike and VSV-G
Authors: Hossain Md Saddam , Kerkvliet Jason G. , Hoppe Adam D. 
Published: November 2022

Abstract
Background
Understanding the cellular host factors that promote and inhibit viral entry is important for identifying viral countermeasures. CRISPR whole genome screens can be used to rapidly discover host factors that contribute to or impair viral entry. However, when using the live viruses and cellular lethality for selection, these screens identify large numbers of genes without any specificity for the stage of the viral infection cycle. New screening methods are needed to identify host machinery contributing to specific steps of viral infection. Here, we developed a CRISPR whole genome screen and counter screen strategy based on a pseudoviral platform that allowed identification of genes specific to SARS-CoV-2 spike and vesicular stomatitis virus glycoprotein VSV-G mediated entry.
Methods
To focus the screen onto the entry step, we used non-lytic fluorescent reporters in combination with a comparative counter screen strategy to distinguish host genes affecting the pseudoviral reporter from those unique to envelope-mediated entry. Screening of SARS-CoV-2 spike and VSV-G on the same lentiviral pseudovirus allowed identification of entry-specific genes relative to genes associated with retro-transcription, integration, and reporter expression from the lentiviral pseudovirus. Second, a Cre-Gag fusion protein in the pseudovirus was used to bypassed retro-transcription and integration by directly activating a floxed GFP reporter upon entry to reduce the number of gene hits and increase specificity for viral entry.
Results
Our approach correctly identified SARS-CoV-2 and VSV-G receptors ACE2 and LDLR, respectively and distinguished genes associated with retroviral reporter expression from envelope-mediated entry. Moreover, the CRE-Gag fusion/flox reporter increased the screen specificity for viral entry associated genes.
Conclusion
Overall, this approach provides a new strategy for identifying host genes influencing viral entry without the confounding complexity of live-viral screens which produce long gene lists associated with all aspects of viral pathogenesis and replication. This approach provides a pathway for increasing the specificity of CRISPR whole genome screens for identifying host genes contributing to specific steps in viral infection.