bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic characterization of a novel Salinicola salarius isolate applied for the bioconversion of agro-industrial wastes into polyhydroxybutyrate
Authors: Abdelrahman Shymaa A. , Barakat Olfat S. , Ahmed Marwa N. 
Published: November 2023

Abstract
Background
PHB is of significant concern due to its potential applications as green alternatives to traditional petrochemical-based plastics. In the present study, a new strain of Salinicola salarius, a halophilic bacterium, was isolated from the New Suez Canal in Egypt and characterized exclusively as a potential PHB producer. Further analysis of the ES021 genome was conducted to identify and elucidate the genes involved in PHB production.
Results
Different PHB-producing marine bacteria were isolated from the New Suez Canal and characterized as PHB producers. Among the 17 bacterial isolates, Salinicola salarius ES021 strain showed the capability to accumulate the highest amount of PHB. Whole genome analysis was implemented to identify the PHB-related genes in Salinicola salarius ES021 strain. Putative genes were identified that can function as phaCAB genes to produce PHB in this strain. These genes include fadA, fabG, and P3W43_16340 (encoding acyl-CoA thioesterase II) for PHB production from glucose. For PHB production from fatty acids, phaJ and fadB are involved. Environmental factors such as aeration and incubation temperature were optimized to attain high productivity of PHB. The results showed that growing Salinicola salarius ES021 strain at 30°C on a shaker incubator (110 rpm) for 48 h resulted in the highest PHB productivity. To maximize PHB production, different raw materials i.e., salted whey and molasses were examined as cheap carbon sources. The PHB productivity was increased two-fold (13.34 g/l) when using molasses (5% sucrose) as a fermentation media. This molasses medium was used to upscale PHB production in a 20 L stirred-tank bioreactor yielding a biomass of 25.12 g/l, and PHB of 12.88 g/l. Furthermore, the produced polymer was confirmed as PHB using Fourier-transform infrared spectroscopy (FTIR) and Gas chromatography-mass spectroscopy (GC-MS) analysis.
Conclusions
Herein, Salinicola salarius ES021 strain was demonstrated as a high natural producer of PHB from agro-industrial wastes. A detailed genome characterization of the ES021 strain showing the PHB-related genes was presented in this study. However, further metabolic engineering is required to confirm the gene networks required for PHB production in this strain.
Zinc homeostasis plays important roles in hypoxia tolerance, a study conducted clinically and in vitro
Authors: Guo Yan , Yu Chao , Lu Zhongsheng , Zhang Menglan , Liu Xiao , Zhang Qiang 
Published: November 2023

Abstract
Objective: To investigate the relationship between zinc homeostasis and hypoxia tolerance.
Methods: Healthy individuals from highland (4500-5000 m, the QH group) and plain (0-200 m, the HH group), as well as high-altitude cerebral edema (HACE) patients. Blood samples were analyzed and transcriptome sequenced. Develop hypoxic model in human brain microvascular endothelial cells (HBMECs), intervene with zinc.
Results: The HACE group demonstrated significant changes in blood transcriptome. Out of over 4000 differentially expressed genes (DEGs) (|log2FC|>2, padj<0.05), more than 300 DEGs were zinc-related, with only the CA1 mRNA being upregulated (log2FC=5.84). Other zinc-related genes showed a more than fourfold reduction in transcription levels, including various zinc-containing enzymes and zinc transport proteins (ZTPs). Compared to QH, the RBC of HACE showed no change (5.6 vs 5.7, P>0.05). However, Hb (147 vs 195) and plasma zinc (37.0 vs 94.0) were reduced, while CA1 (55.4 vs 8.6) and HIF-1α (260 vs 48) were elevated (P<0.01). In vitro studies confirmed that hypoxic exposure (O2 8-8.5%, 24 h) hindered HBMECs proliferation and migration, increased apoptosis and necrosis, and resulted in abnormal expression of CA1 and various ZTPs. Zinc intervention (6 μM, 24 h) significantly reduced these adverse effects, enhancing the cell's tolerance to hypoxia.
Conclusion: During low oxygen periods, the increase in RBC and Hb needs ample zinc and balanced homeostasis. Lack of zinc can disrupt this balance, alter transport proteins and enzyme expression, and possibly lead to severe conditions like HACE. Therefore, maintaining zinc balance is crucial for tolerance to low oxygen.
Lysosomal and synaptic dysfunction markers in longitudinal cerebrospinal fluid spanning from healthy subjects to prodromal and manifest Parkinson’s disease
Authors: Bartl Michael , nilsson johanna , Dakna Mohammed , Weber Sandrina , Schade Sebastian , Xylaki Mary , Gomes Barbara , Ernst Marielle , Muntean Maria-Lucia , Sixel-Döring Friederike , Trenkwalder Claudia , Zetterberg Henrik , Brinkmalm Ann , Mollenhauer Brit 
Published: November 2023

Abstract

Lysosomal and synaptic dysfunctions are hallmarks in multiple neurodegenerative diseases including Alzheimer’s disease and Parkinson’s disease (PD) and could be relevant from a biomarker perspective. Biomarker data on prodromal and early PD are not yet available. We performed targeted mass spectrometry measurements cross-sectionally and longitudinally over 10 years with an established biomarker panel, assessing autophagy and synaptic function in cerebrospinal fluid (CSF) in prodromal subjects with isolated REM sleep behavior disorder (iRBD), drug-naïve de novo PD subjects at baseline, and sex- and age-matched healthy controls. Multiple markers of autophagy, synaptic plasticity, and secretory pathways showed reduced expression in PD and iRBD compared to controls. Machine learning identified neuronal pentraxin receptor and neurosecretory protein VGF as the most relevant for discriminating between groups. CSF levels of LAMP2, neuronal pentraxins, and syntaxins correlated with clinical progression and showed predictive potential for motor- and non-motor symptoms as a valid basis for future drug trials.
Acute leukemia diagnosis through AI-enhanced ATR-FTIR spectroscopy of peripheral blood smear
Authors: Lee Michael , Sy Charles Eryll , Mesina Flordeluna , Caguioa Priscilla , Castillo Ma. Rosario Irene , Bangaoil Ruth , Punay Jeanny , Cobarrubias Mariella Cielo , Tomas Rock Christian , Albano Pia Marie 
Published: November 2023

Abstract

Background
Acute leukemia is a highly perilous cancer, currently diagnosed using invasive procedures like bone marrow aspirate and biopsy (BMA/BMB). There is the pressing need for non-invasive, reagent-free diagnostic approaches with exceptional sensitivity and specificity. Hence, this study explored the potential of combining attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy and artificial intelligence (AI) for diagnosing acute lymphoblastic leukemia (ALL) and acute myelogenous leukemia (AML).
Methods
The study analyzed the spectral data from 50 healthy individuals and 50 BMA/BMB-confirmed acute leukemia patients. Six trained models were used to assess the diagnostic performance, focusing on accuracy, positive predictive value, negative predictive value, F1-score, and area under the ROC curve (AUC). Spectral peak patterns were examined in the 1800 𝑐𝑚−1 to 850 𝑐𝑚−1 range.
Results
Of the six (6) trained models, the SVM model showed remarkable diagnostic performance, including accuracy, positive predictive value, negative predictive value, F1-score and AUC of 83%, 80%, 86%, 82.47% and 90.76%, respectively. Leukemia and healthy blood samples exhibited distinguishable spectral peak patterns in the amides I and II, glycogen, and phosphorylated protein regions.
Conclusion
This study underscores the potential of AI-enhanced FTIR spectroscopy as a valuable adjunct diagnostic tool for acute leukemia. By providing a less invasive and faster alternative to BMA/BMB, this approach offers the possibility of enhancing leukemia diagnosis and ultimately improving patient outcomes through efficient and minimally intrusive diagnostic practices, especially in pediatric and geriatric cases.
Q-Pandora Unboxed: Characterizing Noise Resilience of Quantum Error Correction Codes
Authors: Chatterjee Avimita , Das Subrata , Ghosh Swaroop 
Published: November 2023

Abstract
Quantum error correction codes (QECCs) are crucial for quantum computing, protecting quantum states from noise and errors. This paper compares rotated and unrotated surface codes in different error types and noise models using simulations. Rotated codes outperform with higher thresholds and lower qubit overhead. The study finds QECC noise thresholds surpassing error rates in current quantum processors. Surface code implementation shows a hierarchy based on error or noise types, emphasizing resource demands. Our analysis ranks code-capacity as the most pessimistic and circuit-level as the most realistic model. The research underscores customizing surface codes to hardware needs and balancing reliability with qubit resources, highlighting the importance of addressing qubit efficiency and surface code overhead challenges.
Unveiling the impact of the COVID-19 pandemic on quality indicators of leprosy services in Brazil: an ecological study
Authors: de Souza Carlos Dornels Freire , Machado Melina , Ferreira Ana Carolina Furtado , Aragão José Alves Souza , Fernandes Tânia Rita Moreno Oliveira , Matos Thais Silva , Silva Tarcísio Fulgêncio Alves , Santos Márcio Bezerra , Santos Allan Dantas , Carmo Rodrigo Feliciano 
Published: November 2023

Abstract
Background
The COVID-19 pandemic has affected health services around the world. As a result, the control of endemic infectious diseases has been significantly hampered. This study aimed to quantify the impact of the COVID-19 pandemic on quality indicators of leprosy services in Brazil in 2020 and 2021.
Methods
This is an ecological study with 3 indicators: 1- Proportion of new leprosy cases with degree of physical disability assessed at diagnosis; 2- Proportion of contacts of new cases examined; 3- Proportion of leprosy cured among new cases. To determine the impact, the percentage of variation was used, taking into account the values of the indicators expected for 2020 and 2021, using the average of the last five years, and the values observed in the same years. The impact was quantified as a percentage.
Results
Brazil's performance in the three indicators analyzed was considered regular (between ≥ 75% and 89.9%), both in the pre-pandemic period and in the first two years. In the assessment of the degree of physical disability, the number of countries with a proportion greater than 90% decreased from 11 (expected value) to 7 (in 2020) and 9 (in 2021). In the evaluation of contacts, four states were expected to achieve the target (> 90%), but only three achieved the indicator in 2020 and one in 2021 (Tocantins). As for the cure rate, four states were expected to achieve values above 90%, but only three did so in 2020 and two in 2021.
Conclusion
The study showed a negative impact on the quality indicators of leprosy services in Brazil, which was more pronounced in 2021 (for contact examination and cure indicators) than in 2020, making it even more difficult to control the disease in the country.
Health information delivery to patients at risk of having a small for gestational age/growth restricted baby in Aotearoa New Zealand: what can we learn from lived experience?
Authors: James Joanna , Ngauamo Maria Juliet , Baard Caitlin , Jacobsen Mystie , Burgess Wendy , Clark Alys , Oyston Charlotte , McCool Judith 
Published: November 2023

Abstract
Introduction: The importance of access to reliable information during pregnancy is heightened in pregnancy complications. Impaired fetal growth (including small for gestational age (SGA) and growth restricted (FGR) fetuses) affects up to 10% of pregnancies and is associated with increased risk of morbidity and mortality. However, there is a paucity of accessible, evidence-based, information to support parents told their baby is not growing as expected.This study sought to explore patient experiences of information provision and seeking during pregnancies at risk of impaired fetal growth.
Methods: Focus groups and individual in-depth interviews (totalling 24 participants from across Aotearoa New Zealand) were conducted and recorded via Zoom. Discussions were led using pre-defined prompts to explore the experiences, preferences, and suggested improvements for information delivery. Interviews were transcribed verbatim, and data underwent inductive thematic analysis.
Results: Participants held expectations that their pregnancy would proceed normally; the majority experienced some level of distress at a diagnosis of complications. Information provided by the clinical team was highly valued, particularly when well curated and delivered with empathy. However, for many, this information needed to be supplemented. Additional, nuanced information was sought through online sources, and this included information on causes of impaired fetal growth, the meaning of medical terminology used, and lived experiences of pregnancy and birth. The timing of information provided by their clinical team impacted participant perceived capacity to comprehend information and their response to it. Participants preferred information to be offered at various times, in a range of forms, each adding to the layering of a more complete understanding of their situation. Preferences for information included being able to access a range of credible information in one place to promote greater coherence between the needs and lived experiences of patients and their healthcare providers.
Conclusions: Timely, nuanced and salient information is extremely important to pregnant people and their families when navigating high-risk clinical pathways during pregnancy. Our results provide guidance on improving informational resources in the context of impaired fetal growth.
Exploring the use of COVID-19 Antigen Rapid Diagnostic Tests among displaced populations in Iraq: findings from a pilot project in four IDP camps
Authors: Ammar Lara Abou , Wolfe Caitlin M. , Nagib Lamiaa , Slebei Mohammed , Shawkat Sezan , Amo Dilman , Abdullah Raveen , Abdulmalik Rawshan , Amin Hiwa Muhammed , Shafiq Huda , Hafthalah Shivan , Qahraman Aso , Mohammed Jirjees , Ghawji Hassan , Satyanarayana Srinath , Wilson Nevin , Sarin Sanjay , Kao Kekeletso , Ghusayni Nellie 
Published: November 2023

Abstract

Background
IOM piloted the use of Ag RDTs for COVID-19 in Iraq, in collaboration with FIND, the Global Alliance for Diagnostics, to facilitate access to testing and understand barriers and opportunities for testing in a displacement context. The purpose was to (i) evaluate the performance metrics of the Sure Status COVID-19 Antigen Card Test in this population; (ii) compare Ag RDT results across high- and low-probability cases, vaccination status, and symptom severity; and (iii) report participant perspectives on Ag RDT use for COVID-19 and other diseases.
Methods
Secondary analysis was conducted using de-identified cross-sectional data collected from November 2022-March 2023 in four IDP camps in the Kurdistan region of Iraq. Data was collected during the recording, reporting, and monitoring processes of the pilot project using Ag RDTs for COVID-19 among displaced populations. Descriptive statistics and bivariate analyses were conducted in Stata (version 17).
Results
The observed performance metrics of the Sure Status Ag RDT were as follows: sensitivity = 72.73% (95% CI: 69.56–75.80%); specificity = 99.74% (95% CI: 99.39–100%), PPV = 92.31% (95% CI: 92.31–94.15%), and NPV = 98.85% (95% CI: 98.11–99.58%). Ag RDT uptake was higher among women and symptomatic individuals, and preference for Ag RDTs was especially strong among illiterate respondents. The overall positivity of Ag RDTs and PCR results in this population remained lower than national averages. Concerningly, 23.39% of respondents declined an Ag RDT because they did not believe in COVID-19.
Conclusions
This pilot program was among the first to explore Ag RDT use in Iraqi Kurdistan. Over 99% of respondents reported satisfaction with their Ag RDT experience, and over 90% wanted to see Ag RDTs available for other diseases. These findings can inform implementation of RDTs and screening protocols for other infectious diseases, and patient perspectives on Ag RDTs for testing and screening of COVID-19 among displaced populations can inform health programming within Iraq and globally.
Investigating the Impact of Inter-Set Stretching on Vastus Lateralis Fascicle Dynamics and Knee Extensor Torque during Resistance Training
Authors: Halmenschlager Gustavo , Cabral Hélio , Oliveira Liliam , Matta Thiago 
Published: November 2023

Abstract
Purpose
Although stretching applied between sets can affect performance, it is unknown whether the muscle architecture is associated with the fatigue of subsequent sets. Here we compare the effect of inter-set stretching on maximal concentric and eccentric knee extension torque and vastus lateralis fascicle behavior in physically active men.
Methods
Fifteen men performed 4 × 10 maximal knee extensions. Passive static stretching in the inter-set resting periods was applied to one limb's knee extensors (inter-set stretching protocol), while the other limb recovered passively (passive rest protocol). The vastus lateralis fascicle architecture (pennation angle and fascicle length; proximal and distal regions) and knee extensor torque (peak torque and peak torque angle; concentric and eccentric contractions; set one–four) were compared between the inter-set stretching and passive rest protocols.
Results
Concentric and eccentric peak torques significantly decreased across sets for both protocols (p ≤ 0.001); however, there were no differences between them. There were no significant differences between the inter-set stretching and passive rest protocols for variations in peak torque angle. The fascicle length and pennation angle also did not change significantly between the protocols (p > 0.06 for all cases), regardless of the vastus lateralis region.
Conclusion
Incorporating 30-s intra-set quadriceps stretching during maximal leg extension exercise does not affect the ability to produce maximum force and did not change the fascicle behavior. Coaches and practitioners can benefit from this time-efficient approach for the targeted muscle group without compromising exercise performance across four sets.
Aperiodic spin chains at the boundary of hyperbolic tilings
Authors: Basteiro Pablo , Nath Das Rathindra , Di Giulio Giuseppe , Erdmenger Johanna 
Published: November 2023

In view of making progress towards establishing a holographic duality for theories defined on a discrete tiling of the hyperbolic plane, we consider a recently proposed boundary spin chain Hamiltonian with aperiodic couplings that are chosen such as to reflect the inflation rule, i.e. the construction principle, of the bulk tiling. As a remnant of conformal symmetry, the spin degrees of freedom are arranged in multiplets of the dihedral group under which the bulk lattice is invariant. For the boundary Hamiltonian, we use strong-disorder RG techniques and evaluate correlation functions, the entanglement entropy and mutual information for the case that the ground state is in an aperiodic singlet phase. We find that two-point functions decay as a power-law with exponent equal to one. Furthermore, we consider the case that the spin variables transform in the fundamental representation of SO(N), leading to a gapless system, and find that the effective central charge obtained from the entanglement entropy scales as lnN, reflecting the number of local degrees of freedom. We also determine the dependence of this central charge on the parameters specifying the bulk tiling. Moreover, we obtain an analytical expression for the mutual information, according to which there is no phase transition at any finite value of the distance between the two intervals involved.
A Network Pharmacology Approach and Validation Experiments to
Investigate the Mechanism of Wen-Dan Decoction in the Treatment of
SINFH
Authors: Qi Baochuang , Guo Minzheng , Shi Xiangwen , Li Mingjun , Wu Yipeng , Wang Yi , Lv Qian , Fan Xinyu , Li Chuan , Xu Yongqing 
Published: November 2023

Introduction::
Steroid-induced necrosis of the femoral head (SINFH) is a femoral
head necrotic disease caused by prolonged use of hormones. Wen-Dan decoction is used in
Chinese clinical practice for the treatment of steroid-induced necrosis of the femoral head
(SINFH). However, the mechanism and active compounds of Wen-Dan decoction used to treat
SINFH are not well understood.

Objectives::
We studied the mechanism of action of Wen-Dan decoction in treating steroidinduced
necrosis of the femoral head (SINFH) via network pharmacology and in vivo experiments.

Methods::
The active compounds of Wen-Dan decoction and SINFH-related target genes were
identified through public databases. Then, network pharmacological analysis was conducted to
explore the potential key active compounds, core targets and biological processes of Wen-Dan
decoction in SINFH. The potential mechanisms of Wen-Dan decoction in SINFH obtained by
network pharmacology were validated through in vivo experiments.

Results::
We identified 608 DEGs (differentially expressed genes) (230 upregulated, 378 downregulated)
in SINFH. GO analysis revealed that the SINFH-related genes were mainly involved
in neutrophil activation and the immune response. KEGG (Kyoto Encyclopedia of Genes and
Genomes) pathway analysis showed that the SINFH-related genes were mainly associated with
cytokine receptor interactions, lipids, atherosclerosis, and tuberculosis. We identified 147 active
ingredients of Wen-Dan decoction; the core ingredient was quercetin, and licorice was an active
ingredient. Moreover, 277 target genes in the treatment of SINFH with Wen-Dan decoction
were identified, and NCF1, PTGS2, and RUNX2 were selected as core target genes. QRT-PCR
of peripheral blood from SINFH patients showed higher levels of PGTS2 and NCF1 and
showed lower levels of RUNX2 compared to controls. QRT-PCR analysis of peripheral blood
and femoral bone tissue from a mouse model of SINFH showed higher levels of PGTS2 and
NCF1 and lower levels of RUNX2 in the experimental animals than the controls, which was
consistent with the bioinformatics results. HE, immunohistochemistry, and TUNEL staining
confirmed a significant reduction in hormone-induced femoral head necrosis in the quercetintreated
mice. HE, immunohistochemistry, and TUNEL staining confirmed significant improvement
in hormone-induced femoral head necrosis in the quercetin-treated mice.

Conclusion::
We provide new insights into the genes and related pathways involved in SINFH
and report that PTGS2, RUNX2, and NCF1 are potential drug targets. Quercetin improved
SINFH by promoting osteogenesis and inhibiting apoptosis.