bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Predictive Effect of Tumor Mutation Burden on prognosis in Breast cancer: A Systematic Review and Meta-Analysis
Authors: Ke Liyuan , Li Su , Cui Hongxia 
Published: September 2022

Abstract
Background:

Tumor mutation burden ( TMB ), as a promising predictive factor, has made some progress in predicting response to immune checkpoint inhibitors ( ICIs ) in several cancer types. The association between TMB and the clinical efficacy of ICIs in breast cancer has no conclusion. And it is controversial that whether TMB plays different forecast effects of ICIs and non-ICIs treatment. In this study, we conducted this systematic review and meta-analysis to predict effect of TMB on prognosis in breast cancer.

Methods:

We searched PubMed, Embase, Web of Science and Cochrane databases for articles published up to May 31, 2022. We extracted effective data from included articles and calculated pooled effects of hazard ratio ( HR ) for overall survival ( OS ) and progression-free survival ( PFS ) by STATA 16.0. Heterogeneity was evaluated by the I2 statistic and p-values. Meanwhile, the cause of the heterogeneity was further investigated through publication bias assessment, sensitivity analysis, and subgroup analysis.

Results:

The patients were up to 1,722 collected from sixteen trials included in this analysis. The pooled effects of HR for both OS ( HR: 1.14, 95% CI: 0.83,1.58, p > 0.01 ) and PFS ( HR: 0.96, 95% CI: 0.53,1.71, p > 0.01 ) showed no significant difference between high and low TMB group. Sensitivity analysis showed stability in the pooled effects. The funnel plot and Begg’s test suggested publication bias was absent. Subgroup analysis showed low heterogeneity and indicated that significantly better prognoses were found in ICIs group, TMB cutoff values ＞5 Mut/Mb group, tumor tissue group, and triple-negative breast cancer group.

Conclusion:

Our meta-analysis indicated that TMB as a predictor is not widely applicable in breast cancer. TMB may only forecast the efficacy of ICIs therapy, with better survival in high TMB group, but it is not obvious in non-ICIs therapy.
Tripodal Pd metallenes mediated by Nb2C MXenes for boosting alkynes semihydrogenation
Authors: Wei Zhong-zhe , Zhao Zijiang , Qiu Chenglong , Huang Songtao , Yao Zihao , Wang Mingxuan , Chen Yi , Lin Yue , Zhong Xing , Li Xiaonian , Wang Jianguo 
Published: September 2022

Abstract2D metallene nanomaterials have spurred considerable attention in heterogeneous catalysis by virtue of sufficient unsaturated metal atoms, high specific surface area and surface strain. Nevertheless, the strong metallic bonding in nanoparticles aggravates the difficulty in the controllable regulation of the geometry of metallenes. Here we propose an efficient galvanic replacement strategy to construct Pd metallenes loaded on Nb2C MXenes at room temperature, which is triggered by ultra-strong metal-support interaction based on MD simulation. A combination of electron microscopy, synchrotron X-ray absorption spectroscopy characterizations and theoretical calculations confirm that the Pd metallenes feature a chair structure of six-membered ring with the coordination number of Pd as low as 3. The tripodal Pd metallenes promote the diffusion of alkenes as the effective Pd atoms directly bonded with alkenes decreased compared with traditional Pd (111). As a consequence, the Pd/Nb2C delivers an outstanding turnover frequency of 10372 h− 1and a high selectivity of 96% at 25oC in the semihydrogenation of alkynes without compromising the stability. This strategy is general and scalable considering the plentiful members of the MXene family, which can set a foundation for the design of novel supported-metallene catalysts for demanding transformations.
Unravelling the epidemiological diversity of Zika virus by analyzing key protein variations
Authors: Leiva Santiago , Valdano Marina Bugnon , Gardiol Daniela 
Published: September 2022

Abstract
The consequences of Zika virus (ZIKV) infections were limited to sporadic mild diseases until almost a decade ago, when epidemics outbreaks took place and were followed by virus introduction and quick spread into the Americas. Simultaneously, novel severe neurological manifestations for ZIKV infections were identified, including congenital microcephaly. However, the complete understanding of why the epidemic strains behave differently from previously circulating variants is still missed and many questions still remain about the actual significance of ZIKV genetic variations in the epidemiology and biology of ZIKV. Here, we attained to analyze a high number of sequences to identify genes with different levels of variability and patterns of genomic variations that could be associated with ZIKV diversity. We compared numerous epidemic strains with the pre-epidemic ones from both the Asian and the African lineages, while we also investigated special variations among the epidemic ZIKV strains derived from microcephaly cases. We identified several viral genes with dissimilar mutation rates among the ZIKV strain groups. Moreover, we found novel protein variation profiles that might be associated with the epidemiological particularities of each category of ZIKV strains. Finally, we assessed the impact of the detected changes on the structure and stability of the corresponding viral proteins, finding some interesting non synonymous variations which could help to explain the heterogeneous features among the diverse ZIKA strains. Altogether, this work contributes to identify ZIKV genetic variations that might have a phenotypical impact, as a basis for future experimental analysis to elucidate the recent ZIKV emergency.
Batch alignment of single-cell transcriptomics data using deep metric learning
Authors: Yu Xiaokang , Xu Xinyi , Zhang Jingxiao , Li Xiangjie 
Published: September 2022

Abstract
scRNA-seq has uncovered previously unappreciated levels of heterogeneity. With the increasing scale of scRNA-seq studies, the major challenge is batch effect and accurately detecting the number of cell types, which is inevitable in human studies. The majority of scRNA-seq algorithms have been specifically designed to remove batch effect firstly and then conduct clustering, which may cause loss of some rare cell types. Here we develop scDML, a deep metric learning model to remove batch effect in scRNA-seq data, guided by the initial clusters and the nearest neighbor information intra and inter batches. Comprehensive evaluations spanning different species and tissues demonstrated that scDML can remove batch effect, improve clustering performance, accurately recover true cell types and consistently outperform popular methods such as Seurat 3, scVI, Scanorama, BBKNN, Harmony et al. Most importantly, scDML preserves subtle cell types in raw data and enables discovery of new cell subtypes that are hard to extract by analyzing each batch individually. We also showed that scDML is scalable to large datasets with lower peak memory usage, and we believe that scDML offers a valuable tool to study complex cellular heterogeneity.
Comparison of clinician diagnosis of COVID-19 with real time polymerase chain reaction in an adult-representative population in Sweden
Authors: Quraishi Eman , Jibuaku Chiamaka , Lisik Daniil , Wennergren Göran , Lötvall Jan , Nyberg Fredrik , Ekerljung Linda , Rådinger Madeleine , Kankaanranta Hannu , Nwaru Bright I. 
Published: September 2022

Abstract
Background
Due to the high transmissibility of SARS-CoV-2, accurate diagnosis is essential for effective infection control, but the gold standard, real-time reverse transcriptase-polymerase chain reaction (RT-PCR), is costly, slow, and test capacity has at times been insufficient. We compared the accuracy of clinician diagnosis of COVID-19 against RT-PCR in a general adult population.
Methods
COVID-19 diagnosis data by 30thSeptember 2021 for participants in an ongoing population-based cohort study of adults in Western Sweden were retrieved from registers, based on positive RT-PCR and clinician diagnosis using recommended ICD-10 codes. We calculated accuracy measures of clinician diagnosis using RT-PCR as reference for all subjects and stratified by age, gender, BMI, and comorbidity collected pre-COVID-19.
Results
Of 42,621 subjects, 3,936 (9.2%) and 5,705 (13.4%) had had COVID-19 identified by RT-PCR and clinician diagnosis, respectively. Sensitivity and specificity of clinician diagnosis against RT-PCR were 78% (95%CI 77-80%) and 93% (95%CI 93-93%), respectively. Positive predictive value (PPV) was 54% (95%CI 53-55%), while negative predictive value (NPV) was 98% (95%CI 98-98%) and Youden’s index 71% (95%CI 70-72%). These estimates were similar between men and women, across age groups, BMI categories, and between patients with and without asthma. However, while specificity, NPV, and Youden’s index were similar between patients with and without chronic obstructive pulmonary disease (COPD), sensitivity was slightly higher in patients with (84% [95%CI 74-90%]) than those without (78% [95%CI 77-79%]) COPD.
Conclusions
The accuracy of clinician diagnosis for COVID-19 is adequate, regardless of gender, age, BMI,and asthma, andthus can be used for screening purposes to supplement RT-PCR.
Knowledge of the students of the Faculty of Health Sciences of the University of Lomé on the risk factors of gynecological cancers
Authors: Djiwa Toukilnan , Fouelifa Loïc , Bombonne Mayi , Simgban Panakinao , Darre Tchin 
Published: September 2022

Abstract
Introduction:Gynecological cancers are often diagnosed at a late stage in Togo, due to difficulty of access to means of screening and a lack of technical platform. The objective of our study was to assess the knowledge of Faculty of Health Sciences of University of Lome students on the risk factors of these gynecological cancers.
Methodology:This was a cross-sectional prospective study with a descriptive and analytical aim, carried out among 3rd year bachelor's and 3rd year doctoral students regularly enrolled at the Faculty of Health Sciences for the 2020-2021 academic year.
Results :A total of 640 students correctly completed the form. The mean age was 24.66 ± 2.7 years. The sex ratio (M/F) was 2.5. The students had a good knowledge of the risk factors for cervical cancer ; but knowledge of risk factors of ovarian, endometrial, vaginal, and vulvar cancers was low. The main source of information was the courses at the Faculty of Health Sciences. Factors associated with knowledge of risk factors of cervical cancer were age (p-value = 0.0002), female gender (p-value = 0.0001 ; ORa = 2.46; 95% CI [1.31 -3.36]) and the fact of having followed a course on cervical cancer (p-value = 0.0073 ; ORa = 1.68; 95% CI [1.25-32.08]). Having done an internship in the gynecology department was the only factor associated with knowing the risk factors for ovarian cancer (p-value = 0.00001; ORa = 2.29; 95% CI [1 ,64-2.72]) and endometrial cancer (p-value = 0.0045 ; RCa = 2.63; 95% CI [1.56-3.07]).
Conclusion :The knowledge of risk factors of the gynecological cancer by the students of the FSS is relatively low, varying according to the type of cancer. It appears to promote self-learning for an improvement of this knowledge.
Stable Discharge Plateau Induced by Reversible Ammonium Ion Intercalation in Layered VOPO4·2H2O
Authors: Ye Fei , Pang Ruilvjing , Lu Chengjie , Liu Qiang , Chen Chaoyang , Dong Hongliang , Wu Yuping , Ma Renzhi , Hu Linfeng 
Published: September 2022

AbstractThe non-metal ammonium (NH4+) ion carrier has attracted tremendous interests for aqueous energy storage owing to the light molar mass and small hydrated ionic size. Nevertheless, the NH4+storage is severely challenged by that the as-reported cathode materials generally fail to satisfy the requirements on high capacity and stable working potential simultaneously up to date. Herein, we demonstrated that VOPO4∙2H2O with a layered framework and two-dimensional channels can reversibly host NH4+ion with a high specific capacity of 148.6 mAh g− 1at 0.1 A g− 1. More importantly, very stable discharge potential plateau at 0.4 V was achieved, which comes from the reversible intercalation/de-intercalation of NH4+in the interlayer spacing followed by an alternated stacking configuration. We revealed the crystal water molecules in the interlayer of VOPO4play a critical role in the NH4+ion storage performance. Theoretical DFT calculations suggest a unique crystal water substitution process by ammonium ion during the intercalation process. Our results realize the first inorganic compound with very stable working voltage for NH4+storage, and also contributes the fundamental understanding of the intercalation/de-intercalation of NH4+ions in layered hydrated phosphates for clean energy storage.
Integrated analysis of next generation sequencing minimal residual disease (MRD) and PET scan in transplant eligible myeloma patients
Authors: Fonseca Rodrigo , Arribas Mariano , Wiedmeier-Nutor Julia E. , Kusne Yael N. , Gonzalez-Velez Miguel , Kosiorek Heidi , Butterfield Richard J. , Kirsch Ilan , Mikhael Joseph , Stewart A. Keith , Reeder Craig , Larsen Jeremy , Bergsagel P. , Fonseca Rafael 
Published: September 2022

Abstract
Minimal residual disease (MRD) assays allow response assessment in patients with multiple myeloma (MM), and negativity is associated with improved survival outcomes. The role of highly sensitive next generation sequencing (NGS) MRD in combination with functional imaging remains to be validated. We performed a retrospective analysis on MM patients who underwent frontline autologous stem cell transplant (ASCT). Patients were evaluated at day 100 post-ASCT with NGS MRD and positron emission tomography (PET-CT). Patients with ≥ 2 MRD measurements were included in a secondary analysis for sequential measurements. 186 patients were included in the analysis. At day 100, 45 (24.2%) patients achieved MRD negativity at a sensitivity threshold of 10− 6. MRD negativity was the most predictive factor for longer time to next treatment (TTNT). Negativity rates did not differ according to MM subtype, R-ISS Stage nor cytogenetic risk. PET-CT and MRD positivity had poor agreement. Patients with sustained MRD negativity had longer TTNT, regardless of baseline risk characteristics. Our results show that the “real world” ability to measure deeper and sustainable responses distinguishes a subpopulation of patients with better outcomes. Achieving MRD negativity was the strongest prognostic marker and could help guide therapy-related decisions and serve as a response marker for clinical trials.
Regulation of protein and oxidative energy metabolism are down-regulated in the skeletal muscles of Asiatic black bears during hibernation
Authors: Miyazaki Mitsunori , Shimozuru Michito , Kitaoka Yu , Takahashi Kenya , Tsubota Toshio 
Published: September 2022

Abstract
Hibernating animals exhibit an unexplained physiological characteristic of skeletal muscles being atrophy resistance, in which case muscle mass and strength remain almost unchanged both before and after hibernation. In this study, we examined the alterations in the regulatory systems of protein and energy metabolism in the skeletal muscles of Asiatic black bears during hibernation. Skeletal muscle samples (vastus lateralis muscle) were collected from identical individuals (n = 8) during the active (July) and hibernating (February) periods, while histochemical and biochemical analyses were performed. We observed no significant alterations in body weight, muscle fiber size, and fiber type composition during the active and hibernating periods, indicating that the skeletal muscles of bears are very well preserved during hibernation. In hibernating bear skeletal muscles, both regulatory pathways of muscle protein synthesis (Akt/mechanistic target of rapamycin and mitogen-activated protein kinase systems) and proteolysis (ubiquitin-proteasome and autophagy systems) were down-regulated. Gene expression levels of factors regulating oxidative metabolism were also decreased in hibernating bear skeletal muscles. This is likely an adaptive strategy to minimize the energy wasting of amino acids and lipids during hibernation, which is accompanied by a prolonged period of disuse and starvation.
Diffusion Coefficients of Electrorheological Complex (Dusty) Plasmas
Authors: Shakoori Muhammad Asif , Khan Misbah 
Published: September 2022

Abstract
Equilibrium molecular dynamics (EMD) simulations have been executed to investigate the parallel (D║) and perpendicular (D┴) diffusion coefficients for three-dimensional (3D) strongly coupled (SC) electrorheological complex (dusty) plasmas (ERCPs). The effects of uniaxial (z-axis) ac electric field (MT) on dust grains have been investigated along with various combinations of plasma parameters (Γ, κ). The new outcomes obtained by mean squared displacement of Einstein relation show diffusion coefficients for low-intermediate to high plasma couplings (Γ) for varying MT. The D║ and D┴ at MT = 0.01 are agree well with earlier available data obtained from the Green-Kubo and Einstein relation for 3D SC-Yukawa systems. The simulation data show that D║ increase with an increase of moderate MT strength and D┴ decreased for the intermediate to large MT strength Both (D║, D┴) remained nearly constant for low MT values. The investigations show that the current EMD scheme is more efficient for nonideal gas-like, liquids-like and solid-like states of SC-ERCPs. It has been demonstrated that present simulation outcomes extended the MT range up to 0.01 ≤ MT ≤ 10 to understand the diffusive and rheological behavior of dusty plasmas systems.
Experimental investigation of mechanical properties and energy absorption capabilities of hybrid lattice structures manufactured using Fused Filament Fabrication
Authors: Syrlybayev Daniyar , Perveen Asma , Talamona Didier 
Published: September 2022

Abstract
Hybrid lattice structures are composed of several dissimilar unit cells arranged in specific patterns. Unlike their one-phase counterparts, hybrid lattices remain relatively unexplored. In this work, novel hybrid lattice structures composed of Pillar Octahedral (PO) and Rhombic Dodecahedron (RD) lattices having variable strut diameters are arranged in different orders to form hybrid vertical piles (HVP), 2D and 3D chessboard order (HCh2D and HCh3D) are proposed and their mechanical properties, energy absorption characteristics, and deformation modes are investigated under quasistatic compression. The empirical results indicated that the mechanical properties of hybrid lattice structures are the average of those of their parent lattices. HVP lattice structure has a high yield stress of 1.2, 2.22, and 3.54 MPa when strut diameter is 1.5, 1.75, and 2 mm respectively, and stable post-buckling region. It was also observed that hybrid lattice structures are more efficient in absorbing the energy of the deformation. When strut diameter is 1.5 mm, PO lattice structure has an efficiency of 50%, while HVP, HCh2D, and HCh3D lattices have an efficiency of about 70–80%. Finally, Gibson-Ashby models were proposed to predict the mechanical properties of lattice structures as the function of relative density.
Selective Formose Reaction under Microwave Irradiation
Authors: Hashidzume Akihito , Imai Toru , Deguchi Nanako , Tanibayashi Takashi , Ikeda Takumi , Michitaka Tomohiro , Kuwahara Satoki , Nakahata Masaki , Kamon Yuri , Todokoro Yasuto 
Published: September 2022

Abstract
To realize sustainable societies, production of organic compounds, which is not based on fossil resources, should be developed. Thus, C1 chemistry, utilizing one-carbon compounds as starting materials, has been of increasing importance. In particular, formose reaction is promising because the reaction produces sugars (monosaccharides) from formaldehyde under basic conditions. On the other hand, since microwave (MW) induces the rotational motion of molecules, MW irradiation often improves the selectivity and efficiency of reactions. In this study, formose reaction under MW irradiation was thus investigated under various conditions. Formose reaction proceeded very fast and selectively using 1.0 mol kg− 1 formaldehyde and 55 mmol kg− 1 calcium hydroxide (Ca(OH)2) as a catalyst at a high set temperature (150°C) for a short time (1 min). The major products, i.e., hexose and heptose, were isolated by thin layer chromatography and characterized by NMR and mass spectroscopy. These characterization data elucidated that the hexose and heptose were 2-hydroxymethyl-1,2,4,5-tetrahydroxy-3-pentanone (C6*) and 2,4-bis(hydroxymethyl)-1,2,4,5-tetrahydroxy-3-pentanone (C7*), respectively. On the basis of these observations as well as density functional theory calculations, a plausible reaction pathway was also discussed; Once 1,3-dihydroxyacetone is formed, consecutive aldol reactions favorably occur to form C6* and C7*. This study should provide significant insights not only for production of organic compounds not based on fossil resources but also for the sugar formation under prebiotic conditions.
Combining Reconstructive and Ablative Surgical Treatment of Chronic Breast Cancer-Related Lymphedema (BCRL): Safe and Effective
Authors: Handschin Tristan Michael , Ghazaleh Alina Abu , Buckowiecki Julia , Chammartin Frédéerique Sophie , Andree Christoph , Schaefer Dirk Johannes , Haug Martin , Kappos Elisabeth Artemis , Seidenstuecker Kathrin 
Published: September 2022

Abstract
Purpose: We investigated whether a one-stage combination of vascularized lymph node transfer (VLNT) with water jet-assisted liposuction (WAL) can be safely performed and results in improved patient outcomes when treating chronic breast cancer-related lymphedema (BCRL).
Methods: In this retrospective cohort study, we included all patients from our encrypted lymphedema database treated for chronic BCRL with VLNT or VLNT+WAL who had a minimum follow-up of two years. We analyzed patient-specific variables including arm circumferences as well as patient reported outcomes (PROMs) before and after surgery as well as surgery-related complications.
Results: Only the mean preoperative differences of the circumferences between the lymphedematous and the unaffected arm in individual patients showed a statistically significant difference between treatment groups (p<0.05). Indeed, patients treated with VLNT+WAL had consistently larger differences in individual sets of arms and therefore more pronounced chronic BCRL. Complications were seldom and similar in both groups.
Conclusions: Our findings suggest that a one-stage combination of VLNT with WAL does not result in more complications and might be especially favorable for patients suffering from more severe chronic BCRL.
The first case of monkeypox in Hong Kong presenting as infectious mononucleosis-like syndrome
Authors: Chiu Kelvin Hei-Yeung , Wong Shuk-Ching , Tam Anthony Raymond , Srid Siddharth , Yip Cyril Chik-Yan , Chan Kwok-Hung , Man Kenyon Ka-Yun , Chan Wan-Mui , Ip Jonathan Daniel , Chu Allen Wing-Ho , Lo Janice Yee-Chi , Hung Ivan Fan-Ngai , Yuen Kwok-Yung , To Kelvin Kai-Wang , Cheng Vincent Chi-Chung 
Published: September 2022

Abstract
We report the first imported case of human monkeypox in Hong Kong, manifesting as infectious mononucleosis-like syndrome. Viral load in deep throat saliva was comparable to vesicle swabs collected from face, arm, and back of this patient, suggesting deep throat saliva as an alternative specimen for early diagnosis of monkeypox.