bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular combing and its application in clinical settings
Authors: Wang Yiping , Kumar Kishore Ramesh , Liehr Thomas 
Published: November 2022

AbstractMolecular combing technology (MCT) is an effective means for stretching DNA molecules and making them thus accessible for in situ studies. MCT uses the force exerted in the process of liquid flow via surface tension to stretch DNA molecules and spread them on solid surfaces, i.e. glass cover slips. Many DNA molecules can be stretched at the same time in parallel and neatly arranged side-by-side, making the approach convenient for statistical analysis. Accordingly, DNA replication and transcription can be studied at the single molecule level. In this paper, the principle, experimental methods, important applications, advantages and shortcuts of MCT in medical field are presented and discussed.
A randomised controlled trial to compare clinical and cost-effectiveness of an online parent-led treatment for child anxiety problems with usual care in the context of COVID-19 delivered in Child and Adolescent Mental Health Services in the UK (Co-CAT): a study protocol for a randomised controlled trial
Authors: Taylor Lucy , Giles Sophie , Howitt Sophie , Ryan Zoe , Brooks Emma , Radley Lucy , Thomson Abigail , Whitaker Emily , Knight Fauzia , Hill Claire , Violato Mara , Waite Polly , Raymont Vanessa , Yu Ly-Mee , Harris Victoria , Williams Nicola , Creswell Cathy 
Published: November 2022

Abstract
Background
In the context of COVID-19, NHS Child and Adolescent Mental Health Services (CAMHS) and other children’s mental health services have faced major challenges in providing psychological treatments that (i) work when delivered remotely and (ii) can be delivered efficiently to manage increases in referrals as social distancing measures have been relaxed. Anxiety problems are a common reason for referral to CAMHS, children with pre-existing anxiety problems are particularly vulnerable in the context of COVID-19, and there were concerns about increases in childhood anxiety as schools reopened. The proposed research will evaluate the clinical and cost-effectiveness of a brief online parent-led cognitive behavioural treatment (CBT) delivered by the OSI (Online Support and Intervention for child anxiety) platform with remote support from a CAMHS therapist compared to ‘COVID-19 treatment as usual’ (C-TAU) in CAMHS and other children’s mental health services throughout the COVID-19 pandemic.

Methods
We will conduct a two-arm, multi-site, randomised controlled non-inferiority trial to evaluate the clinical and cost-effectiveness of OSI with therapist support compared to CAMHS and other child mental health services ‘COVID-19 treatment as usual’ (C-TAU) during the COVID-19 outbreak and to explore parent and therapists’ experiences.

Discussion
If non-inferiority is shown, the research will provide (1) a solution for efficient psychological treatment for child anxiety disorders while social distancing (for the COVID-19 context and future pandemics); (2) an efficient means of treatment delivery as ‘normal service’ resumes to enable CAMHS to cope with the anticipated increase in referrals; and (3) a demonstration of rapid, high-quality evaluation and application of online interventions within NHS CAMHS to drive forward much-needed further digital innovation and evaluation in CAMHS settings. The primary beneficiaries will be children with anxiety disorders and their families, NHS CAMHS teams, and commissioners who will access a potentially effective, cost-effective, and efficient treatment for child anxiety problems.

Trial registration
ISRCTN ISRCTN12890382. Registered prospectively on 23 October 2020.
Adaptation of a microbial community to demand-oriented biological methanation
Authors: Khesali Aghtaei Hoda , Püttker Sebastian , Maus Irena , Heyer Robert , Huang Liren , Sczyrba Alexander , Reichl Udo , Benndorf Dirk 
Published: November 2022

AbstractBackgroundBiological conversion of the surplus of renewable electricity and carbon dioxide (CO2) from biogas plants to biomethane (CH4) could support energy storage and strengthen the power grid. Biological methanation (BM) is linked closely to the activity of biogas-producingBacteriaand methanogenicArchaea. During reactor operations, the microbiome is often subject to various changes, e.g., substrate limitation or pH-shifts, whereby the microorganisms are challenged to adapt to the new conditions. In this study, various process parameters including pH value, CH4production rate, conversion yields and final gas composition were monitored for a hydrogenotrophic-adapted microbial community cultivated in a laboratory-scale BM reactor. To investigate the robustness of the BM process regarding power oscillations, the biogas microbiome was exposed to five hydrogen (H2)-feeding regimes lasting several days.ResultsApplying various “on–off” H2-feeding regimes, the CH4production rate recovered quickly, demonstrating a significant resilience of the microbial community. Analyses of the taxonomic composition of the microbiome revealed a high abundance of the bacterial phylaFirmicutes,BacteroidotaandThermotogotafollowed by hydrogenotrophicArchaeaof the phylumMethanobacteriota. Homo-acetogenic and heterotrophic fermentingBacteriaformed a complex food web with methanogens. The abundance of the methanogenicArchaearoughly doubled during discontinuous H2-feeding, which was related mainly to an increase in acetoclasticMethanothrixspecies. Results also suggested thatBacteriafeeding on methanogens could reduce overall CH4production. On the other hand, using inactive biomass as a substrate could support the growth of methanogenicArchaea. During the BM process, the additional production of H2by fermentingBacteriaseemed to support the maintenance of hydrogenotrophic methanogens at non-H2-feeding phases. Besides the elusive role ofMethanothrixduring the H2-feeding phases, acetate consumption and pH maintenance at the non-feeding phase can be assigned to this species.ConclusionsTaken together, the high adaptive potential of microbial communities contributes to the robustness of BM processes during discontinuous H2-feeding and supports the commercial use of BM processes for energy storage. Discontinuous feeding strategies could be used to enrich methanogenicArchaeaduring the establishment of a microbial community for BM. Both findings could contribute to design and improve BM processes from lab to pilot scale.
Universal clinical Parkinson’s disease axes identify a major influence of neuroinflammation
Authors: Sandor Cynthia , Millin Stephanie , Dahl Andrew , Schalkamp Ann-Kathrin , Lawton Michael , Hubbard Leon , Rahman Nabila , Williams Nigel , Ben-Shlomo Yoav , Grosset Donald G. , Hu Michele T. , Marchini Jonathan , Webber Caleb 
Published: November 2022

Abstract

Background
There is large individual variation in both clinical presentation and progression between Parkinson’s disease patients. Generation of deeply and longitudinally phenotyped patient cohorts has enormous potential to identify disease subtypes for prognosis and therapeutic targeting.

Methods
Replicating across three large Parkinson’s cohorts (Oxford Discovery cohort (n = 842)/Tracking UK Parkinson’s study (n = 1807) and Parkinson’s Progression Markers Initiative (n = 472)) with clinical observational measures collected longitudinally over 5–10 years, we developed a Bayesian multiple phenotypes mixed model incorporating genetic relationships between individuals able to explain many diverse clinical measurements as a smaller number of continuous underlying factors (“phenotypic axes”).

Results
When applied to disease severity at diagnosis, the most influential of three phenotypic axes “Axis 1” was characterised by severe non-tremor motor phenotype, anxiety and depression at diagnosis, accompanied by faster progression in cognitive function measures. Axis 1 was associated with increased genetic risk of Alzheimer’s disease and reduced CSF Aβ1-42 levels. As observed previously for Alzheimer’s disease genetic risk, and in contrast to Parkinson’s disease genetic risk, the loci influencing Axis 1 were associated with microglia-expressed genes implicating neuroinflammation. When applied to measures of disease progression for each individual, integration of Alzheimer’s disease genetic loci haplotypes improved the accuracy of progression modelling, while integrating Parkinson’s disease genetics did not.

Conclusions
We identify universal axes of Parkinson’s disease phenotypic variation which reveal that Parkinson’s patients with high concomitant genetic risk for Alzheimer’s disease are more likely to present with severe motor and non-motor features at baseline and progress more rapidly to early dementia.
A desmoid tumor with fluorodeoxyglucose accumulation arising from the anastomotic site of postoperative gastric cancer: a case report
Authors: Kawashima Kento , Hiramatsu Kazuhiro , Kato Takehito , Fukaya Masahide , Aoba Taro , Arimoto Atsuki , Yamaguchi Takayuki 
Published: November 2022

Abstract
Background
Desmoid tumors are extremely rare borderline benign and malignant tumors that do not exhibit accumulation on fluorodeoxyglucose positron emission tomography–computed tomography. In the present study, we report a rare case of a desmoid tumor with fluorodeoxyglucose accumulation at the anastomotic postoperative gastric cancer site.

Case presentation
A 68-year-old Japanese man underwent robot-assisted laparoscopic distal gastrectomy for early-stage gastric cancer in 2019. The pathological diagnosis was stage IA cancer, and no adjuvant chemotherapy was administered. Two years after surgery, a soft mass appeared on the greater curvature side of the anastomosis on computed tomography. Fluorodeoxyglucose positron emission tomography–computed tomography revealed fluorodeoxyglucose accumulation, which suggested a malignancy; therefore, surgery was performed for diagnostic treatment. The histopathological findings led to the diagnosis of a desmoid tumor. The patient has not experienced recurrence to date.

Conclusions
In the present study, we encountered a desmoid tumor arising from the anastomotic site of a postoperative gastric cancer. This case is rare as fluorodeoxyglucose positron emission tomography–computed tomography showed fluorodeoxyglucose accumulation in the desmoid tumor, and a preoperative diagnosis could not be reached. We hope that further studies will improve the accuracy of preoperative diagnosis.
Insufficiency fracture of the supra-acetabulum that required differentiation from a pathological fracture secondary to a malignant bone tumor: a case report
Authors: Morinaga Sei , Yamamoto Norio , Hayashi Katsuhiro , Takeuchi Akihiko , Miwa Shinji , Igarashi Kentaro , Yonezawa Hirotaka , Asano Yohei , Saito Shiro , Tsuchiya Hiroyuki 
Published: November 2022

Abstract
Background
The supra-acetabulum is a common site for malignant bone tumors, which can be difficult to differentiate from insufficiency fractures. We report a rare case of a stress fracture of the supra-acetabulum that required differentiation from a malignant bone tumor.

Case presentation
A 74-year-old Japanese man presented to the hospital because of right hip joint pain. X-rays showed no obvious abnormalities. Magnetic resonance imaging showed an abnormality in the right supra-acetabulum, and he was referred to our department. A linear, low-signal region and its surrounding equal signal region were observed at the same site in the T1-weighted image, and a linear low-signal region and high signal region were observed in the surrounding area in the T2-weighted image. On the contrast-enhanced magnetic resonance imaging, the lesion was still unclear and the whole area was gradually enhanced. A computed tomography-guided needle biopsy was performed, but no tumor cells were observed, therefore the lesion was presumed to be a fracture healing. The bone density was 66% for the lumbar spine (young adult mean, L2–4), and blood biochemistry showed an increase in alkaline phosphatase and total type I procollagen N-terminal propeptide.

Conclusion
This case was diagnosed as an insufficiency fracture of the supra-acetabulum in a male patient with primary osteoporosis by biopsy specimen. Initially, a pathological fracture associated with a malignant lesion was considered. On magnetic resonance imaging, the boundary around the fracture line was unclear and a signal change that was gradually enhanced by gadolinium was observed. This is likely to be bone marrow edema associated with the stress fracture, and we believe this to be a useful finding that may help in differentiating a stress fracture from a pathological fracture secondary to a malignant lesion.
Sustainable energy recovery from thermal processes: a review
Authors: Chen Weidong , Huang Zhifeng , Chua Kian Jon 
Published: November 2022

Abstract
Background
With the increasing concerns on the energy shortage and carbon emission issues worldwide, sustainable energy recovery from thermal processes is consistently attracting extensive attention. Nowadays, a significant amount of usable thermal energy is wasted and not recovered worldwide every year. Meanwhile, discharging the wasted thermal energy often causes environmental hazards. Significant social and ecological impacts will be achieved if waste thermal energy can be effectively harnessed and reused. Hence, this study aims to provide a comprehensive review on the sustainable energy recovery from thermal processes, contributing to achieving energy security, environmental sustainability, and a low-carbon future.

Main text
To better understand the development of waste thermal energy utilization, this paper reviews the sustainable thermal energy sources and current waste energy recovery technologies, considering both waste heat and cold energy. The main waste heat sources are prime movers, renewable heat energy, and various industrial activities. Different waste heat recovery technologies to produce electricity, heating, and cooling are analyzed based on the types and temperatures of the waste heat sources. The typical purposes for waste heat energy utilization are power generation, spacing cooling, domestic heating, dehumidification, and heat storage. In addition, the performance of different waste heat recovery systems in multigeneration systems is introduced. The cold energy from the liquified natural gas (LNG) regasification process is one of the main waste cold sources. The popular LNG cold energy recovery strategies are power generation, combined cooling and power, air separation, cryogenic CO2 capture, and cold warehouse. Furthermore, the existing challenges on the waste thermal energy utilization technologies are analyzed. Finally, potential prospects are discussed to provide greater insights for future works on waste thermal energy utilization.

Conclusions
Novel heat utilization materials and advanced heat recovery cycles are the key factors for the development of waste high-temperature energy utilization. Integrated systems with multiply products show significant application potential in waste thermal energy recovery. In addition, thermal energy storage and transportation are essential for the utilization of harnessed waste heat energy. In contrast, the low recovery rate, low utilization efficiency, and inadequate assessment are the main obstacles for the waste cold energy recovery systems.
In vitro antibacterial, antioxidant activities, molecular docking, and ADMET analysis of phytochemicals from roots of Hydnora johannis
Authors: Degfie Teshome , Endale Milkyas , Tafese Tarekegn , Dekebo Aman , Shenkute Kebede 
Published: November 2022

AbstractHydnora johannisis a medicinal plant traditionally used to treat various ailments. Chemical investigation of the dichloromethane (DCM)/methanol (MeOH) (1:1) roots extract ofHydnora johannisafforded three compounds (1–3), reported herein for the first time from the species. The structures of the isolated compounds1–3were elucidated using 1D and 2D NMR spectroscopic analysis and comparison with literature data. The highest zone of inhibition value was measured for DCM/MeOH extract (10.75 ± 0.25 mm) againstStaphylococcus aureusat concentration of 0.25 mg/mL, promising in comparison to the standard amoxicillin (16.0 ± 0.0 mm, 0.25 mg/mL). At concentration of 0.25 mg/mL, the largest mean inhibition zone of 12.0 ± 0.0 mm was measured for compound2againstPseudomonas aeruginosa, comparable to the standard drug amoxicillin (16.0 ± 0.0 mm, 0.25 mg/mL). Compound2displayed better binding affinity with minimum binding energy of − 8.7 kcal/mol (PqsA), − 7.6 kcal/mol (DNA gyrase), and − 7.4 kcal/mol (S aureusPK) than amoxicillin (− 7.3, − 6.1, and − 7.0 kcal/mol, respectively). This suggests that compound2may act as potential inhibitor of the tested bacterial proteins. Compound1satisfies the Lipinski’s rule of five with zero violations. Compound2obey the MW (452.4 g/mol) and iLogP (< 5) rules, and compound3obey the NHD (4) and NHA (6) rules. Compounds2recorded iLogP value less enough than five (1.55), implying its optimal lipophilicity. Compounds1and3satisfy the veber’s rule (NRB < 12, and TPSA < 140 unit). Compound2and3exhibited negligible acute toxicity (LD50 > 5000, Toxicity class > 5. Compound2demonstrated maximum scavenging activity (67.87%) with IC50value of 0.190 µg/mL, compared to ascorbic acid (78.21%) with IC50value of 0.014 µg/mL at concentration of 12.5 µg/mL. Overall, the in vitro antibacterial activity of the extracts and compounds, molecular docking analysis and radical scavenging activity results of the isolated compounds suggest DCM/MeOH crude extract and compound2are promising antibacterial agents whereas compound2and3are promising antioxidants which corroborates with the traditional uses of the roots ofH. johannis.
FMO3 deficiency of duck leads to decreased lipid deposition and increased antibacterial activity
Authors: Li Xingzheng , Song Jianlou , Shi Xuefeng , Huang Mingyi , Liu Lei , Yi Guoqiang , Yang Ning , Xu Guiyun , Zheng Jiangxia 
Published: November 2022

Abstract
Background
Most duck eggs possess a fishy odor, indicating that ducks generally exhibit impaired trimethylamine (TMA) metabolism. TMA accumulation is responsible for this unpleasant odor, and TMA metabolism plays an essential role in trimethylaminuria (TMAU), also known as fish odor syndrome. In this study, we focused on the unusual TMA metabolism mechanism in ducks, and further explored the unclear reasons leading to the debilitating TMA metabolism.

Methods
To achieve this, transcriptome, proteome, and metagenome analyses were first integrated based on the constructed duck populations with high and low TMA metabolism abilities. Additionally, further experiments were conducted to validate the hypothesis regarding the limited flavin-containing monooxygenase 3 (FMO3) metabolism ability of ducks.

Results
The study demonstrated that liver FMO3 and cecal microbes, including Akkermansia and Mucispirillum, participated in TMA metabolism in ducks. The limited oxidation ability of FMO3 explains the weakening of TMA metabolism in ducks. Nevertheless, it decreases lipid deposition and increases antibacterial activity, contributing to its survival and reproduction during the evolutionary adaptation process.

Conclusions
This study demonstrated the function of FMO3 and intestinal microbes in regulating TMA metabolism and illustrated the biological significance of FMO3 impairment in ducks.
Blood neutrophil extracellular traps: a novel target for the assessment of mammary health in transition dairy cows
Authors: Jiang Luyi , Sun Huizeng , Gu Fengfei , He Jin , Zhao Fengqi , Liu Jianxin 
Published: November 2022

Abstract
Background
Mammary health is important for transition dairy cows and has been well recognized to exert decisive effects on animal welfare. However, the factors influencing mammary health are still unclear. Differential somatic cell count (DSCC) could reflect the mastitis risk since it is the percentage of neutrophils plus lymphocytes in total somatic cells and could be reflective of mammary health of dairy cows. This work aimed to investigate the assessment and prognosis of the health of transition cows based on blood neutrophil extracellular traps (NETs).

Results
Eighty-four transition Holstein dairy cows were selected. The serum was sampled in all the animals at week 1 pre- and postpartum, and milk was sampled at week 1 postpartum. Based on the DSCC in milk at week 1, cows with lower (7.4% ± 4.07%, n = 15) and higher (83.3% ± 1.21%, n = 15) DSCCs were selected. High DSCC cows had higher levels of red blood cell counts (P < 0.05), hemoglobin (P = 0.07), and hematocrit (P = 0.05), higher concentrations of serum oxidative variables [(reactive oxygen species (P < 0.05), malondialdehyde (P < 0.05), protein carbonyl (P < 0.05), and 8-hydroxy-2-deoxyguanosine (P = 0.07)], higher levels of serum and milk NETs (P < 0.05) and blood-milk barrier indicators, including serum β-casein (P = 0.05) and milk immunoglobulin G2 (P = 0.09), than those of low DSCC cows. In addition, lower concentrations of serum nutrient metabolites (cholesterol and albumin) (P < 0.05) and a lower level of serum deoxyribonuclease I (P = 0.09) were observed in high DSCC cows than in low DSCC cows. Among the assessments performed using levels of the three prepartum serum parameters (NETs, deoxyribonuclease I and β-casein), the area under the curve (0.973) of NETs was the highest. In addition, the sensitivity (1.00) and specificity (0.93) were observed for the discrimination of these cows using NETs levels with a critical value of 32.2 ng/mL (P < 0.05).

Conclusions
The formation of NETs in blood in transition dairy cows may damage the integrity of the blood-milk barrier and thereby increase the risk for mastitis in postpartum cows.
Body composition and energy expenditure in anorexia nervosa: preliminary data of outpatients with recovering and active disease
Authors: dos Reis Tâmara Oliveira , de Magalhães Oliveira Fernanda , Kattah Fabiana Martins , Pena Natalia Fenner , Soares Maria Marta Sarquis , da Gama Torres Henrique Oswaldo 
Published: November 2022

Abstract
Background
In Anorexia Nervosa (AN) recovery, body mass index (BMI) may not reflect body composition. To investigate recovery, bioelectrical impedance (BIA) parameters and energy expenditure were investigated in patients with active and recovering AN, with emphasis on phase angle (PA), a BIA parameter.

Methods
BMI, PA, indirect BIA parameters (fat free mass, fat mass, total body water, fat free mass index, fat mass index) and resting metabolic rate (RMR) were obtained. Data from subjects distributed to active AN (ANact, n = 9), recovered AN (ANrec, n = 9) and healthy individuals (HI) (n = 16) were compared employing univariate methods and ordinal logistic regression.

Results
In univariate comparison, the BMI would not distinguish recovered individuals; this distinction was observed for the PA (p =  < 0,001). PA showed a good capacity to discriminate, between ANrec and HI (AUC = 0.792; CI = 0.564- 1.000; p = 0.017). In 2 models of ordinal logistic regression PA (OR = 0.123; 95% CI 0.030; 0.503 and OR = 0.091; 95% CI 0.016; 0.528) remained as a significant independent variable, indicating that increases in PA are related to higher probabilities of moving from ANact, to ANrec and to HI group. Bivariate regression indicated the presence of a relationship between PA and (R2 = 0.266, p = 0.002).

Conclusions
Changes in body composition and energy expenditure were observed in recovered anorexics with normal BMI. PA can play an important role in the assessment of recovering anorexic patients.