bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptionally imprinted glycomic signatures of acute myeloid leukemia
Authors: Blöchl Constantin , Wang Di , Mayboroda Oleg A. , Lageveen-Kammeijer Guinevere S. M. , Wuhrer Manfred 
Published: February 2023

Abstract
Background
Acute myeloid leukemia (AML) is a genetically and phenotypically heterogeneous disease that has been suffering from stagnant survival curves for decades. In the endeavor toward improved diagnosis and treatment, cellular glycosylation has emerged as an interesting focus area in AML. While mechanistic insights are still limited, aberrant glycosylation may affect intracellular signaling pathways of AML blasts, their interactions within the microenvironment, and even promote chemoresistance. Here, we performed a meta-omics study to portray the glycomic landscape of AML, thereby screening for potential subtypes and responsible glyco-regulatory networks.

Results
Initially, by integrating comprehensive N-, O-, and glycosphingolipid (GSL)-glycomics of AML cell lines with transcriptomics from public databases, we were able to pinpoint specific glycosyltransferases (GSTs) and upstream transcription factors (TFs) associated with glycan phenotypes. Intriguingly, subtypes M5 and M6, as classified by the French-American-British (FAB) system, emerged with distinct glycomic features such as high (sialyl) Lewisx/a ((s)Lex/a) and high sialylation, respectively. Exploration of transcriptomics datasets of primary AML cells further substantiated and expanded our findings from cell lines as we observed similar gene expression patterns and regulatory networks that were identified to be involved in shaping AML glycan signatures.

Conclusions
Taken together, our data suggest transcriptionally imprinted glycomic signatures of AML, reflecting their differentiation status and FAB classification. This study expands our insights into the emerging field of AML glycosylation and paves the way for studies of FAB class-associated glycan repertoires of AML blasts and their functional implications.
Renewable energy from secondary wood products contributes to local green development: the case of small-scale privately owned forests in Ciamis Regency, Indonesia
Authors: Siarudin Mohamad , Awang San Afri , Sadono Ronggo , Suryanto Priyono 
Published: February 2023

Abstract
Background
Wood biomass from forests is a renewable energy source that has the potential to support global green development. However, the process of traditional firewood extraction and its contribution to the energy supply varies and is usually underrecognized, especially in the local context. Therefore, this study aimed to describe the traditional use and estimate the supply and demand for wood bioenergy from small-scale privately owned forests (SSPF) in Ciamis Regency, West Java Province, Indonesia.

Methods
The sample location was determined in 3 subdistricts, namely, Sukamantri, Ciamis, and Banjaranyar, which represent the northern, central, and southern regions, respectively. The data were collected through observations on stands, interviews with respondents, key informants from users and business actors of wood in the SSPF, and observations on the processes taking place in the flow and use of biomaterials and firewoods.

Results and conclusion
Firewood is a secondary product that cannot be separated from the main products along SSPF’s chain of production based on the integration of raw material sources, linkages between actors, and volume sharing. The local knowledge and wisdom entanglements included the identification of the type and quality of firewood, distribution of resource allocation for household and industrial needs, and sharing of firewood for household needs. Although wood biomass contributes to the fulfillment of households and industrial needs of 8.51 million m3, there are indications of an imbalance between the potential supply and the demand for firewood due to its high intensity of use in industries. Therefore, multistakeholder and cross-regional support are needed to achieve sustainable SSPF management and fulfill the self-sufficiency of wood energy.
The human gut microbiome of athletes: metagenomic and metabolic insights
Authors: Fontana Federico , Longhi Giulia , Tarracchini Chiara , Mancabelli Leonardo , Lugli Gabriele Andrea , Alessandri Giulia , Turroni Francesca , Milani Christian , Ventura Marco 
Published: February 2023

Abstract
Background
The correlation between the physical performance of athletes and their gut microbiota has become of growing interest in the past years, since new evidences have emerged regarding the importance of the gut microbiota as a main driver of the health status of athletes. In addition, it has been postulated that the metabolic activity of the microbial population harbored by the large intestine of athletes might influence their physical performances. Here, we analyzed 418 publicly available shotgun metagenomics datasets obtained from fecal samples of healthy athletes and healthy sedentary adults.

Results
This study evidenced how agonistic physical activity and related lifestyle can be associated with the modulation of the gut microbiota composition, inducing modifications of the taxonomic profiles with an enhancement of gut microbes able to produce short-fatty acid (SCFAs). In addition, our analyses revealed a correlation between specific bacterial species and high impact biological synthases (HIBSs) responsible for the generation of a range of microbially driven compounds such vitamin B12, amino acidic derivatives, and other molecules linked to cardiovascular and age-related health-risk reduction.

Conclusions
Notably, our findings show how subsist an association between competitive athletes, and modulation of the gut microbiota, and how this modulation is reflected in the potential production of microbial metabolites that can lead to beneficial effects on human physical performance and health conditions.
The promising role of bacteriophage therapy in managing total hip and knee arthroplasty related periprosthetic joint infection, a systematic review
Authors: Khalifa Ahmed A. , Hussien Sarah M. 
Published: February 2023

AbstractPurposeTotal hip and knee arthroplasty periprosthetic joint infection (PJI) poses a management dilemma owing to the emergence of resistant organisms. A promising option is Bacteriophage therapy (BT) was used as an adjuvant for PJI management, aiming at treating resistant infections, decreasing morbidity, and mortality. The current review aimed to demonstrate the role and safety of using BT as an adjuvant to treat PJIs.MethodsA systematic search was performed through four databases (Embase, PubMed, Web of Science, and Scopus) up to March 2022, according to the predetermined inclusion and exclusion criteria.ResultsOur systematic review included 11 case reports of 13 patients in which 14 joints (11 TKAs and three THAs) were treated. The patients’ average age was 73.7 years, underwent an average of 4.5 previous surgeries. The most common organism was the Staphylococcus aureus species. All patients underwent surgical debridement; for the 13 patients, eight received a cocktail, and five received monophage therapy. All patients received postoperative suppressive antibiotic therapy. After an average follow‐up of 14.5 months, all patients had satisfactory outcomes. No recurrence of infection in any patient. Transaminitis complicating BT was developed in three patients, needed stoppage in only one, and the condition was reversible and non‐life‐threatening.ConclusionBT is a safe and potentially effective adjuvant therapy for treating resistant and relapsing PJIs. However, further investigations are needed to clarify some BT‐related issues to create effective and reproducible therapeutics. Furthermore, new ethical regulations should be implemented to facilitate its widespread use.
Transforaminal Interbody Fusion Using the Unilateral Biportal Endoscopic Technique Compared With Transforaminal Lumbar Interbody Fusion for the Treatment of Lumbar Spine Diseases: Analysis of Clinical and Radiological Outcomes
Authors: Zheng Bo , Zhang Xiu-Li , Li Peng 
Published: February 2023

BACKGROUND:
There has been a widespread application of minimally invasive spinal surgery techniques in the past few years. Unilateral biportal endoscopic has been successfully used in a variety of lumbar spine diseases, but there are few studies on lumbar fusion assisted by unilateral biportal endoscopy.

OBJECTIVE:
To compare the clinical and radiological outcomes of transforaminal interbody fusion using the unilateral biportal endoscopic technique (UBEIF) and transforaminal lumbar interbody fusion (TLIF) in patients with lumbar disease.

METHODS:
We studied 128 patients, 58 in the UBEIF group and 70 in the TLIF group. The Oswestry disability index, creatine kinase, visual analog score (VAS) for leg and back pain were used to assess clinical outcomes. Radiographic outcomes were assessed using the fusion rate, internal fixation loosening, and adjacent segment degeneration.

RESULTS:
Back and leg pain VAS scores in both groups were significantly lower 3, 6, and 12 months after surgery (P < .05). A significant reduction in Oswestry disability index in both groups was observed 6 and 12 months after surgery (P < .05). Compared with the TLIF group at 1 week after surgery, UBEIF patients' VAS score for back pain significantly improved (P < .05). There was no difference in fusion rate between the 2 groups (98.27% vs 98.57%).

CONCLUSION:
UBEIF and TLIF have similar clinical and radiographic outcomes in the treatment of single-segment lumbar disease with lumbar instability, including improved back and leg pain, improved disability, and high fusion rates. Furthermore, with UBEIF, less blood is lost, there is better relief of early back pain, and hospital stays are shorter.
In vivoquantitative high-throughput screening for drug discovery and comparative toxicology
Authors: Dranchak Patricia K. , Oliphant Erin , Queme Bryan , Lamy Laurence , Wang Yuhong , Huang Ruili , Xia Menghang , Tao Dingyin , Inglese James 
Published: February 2023

ABSTRACTQuantitative high-throughput screening (qHTS) pharmacologically evaluates chemical libraries for therapeutic uses, toxicological risk and, increasingly, for academic probe discovery. Phenotypic high-throughput screening assays interrogate molecular pathways, often relying on cell culture systems, historically less focused on multicellular organisms. Caenorhabditis elegans has served as a eukaryotic model organism for human biology by virtue of genetic conservation and experimental tractability. Here, a paradigm enabling C. elegans qHTS using 384-well microtiter plate laser-scanning cytometry is described, in which GFP-expressing organisms revealing phenotype-modifying structure–activity relationships guide subsequent life-stage and proteomic analyses, and Escherichia coli bacterial ghosts, a non-replicating nutrient source, allow compound exposures over two life cycles, mitigating bacterial overgrowth complications. We demonstrate the method with libraries of anti-infective agents, or substances of toxicological concern. Each was tested in seven-point titration to assess the feasibility of nematode-based in vivo qHTS, and examples of follow-up strategies were provided to study organism-based chemotype selectivity and subsequent network perturbations with a physiological impact. We anticipate that this qHTS approach will enable analysis of C. elegans orthologous phenotypes of human pathologies to facilitate drug library profiling for a range of therapeutic indications.
Spatial transcriptomics dimensionality reduction using wavelet bases
Authors: Xu Zhuoyan , Sankaran Kris 
Published: February 2023

Background: Spatially resolved transcriptomics (ST) measures gene expression along with the spatial coordinates of the measurements. The analysis of ST data involves significant computation complexity. In this work, we propose a gene expression dimensionality reduction algorithm that retains spatial structure. Methods: We combine the wavelet transformation with matrix factorization to select spatially-varying genes. We extract a low-dimensional representation of these genes. We adopt an Empirical Bayes perspective, imposing regularization through the prior distribution of factor genes. Additionally, we visualize the extracted representations, providing an overview of global spatial patterns. We illustrate the performance of our methods through spatial structure recovery and gene expression reconstruction using a simulation and real data analysis. Results: In real data experiments, our method identifies spatial structure of gene factors and outperforms regular decomposition regarding reconstruction error. We find a connection between the fluctuation of gene patterns and wavelet estimates, and this allows us to provide smoother visualizations. We develop the package and share the workflow generating reproducible quantitative results and gene visualization. The package is available at https://github.com/OliverXUZY/waveST. Conclusions: We have proposed a pipeline for dimensionality reduction that respects spatial structure. Both simulations and real data experiments demonstrate that wavelet and shrinkage techniques show positive results in spatially resolved transcriptomics data. We highlight the idea of combining image processing techniques and statistical methods for application in a spatial genomics context
The coronavirus disease 2019 (COVID-19) pandemic in nursing homes – the experience of care workers in Poland
Authors: Necel Ryszard 
Published: February 2023

Background: Nursing homes in Poland are the most common formal care institutions for dependent people. During the coronavirus disease 2019 (COVID-19) pandemic, nursing homes had particularly high infection rates. In this context, it is important to ask about the experiences of the care workers working in these institutions. Methods: This research was conducted using the computer-assisted web interviewing (CAWI) technique in five provinces in Poland. The field research was carried out in April 2021. The research sample included, among others, nurses, care workers, therapists, social workers and the management staff of institutions whose representatives worked during the COVID-19 pandemic. Respondents were asked to assess the care provided to residents. Results: It turned out that the vast majority of respondents positively assessed the fulfillment of the basic living needs of residents and the availability of care. The assessment of the organization of residents’ leisure time, the fulfillment of their religious and cultural needs, and the issue of maintaining contacts with the social environment was less satisfactory. The article also describes the results of care institution employees’ self-assessment of their mental health. For the majority, the most stressful factor was the need to work in a health-threatening environment and the sense of responsibility for the residents. Regarding the availability of the forms of support offered to workers experiencing deteriorating mental health due to working in the pandemic situation, more than a third said that their institution did not offer any form of assistance. Conclusions: The article lists a number of recommendations. In the light of the data obtained, it is necessary to increase the intensity of services provided to residents of nursing homes in terms of organizing their free time, meeting their religious and cultural needs and maintaining contact with the social environment.
The Well-Being of the Academic Community During the COVID-19 Pandemic
Authors: Przyborowska Beata , Błajet Piotr , Fopka-Kowalczyk Małgorzata 
Published: February 2023

Since 2020, the entire world has been struggling with the SARS-CoV-2 pandemic. The constant increase in the number of sick and dying people and the need for quarantine and social distancing have significantly affected the functioning of people, regardless of their background, age and activities. This article aims to examine the level of well-being among the academic community of Nicolaus Copernicus University in Poland based on the concept of Ken Wilber. To this end, a self-administered questionnaire was developed to assess the overall well-being, as well as the respondents’ well-being related to emotions, relationships, health, and the sense of security and satisfaction experienced during the pandemic. A total of 1,164 university employees and 1,601 doctoral and other students participated in the study. Teachers represented the highest levels of overall well-being, scoring higher than doctoral students and undergraduates. The older the respondents, the higher the perceived levels of overall well-being. These findings indicate that doctoral and other students are struggling with reduced levels of well-being and a reduced sense of the quality of life, displaying signs of emotional difficulties, anxiety and fear.
Climate Change and Uncertainty: An Asset Pricing Perspective
Authors: Barnett Michael 
Published: February 2023

Climate change and uncertainty about its potential consequences has become a central concern for economists, investors, and policymakers alike. I use a stochastic, dynamic general equilibrium model where final output is produced using a mix of cheap, dirty inputs and expensive, clean inputs and preferences incorporate aversion to climate model misspecification to analyze the implications of climate change and climate model uncertainty on economic and financial market outcomes. I find that climate change leads to increased clean input production and reduced emissions and that there is a negative price of climate risk that is significantly amplified and increasing in magnitude as climate change increases due to aversion to climate model uncertainty. Existing empirical estimates are consistent with the model implications, highlighting the potentially significant influence of climate model uncertainty on macroeconomic and asset pricing outcomes. This paper was accepted by Elke Weber, Special Section of Management Science on Business and Climate Change. Funding: This work was supported by the Energy Policy Institute at Chicago [Dissertation Support Fellowship], the Fama-Miller Center [Liew Fama-Miller Fellowship], the National Science Foundation [Graduate Research Fellowship Award D], and the University of Chicago [Harper (Provost) Dissertation Fellowship]. Supplemental Material: The data files and online appendices are available at https://doi.org/10.1287/mnsc.2022.4635 .
Examination of early treatment effects and related biases during the conduct of two UK-wide pragmatic orthopaedic surgical trials: ProFHER and UK FROST
Authors: Knowlson Catherine N. , Brealey Stephen , Keding Ada , Torgerson David , Rangan Amar 
Published: February 2023

AimsEarly large treatment effects can arise in small studies, which lessen as more data accumulate. This study aimed to retrospectively examine whether early treatment effects occurred for two multicentre orthopaedic randomized controlled trials (RCTs) and explore biases related to this.MethodsIncluded RCTs were ProFHER (PROximal Fracture of the Humerus: Evaluation by Randomisation), a two-arm study of surgery versus non-surgical treatment for proximal humerus fractures, and UK FROST (United Kingdom Frozen Shoulder Trial), a three-arm study of two surgical and one non-surgical treatment for frozen shoulder. To determine whether early treatment effects were present, the primary outcome of Oxford Shoulder Score (OSS) was compared on forest plots for: the chief investigator’s (CI) site to the remaining sites, the first five sites opened to the other sites, and patients grouped in quintiles by randomization date. Potential for bias was assessed by comparing mean age and proportion of patients with indicators of poor outcome between included and excluded/non-consenting participants.ResultsNo bias in treatment effect was observed overall for the CI site, or the first five sites, compared with the remaining sites in either trial. An early treatment effect on the OSS was observed for the first quintile of participants recruited to ProFHER only (clinically relevant difference of seven points). Selection bias for age was observed in the ProFHER trial only, with slightly younger patients being recruited into the study. Both trials showed some selection bias for markers of poor prognosis, although these did not appear to change over time.ConclusionNo bias in treatment effects overall were found at the CI or early sites set-up. An early treatment effect was found in one of the two trials, which was likely a chance effect as this did not continue during the study. Selection bias was observed in both RCTs, however this was minimal and did not impact on outcome.Cite this article: Bone Jt Open 2023;4(2):96–103.
Images of Inhomogeneous Turbid Media Using Diffuse Photon Density Waves
Authors: O'Leary M. A. , Boas D. A. , Chance B. , Yodh A. G. 
Published: February 2023

In this paper we present images derived from measurements of diffuse photon density waves in turbid media. After a brief introduction and description of the experimental set-up, this document is divided into two sections.
In the first, we present an analytic solution for the scattering of diffuse photon density waves by spherical and cylindrical inhomogeneities within turbid media and discuss the application of this solution to systems containing multiple objects and multiple sources. This exact solution is a useful tool for simulating the distortion of a diffuse photon density wave due to simple inhomogeneities. Until recently, simulations of heterogeneous media were achieved by Monte-Carlo methods, finite element analysis, or other time consuming techniques. More recently, Feng et al. [1] presented a perturbative solution for a single, point-like heterogeneity. The exact calculation we present is not limited to small objects, and numerical calculations using this solution are fast compared to Monte Carlo simulations[2]. Finally, we experimentally demonstrate that this analytic solution enables us to fit for the optical and geometric properties of arbitrary spherical and cylindrical objects, and we discuss the detector sensitivity required to characterize such objects.
In the second section we derive images of more general inhomogeneous scattering media. Our method is based on the diffusion approximation, but is not an iterative approach; it is a direct inversion that is exact to first order in variations of the sample absorption. An increase in sensitivity is achieved through the use of multiple-source/single-detector units placed around the turbid medium. In our particular case, each unit consisted of a set of two modulated diffuse light sources phased 180° out of phase with respect to one another, and a single detector located at positions equidistant from each source. In this report we will describe the general theoretical approach, provide experimental evidence of its utility, and discuss potential applications.
Mirror tilt effects in free electron lasers with a hole coupling
Authors: Zhulin V. I. 
Published: February 2023

In an ordinary laser operation a misalignment of resonator mirrors leads usually to undesirable effects and has to be avoided. But in some certain types of cavity configurations deliberate introduction of misalignment makes it possible to improve considerably the characteristics of output radiation. An example of such configurations is an optical scheme with hole coupling. We considered two options:
• the free electron laser (FEL) with the radiation output through the on-axis hole at the exit mirror;1
• the external resonator (used for pulse stacking) where the exit FEL radiation enters this resonator through the on-axis hole at the input mirror.2
These configurations were investigated with the continuous wave 3-D code developed earlier.3