bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the cellulolytic and hemicellulolytic activities of manganese peroxidase for lignocellulose deconstruction
Authors: Liu Xiaoqing , Ding Sunjia , Gao Fang , Wang Yaru , Taherzadeh Mohammad J. , Wang Yuan , Qin Xing , Wang Xiaolu , Luo Huiying , Yao Bin , Huang Huoqing , Tu Tao 
Published: September 2023

Abstract
Background
A cost-effective pretreatment and saccharification process is a necessary prerequisite for utilizing lignocellulosic biomass (LCB) in biofuel and biomaterials production. Utilizing a multifunctional enzyme with both pretreatment and saccharification functions in a single step for simultaneous biological pretreatment and saccharification process (SPS) will be a green method of low cost and high efficiency. Manganese peroxidase (MnP, EC 1.11.1.13), a well-known lignin-degrading peroxidase, is generally preferred for the biological pretreatment of biomass. However, exploring the role and performance of MnP in LCB conversion will promote the application of MnP for lignocellulose-based biorefineries.

Results
In this study, we explored the ability of an MnP from Moniliophthora roreri, MrMnP, in LCB degradation. With Mn2+ and H2O2, MrMnP decomposed 5.0 g/L carboxymethyl cellulose to 0.14 mM of reducing sugar with a conversion yield of 5.0 mg/g, including 40 μM cellobiose, 70 μM cellotriose, 20 μM cellotetraose, and 10 μM cellohexaose, and degraded 1.0 g/L mannohexaose to 0.33 μM mannose, 4.08 μM mannotriose, and 4.35 μM mannopentaose. Meanwhile, MrMnP decomposed 5.0 g/L lichenan to 0.85 mM of reducing sugar with a conversion yield of 30.6 mg/g, including 10 μM cellotriose, 20 μM cellotetraose, and 80 μM cellohexose independently of Mn2+ and H2O2. Moreover, the versatility of MrMnP in LCB deconstruction was further verified by decomposing locust bean gum and wheat bran into reducing sugars with a conversion yield of 54.4 mg/g and 29.5 mg/g, respectively, including oligosaccharides such as di- and tri-saccharides. The catalytic mechanism underlying MrMnP degraded lignocellulose was proposed as that with H2O2, MrMnP oxidizes Mn2+ to Mn3+. Subsequently, it forms a complex with malonate, facilitating the degradation of CMC and mannohexaose into reducing sugars. Without H2O2, MrMnP directly oxidizes malonate to hydroperoxyl acetic acid radical to form compound I, which then attacks the glucosidic bond of lichenan.

Conclusion
This study identified a new function of MrMnP in the hydrolysis of cellulose and hemicellulose, suggesting that MrMnP exhibits its versatility in the pretreatment and saccharification of LCB. The results will lead to an in-depth understanding of biocatalytic saccharification and contribute to forming new enzymatic systems for using lignocellulose resources to produce sustainable and economically viable products and the long-term development of biorefinery, thereby increasing the productivity of LCB as a green resource.
Urban malaria vector bionomics and human sleeping behavior in three cities in Senegal
Authors: Diop Abdoulaye , Ndiaye Fatou , Sturm-Ramirez Katherine , Konate Lassana , Senghor Massila , Diouf El Hadji , Dia Abdoulaye Kane , Diedhiou Seynabou , Samb Badara , Sene Doudou , Zohdy Sarah , Dotson Ellen , Diouf Mame Birame , Koscelnik Valerie , Gerberg Lilia , Bangoura Abdoulaye , Faye Ousmane , Clark Tiffany , Niang El Hadji Amadou , Chabi Joseph 
Published: September 2023

AbstractBackgroundMalaria is endemic in Senegal, with seasonal transmission, and the entire population is at risk. In recent years, high malaria incidence has been reported in urban and peri-urban areas of Senegal. An urban landscape analysis was conducted in three cities to identify the malaria transmission indicators and human behavior that may be driving the increasing malaria incidence occurring in urban environments. Specifically, mosquito vector bionomics and human sleeping behaviors including outdoor sleeping habits were assessed to guide the optimal deployment of targeted vector control interventions.MethodsLongitudinal entomological monitoring using human landing catches and pyrethrum spray catches was conducted from May to December 2019 in Diourbel, Kaolack, and Touba, the most populous cities in Senegal after the capital Dakar. Additionally, a household survey was conducted in randomly selected houses and residential Koranic schools in the same cities to assess house structures, sleeping spaces, sleeping behavior, and population knowledge about malaria and vector control measures.ResultsOf the 8240Anophelesmosquitoes collected from all the surveyed sites, 99.4% (8,191) wereAn. gambiaes.l., and predominantlyAn. arabiensis(99%). A higher number ofAn. gambiaes.l. were collected in Kaolack (77.7%,n = 6496) than in Diourbel and Touba. The overall mean human biting rate was 14.2 bites per person per night (b/p/n) and was higher outdoors (15.9 b/p/n) than indoors (12.5 b/p/n). The overall mean entomological inoculation rates ranged from 3.7 infectious bites per person per year (ib/p/y) in Diourbel to 40.2 ib/p/y in Kaolack. Low anthropophilic rates were recorded at all sites (average 35.7%). Of the 1202 households surveyed, about 24.3% of household members slept outdoors, except during the short rainy season between July and October, despite understanding how malaria is transmitted and the vector control measures used to prevent it.ConclusionAnopheles arabiensiswas the primary malaria vector in the three surveyed cities. The species showed an outdoor biting tendency, which represents a risk for the large proportion of the population sleeping outdoors. As all current vector control measures implemented in the country target endophilic vectors, these data highlight potential gaps in population protection and call for complementary tools and approaches targeting outdoor biting malaria vectors.Graphical Abstract
Identification of novel protein biomarkers and drug targets for colorectal cancer by integrating human plasma proteome with genome
Authors: Sun Jing , Zhao Jianhui , Jiang Fangyuan , Wang Lijuan , Xiao Qian , Han Fengyan , Chen Jie , Yuan Shuai , Wei Jingsun , Larsson Susanna C. , Zhang Honghe , Dunlop Malcolm G , Farrington Susan M , Ding Kefeng , Theodoratou Evropi , Li Xue 
Published: September 2023

Abstract
Background
The proteome is a major source of therapeutic targets. We conducted a proteome-wide Mendelian randomization (MR) study to identify candidate protein markers and therapeutic targets for colorectal cancer (CRC).

Methods
Protein quantitative trait loci (pQTLs) were derived from seven published genome-wide association studies (GWASs) on plasma proteome, and summary-level data were extracted for 4853 circulating protein markers. Genetic associations with CRC were obtained from a large-scale GWAS meta-analysis (16,871 cases and 26,328 controls), the FinnGen cohort (4957 cases and 304,197 controls), and the UK Biobank (9276 cases and 477,069 controls). Colocalization and summary-data-based MR (SMR) analyses were performed sequentially to verify the causal role of candidate proteins. Single cell-type expression analysis, protein-protein interaction (PPI), and druggability evaluation were further conducted to detect the specific cell type with enrichment expression and prioritize potential therapeutic targets.

Results
Collectively, genetically predicted levels of 13 proteins were associated with CRC risk. Elevated levels of two proteins (GREM1, CHRDL2) and decreased levels of 11 proteins were associated with an increased risk of CRC, among which four (GREM1, CLSTN3, CSF2RA, CD86) were prioritized with the most convincing evidence. These protein-coding genes are mainly expressed in tissue stem cells, epithelial cells, and monocytes in colon tumor tissue. Two interactive pairs of proteins (GREM1 and CHRDL2; MMP2 and TIMP2) were identified to be involved in osteoclast differentiation and tumorigenesis pathways; four proteins (POLR2F, CSF2RA, CD86, MMP2) have been targeted for drug development on autoimmune diseases and other cancers, with the potentials of being repurposed as therapeutic targets for CRC.

Conclusions
This study identified several protein biomarkers to be associated with CRC risk and provided new insights into the etiology and promising targets for the development of screening biomarkers and therapeutic drugs for CRC.
Unveiling difficult-to-treat rheumatoid arthritis: long-term impact of biologic or targeted synthetic DMARDs from the KOBIO registry
Authors: Jung Ju-Yang , Lee Eunyoung , Kim Ji-Won , Suh Chang-Hee , Shin Kichul , Kim Jinhyun , Kim Hyoun-Ah 
Published: September 2023

Abstract
Background
While the availability of biological or targeted synthetic disease-modifying anti-rheumatic drugs (b/tsDMARDs) has improved outcomes for rheumatoid arthritis (RA) patients, there remains a subset of individuals who fail to achieve low disease activity or remission despite multiple cycles of b/tsDMARDs. This state is referred to as 'difficult-to-treat (D2T)' RA.

Methods
Data from the Korean College of Rheumatology Biologics registry were utilized to analyze patients with RA who were treated with b/tsDMARDs.

Results
Among 2,321 RA patients with RA treated with b/tsDMARDs, 271 (11.7%) were diagnosed with D2T RA. Lower age (OR = 0.98, p < 0.001), longer disease duration (OR = 1.06, p < 0.001), lower patient global assessment (OR = 0.89, p = 0.045), higher SDAI (OR = 1.06, p = 0.014) and RAPID3 (OR = 1.06, p = 0.002), lower RF positivity (OR = 0.65, p = 0.04), and lower prior use of methotrexate (OR = 0.44, p = 0.008), sulfasalazine (OR = 0.59, p = 0.003), and leflunomide (OR = 0.67, p = 0.013) were associated with D2T RA. The drug survival rate of b/tsDMARDs did not differ between patients with D2T RA and non-D2T RA (p = 0.35). However, the drug survival of individual b/tsDMARD differed between patients with D2T RA and non-D2T RA after eight years. Patients with D2T RA withdrew from b/tsDMARDs due to inefficacy more frequently than those without D2T RA (p < 0.001).

Conclusions
D2T RA patients experienced higher disease activity despite maintaining b/tsDMARD therapy. Withdrawal rates due to inefficacy were higher in D2T RA. Effective therapeutic strategies are needed to improve disease control and treatment outcomes in this unique patient population.
Dynamic household structure and composition: a manual for longitudinal analysis of living arrangements
Authors: Menashe-Oren Ashira , Compaoré Yacouba , Bocquier Philippe , Ginsburg Carren 
Published: September 2023

Abstract
Objective
This research note introduces a set of tools to conduct analysis of household structure and composition with either limited or comprehensive longitudinal data. The data used here are from Health and Demographic Surveillance Systems in Africa, but the methods can be adapted and applied to other longitudinal micro-data such as register data. A training manual describing the procedures for creating time-varying household measures step-by-step is supplied as supplementary material to this note. Code is provided in STATA but can easily be translated for other statistical software, and the logic for each step remains the same.

Results
The analysis of household structure demonstrates how with limited data (such as a household identifier), it is possible to construct time-varying measures of household membership, including household size or the number of members in specific age and sex groups. The analysis of household composition demonstrates how with expanded data (including links to parents in addition to residence status in the same household), it is possible to construct time-varying measures of household membership of specific kin, i.e. mother, sibling or grandparent. The results illustrated in this research note are a taste of what can be achieved by following the training manual in the supplementary material.
Impact of planting Phallus rubrovolvatus on physicochemical and microbial properties and functional groups of soil
Authors: Gao Xu , Ding Mengjiao , Wu Tao , Deng Xiaohua , Li Qiang 
Published: September 2023

Abstract
Purpose
Soil microbial communities are critically important to agricultural ecosystems. The present study aimed to evaluate the changes in soil microbial community composition and functional groups after planting Phallus rubrovolvatus.

Methods
Illumina platform were adopted to characterize the bacterial and fungal diversity in the soil cropped with P. rubrovolvatus for 0 and 1 year.

Results
The results showed that planting P. rubrovolvatus reduced the bacterial and fungal diversity in the soil, and the dynamics of the soil bacterial diversity changed more drastically. This study also indicated that, as keystone taxa, the dominant bacteria (Actinobacteria, Sphingomonas, Xanthobacteraceae, and Gemmatimonadaceae) and dominant fungi (Mortierellales and Eurotiales) served as a key component in the network of soil microbial communities. Moreover, the bacterial and fungal communities in the soil planted with P. rubrovolvatus formed more similar and weak networks.

Conclusion
Planting P. rubrovolvatus significantly influenced the structure and composition of microbial communities. In the future, we will focus on ways to improve the soil environment after planting P. rubrovolvatus.
Natural language processing for automatic evaluation of free-text answers — a feasibility study based on the European Diploma in Radiology examination
Authors: Stoehr Fabian , Kämpgen Benedikt , Müller Lukas , Zufiría Laura Oleaga , Junquero Vanesa , Merino Cristina , Mildenberger Peter , Kloeckner Roman 
Published: September 2023

Abstract
Background
Written medical examinations consist of multiple-choice questions and/or free-text answers. The latter require manual evaluation and rating, which is time-consuming and potentially error-prone. We tested whether natural language processing (NLP) can be used to automatically analyze free-text answers to support the review process.

Methods
The European Board of Radiology of the European Society of Radiology provided representative datasets comprising sample questions, answer keys, participant answers, and reviewer markings from European Diploma in Radiology examinations. Three free-text questions with the highest number of corresponding answers were selected: Questions 1 and 2 were “unstructured” and required a typical free-text answer whereas question 3 was “structured” and offered a selection of predefined wordings/phrases for participants to use in their free-text answer. The NLP engine was designed using word lists, rule-based synonyms, and decision tree learning based on the answer keys and its performance tested against the gold standard of reviewer markings.

Results
After implementing the NLP approach in Python, F1 scores were calculated as a measure of NLP performance: 0.26 (unstructured question 1, n = 96), 0.33 (unstructured question 2, n = 327), and 0.5 (more structured question, n = 111). The respective precision/recall values were 0.26/0.27, 0.4/0.32, and 0.62/0.55.

Conclusion
This study showed the successful design of an NLP-based approach for automatic evaluation of free-text answers in the EDiR examination. Thus, as a future field of application, NLP could work as a decision-support system for reviewers and support the design of examinations being adjusted to the requirements of an automated, NLP-based review process.

Clinical relevance statement
Natural language processing can be successfully used to automatically evaluate free-text answers, performing better with more structured question-answer formats. Furthermore, this study provides a baseline for further work applying, e.g., more elaborated NLP approaches/large language models.

Key points
• Free-text answers require manual evaluation, which is time-consuming and potentially error-prone.
• We developed a simple NLP-based approach — requiring only minimal effort/modeling — to automatically analyze and mark free-text answers.
• Our NLP engine has the potential to support the manual evaluation process.
• NLP performance is better on a more structured question-answer format.

Graphical Abstract
CDC42-mediated Wnt signaling facilitates odontogenic differentiation of DPCs during tooth root elongation
Authors: Zhou Tao , Chen Guoqing , Xu Yuchan , Zhang Shuning , Tang Huilin , Qiu Tao , Guo Weihua 
Published: September 2023

Abstract
Background
CDC42 is a member of Rho GTPase family, acting as a molecular switch to regulate cytoskeleton organization and junction maturation of epithelium in organ development. Tooth root pattern is a highly complicated and dynamic process that dependens on interaction of epithelium and mesenchyme. However, there is a lack of understanding of the role of CDC42 during tooth root elongation.

Methods
The dynamic expression of CDC42 was traced during tooth development through immunofluorescence staining. Then we constructed a model of lentivirus or inhibitor mediated Cdc42 knockdown in Herwig’s epithelial root sheath (HERS) cells and dental papilla cells (DPCs), respectively. Long-term influence of CDC42 abnormality was assessed via renal capsule transplantation and in situ injection of alveolar socket.

Results
CDC42 displayed a dynamic spatiotemporal pattern, with abundant expression in HERS cells and apical DPCs in developing root. Lentivirus-mediated Cdc42 knockdown in HERS cells didn’t disrupt cell junctions as well as epithelium-mesenchyme transition. However, inhibition of CDC42 in DPCs undermined cell proliferation, migration and odontogenic differentiation. Wnt/β-catenin signaling as the downstream target of CDC42 modulated DPCs’ odontogenic differentiation. The transplantation and in situ injection experiments verified that loss of CDC42 impeded root extension via inhibiting the proliferation and differentiation of DPCs.

Conclusions
We innovatively revealed that CDC42 was responsible for guiding root elongation in a mesenchyme-specific manner. Furthermore, CDC42-mediated canonical Wnt signaling regulated odontogenic differentiation of DPCs during root formation.
Paracrine signalling between keratinocytes and SVF cells results in a new secreted cytokine profile during wound closure
Authors: Balko Stefan , Kerr Evan , Buchel Ed , Logsetty Sarvesh , Raouf Afshin 
Published: September 2023

AbstractStromal vascular fraction (SVF) cells, and the adipose-derived mesenchymal stem cells they contain, have shown enhanced wound healing in vitro and in vivo, yet their clinical application has been limited. In this regard, understanding the mechanisms that govern SVF-enhanced wound healing would improve their application in the clinic. Here, we show that the SVF cells and keratinocytes engage in a paracrine crosstalk during wound closure, which results in a new cytokine profile that is distinct from the cytokines regularly secreted by either cell type on their own. We identify 11 cytokines, 5 of which are not regularly secreted by the SVF cells, whose expressions are significantly increased during wound closure by the keratinocytes. This new cytokine profile could be used to accelerate wound closure and initiate re-epithelialization without the need to obtain the SVF cells from the patient.
Application of mesenchymal stem cells for anti-senescence and clinical challenges
Authors: Wang Yaping , Gao Tianyun , Wang Bin 
Published: September 2023

AbstractSenescence is a hot topic nowadays, which shows the accumulation of senescent cells and inflammatory factors, leading to the occurrence of various senescence-related diseases. Although some methods have been identified to partly delay senescence, such as strengthening exercise, restricting diet, and some drugs, these only slow down the process of senescence and cannot fundamentally delay or even reverse senescence. Stem cell-based therapy is expected to be a potential effective way to alleviate or cure senescence-related disorders in the coming future. Mesenchymal stromal cells (MSCs) are the most widely used cell type in treating various diseases due to their potentials of self-replication and multidirectional differentiation, paracrine action, and immunoregulatory effects. Some biological characteristics of MSCs can be well targeted at the pathological features of aging. Therefore, MSC-based therapy is also a promising strategy to combat senescence-related diseases. Here we review the recent progresses of MSC-based therapies in the research of age-related diseases and the challenges in clinical application, proving further insight and reference for broad application prospects of MSCs in effectively combating senesce in the future.
Evaluation of safety and efficacy of allogeneic adipose tissue-derived mesenchymal stem cells in pediatric bronchiolitis obliterans syndrome (BoS) after allogeneic hematopoietic stem cell transplantation (allo-HSCT)
Authors: Mohseni Rashin , Mahdavi Sharif Pouya , Behfar Maryam , Modaresi Mohammad Reza , Shirzadi Rohola , Mardani Mahta , Jafari Leila , Jafari Fahimeh , Nikfetrat Zeynab , Hamidieh Amir Ali 
Published: September 2023

Abstract
Background
Allo-HSCT is a definite approach for the management of a wide variety of lethal and debilitating malignant and non-malignant disorders. However, its two main complications, acute and chronic graft-versus-host disease (GVHD), exert significant morbidities and mortalities. BoS, as a manifestation of chronic lung GVHD, is a gruesome complication of allo-HSCT, and for those with steroid-refractory disease, no approved second-line therapies exist. Mesenchymal stem cells (MSCs) exert anti-inflammatory and growth-promoting effects, and their administration against a wide range of inflammatory and neurologic disorders, as well as GVHD, has been associated with promising outcomes. However, literature on the safety and effectiveness of MSC therapy for BoS and pediatric cGVHD is scarce.

Methods
We designed a single-arm trial to administer adipose tissue (AT)-derived MSCs to pediatric patients with refractory BoS after allo-HSCT. AT-MSCs from obese, otherwise healthy donors were cultured in an ISO class 1 clean room and injected into the antecubital vein of eligible patients with a dose of 1 × 106/kg. The primary endpoints included a complete or partial response to therapy [in terms of increased forced expiratory volume in one second (FEV1) values and steroid dose reduction] and its safety profile.

Results
Four eligible patients with a median age of 6.5 years were enrolled in the study. Steroid-induced osteoporosis and myopathy were present in three cases. A partial response was evident in three cases after a single injection of AT-MSCs. The treatment was safe and tolerable, and no treatment-related adverse events were noted. Two patients developed manageable COVID-19 infections one and 4 months after AT-MSC injection. After a median follow-up duration of 19 months, all cases are still alive and have had no indications for lung transplantation.

Conclusions
AT-MSCs could be safely administered to our pediatric cases with BoS post-allo-HSCT. Considering their advanced stage of disease, their sub-optimal functional capacity due to steroid-induced complications, and COVID-19 infection post-treatment, we believe that AT-MSC therapy can have possible efficacy in the management of pediatric BoS. The conduction of further studies with larger sample sizes and more frequent injections is prudent for further optimization of AT-MSC therapy against BoS.
Trial registration Iranian Registry of Clinical Trials (IRCT), IRCT20201202049568N2. Registered 22 February 2021, https://en.irct.ir/trial/53143.