bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country
Authors: Vogel Monica , Utpatel Christian , Corbett Caroline , Kohl Thomas A. , Iskakova Altyn , Ahmedov Sevim , Antonenka Uladzimir , Dreyer Viola , Ibrahimova Ainura , Kamarli Chynara , Kosimova Dilorom , Mohr Vanessa , Sahalchyk Evgeni , Sydykova Meerim , Umetalieva Nagira , Kadyrov Abdylat , Kalmambetova Gulmira , Niemann Stefan , Hoffmann Harald 
Published: July 2021

AbstractWhole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implementation in such a setting. WGS was implemented in the Kyrgyz Republic. We estimated needs of up to 55 TB-WGS per week and chose the MiSeq platform (Illumina, USA) because of its capacity of up to 60 TB-WGS per week. The project’s timeline was completed in 93-weeks. Costs of large equipment and accompanying costs were 222,065 USD and 8462 USD, respectively. The first 174 WGS costed 277 USD per sequence, but this was skewed by training inefficiencies. Based on real prices and presuming optimal utilization of WGS capacities, WGS costs could drop to 167 and 141 USD per WGS using MiSeq Reagent Kits v2 (500-cycles) and v3 (600-cycles), respectively. Five trainings were required to prepare the staff for autonomous WGS which cost 48,250 USD. External assessment confirmed excellent performance of WGS by the Kyrgyz laboratory in an interlaboratory comparison of 30 M. tuberculosis genomes showing complete agreeance of results.
Semantic segmentation of PolSAR image data using advanced deep learning model
Authors: Garg Rajat , Kumar Anil , Bansal Nikunj , Prateek Manish , Kumar Shashi 
Published: July 2021

AbstractUrban area mapping is an important application of remote sensing which aims at both estimation and change in land cover under the urban area. A major challenge being faced while analyzing Synthetic Aperture Radar (SAR) based remote sensing data is that there is a lot of similarity between highly vegetated urban areas and oriented urban targets with that of actual vegetation. This similarity between some urban areas and vegetation leads to misclassification of the urban area into forest cover. The present work is a precursor study for the dual-frequency L and S-band NASA-ISRO Synthetic Aperture Radar (NISAR) mission and aims at minimizing the misclassification of such highly vegetated and oriented urban targets into vegetation class with the help of deep learning. In this study, three machine learning algorithms Random Forest (RF), K-Nearest Neighbour (KNN), and Support Vector Machine (SVM) have been implemented along with a deep learning model DeepLabv3+ for semantic segmentation of Polarimetric SAR (PolSAR) data. It is a general perception that a large dataset is required for the successful implementation of any deep learning model but in the field of SAR based remote sensing, a major issue is the unavailability of a large benchmark labeled dataset for the implementation of deep learning algorithms from scratch. In current work, it has been shown that a pre-trained deep learning model DeepLabv3+ outperforms the machine learning algorithms for land use and land cover (LULC) classification task even with a small dataset using transfer learning. The highest pixel accuracy of 87.78% and overall pixel accuracy of 85.65% have been achieved with DeepLabv3+ and Random Forest performs best among the machine learning algorithms with overall pixel accuracy of 77.91% while SVM and KNN trail with an overall accuracy of 77.01% and 76.47% respectively. The highest precision of 0.9228 is recorded for the urban class for semantic segmentation task with DeepLabv3+ while machine learning algorithms SVM and RF gave comparable results with a precision of 0.8977 and 0.8958 respectively.
Gene expression profile of the murine ischemic retina and its response to Aflibercept (VEGF-Trap)
Authors: Rojo Arias Jesús Eduardo , Jászai József 
Published: July 2021

AbstractIschemic retinal dystrophies are leading causes of acquired vision loss. Although the dysregulated expression of the hypoxia-responsive VEGF-A is a major driver of ischemic retinopathies, implication of additional VEGF-family members in their pathogenesis has led to the development of multivalent anti-angiogenic tools. Designed as a decoy receptor for all ligands of VEGFR1 and VEGFR2, Aflibercept is a potent anti-angiogenic agent. Notwithstanding, the molecular mechanisms mediating Aflibercept’s efficacy remain only partially understood. Here, we used the oxygen-induced retinopathy (OIR) mouse as a model system of pathological retinal vascularization to investigate the transcriptional response of the murine retina to hypoxia and of the OIR retina to Aflibercept. While OIR severely impaired transcriptional changes normally ensuing during retinal development, analysis of gene expression patterns hinted at alterations in leukocyte recruitment during the recovery phase of the OIR protocol. Moreover, the levels of Angiopoietin-2, a major player in the progression of diabetic retinopathy, were elevated in OIR tissues and consistently downregulated by Aflibercept. Notably, GO term, KEGG pathway enrichment, and expression dynamics analyses revealed that, beyond regulating angiogenic processes, Aflibercept also modulated inflammation and supported synaptic transmission. Altogether, our findings delineate novel mechanisms potentially underlying Aflibercept’s efficacy against ischemic retinopathies.
Spectroscopic studies on photodegradation of atorvastatin calcium
Authors: Oprica Madalina , Iota Miruna , Daescu Monica , Fejer Szilard N. , Negrila Catalin , Baibarac Mihaela 
Published: July 2021

AbstractIn this work, the photodegradation process of atorvastatin calcium (ATC) is reported as depending on: (1) the presence and the absence of excipients in the solid state; (2) the chemical interaction of ATC with phosphate buffer (PB) having pH equal to 7 and 8; and (3) hydrolysis reaction of ATC in the presence of aqueous solution of NaOH. The novelty of this work consists in the monitoring of the ATC photodegradation by photoluminescence (PL). The exposure of ATC in solid state to UV light induces the photo-oxygenation reactions in the presence of water vapors and oxygen from air. According to the X-ray photoelectron spectroscopic studies, we demonstrate that the photo-oxygenation reaction leads to photodegradation compounds having a high share of C=O bonds compared to ATC before exposure to UV light. Both in the presence of PB and NaOH, the photodegradation process of ATC is highlighted by a significant decrease in the intensity of the PL and photoluminescence excitation (PLE) spectra. According to PLE spectra, the exposure of ATC in the presence of NaOH to UV light leads to the appearance of a new band in the spectral range 340–370 nm, this belonging to the photodegradation products. Arguments concerning the chemical compounds, that resulted in this last case, are shown by Raman scattering and FTIR spectroscopy.
Human chromosome 3p21.3 carries TERT transcriptional regulators in pancreatic cancer
Authors: Yagyu Takuki , Ohira Takahito , Shimizu Ryutaro , Morimoto Masaki , Murakami Yuki , Hanaki Takehiko , Kihara Kyoichi , Matsunaga Tomoyuki , Yamamoto Manabu , Tokuyasu Naruo , Sakamoto Teruhisa , Fujiwara Yoshiyuki , Kugoh Hiroyuki 
Published: July 2021

AbstractFrequent loss of heterozygosity (LOH) on the short arm of human chromosome 3 (3p) region has been found in pancreatic cancer (PC), which suggests the likely presence of tumor suppressor genes in this region. However, the functional significance of LOH in this region in the development of PC has not been clearly defined. The human telomerase reverse transcriptase gene (hTERT) contributes to unlimited proliferative and tumorigenicity of malignant tumors. We previously demonstrated that hTERT expression was suppressed by the introduction of human chromosome 3 in several cancer cell lines. To examine the functional role of putative TERT suppressor genes on chromosome 3 in PC, we introduced an intact human chromosome 3 into the human PK9 and murine LTPA PC cell lines using microcell-mediated chromosome transfer. PK9 microcell hybrids with an introduced human chromosome 3 showed significant morphological changes and rapid growth arrest. Intriguingly, microcell hybrid clones of LTPA cells with an introduced human chromosome 3 (LTPA#3) showed suppression of mTert transcription, cell proliferation, and invasion compared with LTPA#4 cells containing human chromosome 4 and parental LTPA cells. Additionally, the promoter activity of mTert was downregulated in LTPA#3. Furthermore, we confirmed that TERT regulatory gene(s) are present in the 3p21.3 region by transfer of truncated chromosomes at arbitrary regions. These results provide important information on the functional significance of the LOH at 3p for development and progression of PC.
Anatomical characterization and technological properties of Pterogyne nitens wood, a very interesting species of the Brazilian Caatinga biome
Authors: Pereira Allana Katiussya Silva , Longue Júnior Dalton , Carvalho Ana Márcia Macedo Ladeira , Mafra Neto Caio da Silva 
Published: July 2021

AbstractPterogyne nitens is commonly known in northeastern Brazil as a lesser-known fast-growing species in the Caatinga biome, which is a difficult place for tree development due to the low natural fertility soils and low availability of water. Due to the importance of expanding information about the anatomical wood properties of Caatinga native species, the aim of this work was to characterize the anatomical elements, to macroscopically describe the wood and make inferences about its possible end-uses. Maceration was performed which enabled measuring fiber dimensions, pore frequency and the following technological indexes: cell wall fraction, slenderness ratio, Runkel index and flexibility coefficient. Histological sections enabled describing the arrangements of the cellular elements in different observation sections and to determine the pore diameter. P. nitens wood has anatomical arrangements characterized by confluent axial parenchyma, being diffuse-porous with the presence of tylosis and heterogeneous/stratified rays (biseriate). The fibers were classified as very short (length 0.81 mm), not flexible and Runkel index 0.82. The pores were few in number with a frequency of 32.9 pores/mm2, distributed in a diffuse format and many were obstructed by tylosis. Based on the anatomical results and considering other technological studies, P. nitens wood is most suitable for charcoal production.
A novel anatomic titanium mesh cage for reducing the subsidence rate after anterior cervical corpectomy: a finite element study
Authors: Wang Yuhang , Zhan Yi , Yang Huiming , Guo Hua , Zhang Haiping , Zhao Qinpeng , Hao Dingjun , Wang Biao 
Published: July 2021

AbstractFusion with a titanium mesh cage (TMC) has become popular as a conventional method after cervical anterior corpectomy, but postoperative TMC subsidence has often been reported in the literature. We designed a novel anatomic cervical TMC to reduce the postoperative subsidence rate. According to the test process specified in the American Society of Testing Materials (ASTM) F2267 standard, three-dimensional finite element analysis was used to compare the anti-subsidence characteristics of a traditional TMC (TTMC) and novel TMC (NTMC). Through analysis, the relative propensity values of a device to subside (Kp) of the TTMC and NTMC were 665.5 N/mm and 1007.2 N/mm, respectively. A higher Kp measurement is generally expected to indicate that the device is more resistant to subsidence into a vertebral body. The results showed that the novel anatomic titanium mesh cage (NTMC) significantly improved the anti-subsidence performance after anterior cervical corpectomy and fusion (ACCF), which was approximately 51.3% higher than that of the traditional titanium mesh cage.
Influence of coal gangue mulching with various thicknesses and particle sizes on soil water characteristics
Authors: Han Xiu-Na , Dong Ying , Geng Yu-qing , Li Na , Zhang Chao-Ying 
Published: July 2021

AbstractWater availability seriously affects vegetation restoration in arid mining areas, and mulching is an effective way to improve soil water conditions. Coal gangue occupies large swathes of land resources, resulting in ecological fragility and various environmental problems. Despite coal gangue having mineral elements similar to those in soil, its potential function as a mulch for soil water conservation has been unclear. Herein, mulching on the surfaces of soil columns with 30 cm height and 15 cm inner diameter was conducted using coal gangue with four particle size ranges (0–0.5, 0.5–1, 1–2, and 2–4 cm) and four thicknesses (4, 8, 12, and 16 cm) under laboratory conditions to investigate water infiltration and evaporation under different conditions. The cumulative infiltration of the treatments with mulching thicknesses of 4 cm (T1), 8 cm (T2), 12 cm (T3), and 16 cm (T4) was 16.1%, 22.9%, 28.6%, and 41.6% greater than that of the control, respectively. The cumulative evaporation of the treatments with particle size ranges of 0–0.5 cm (P1), 0.5–1 cm (P2), 1–2 cm (P3), and 2–4 cm (P4) was 6.5%, 28.6%, 22.9%, and 18.6% lower than the control, respectively. Overall, to enhance the soil water storage capacity in mining areas, the results suggest that coal gangue mulching with a thickness of 8–16 cm and particle size range of 0.5–2 cm is suitable.
Specificity of UV-C LED disinfection efficacy for three N95 respirators
Authors: Ontiveros C. Carolina , Shoults David C. , MacIsaac Sean , Rauch Kyle D. , Sweeney Crystal L. , Stoddart Amina K. , Gagnon Graham A. 
Published: July 2021

AbstractThe recent surge in the use of UV technology for personal protective equipment (PPE) has created a unique learning opportunity for the UV industry to deepen surface disinfection knowledge, especially on surfaces with complex geometries, such as the N95 filter facepiece respirators (FFR). The work outlined in this study addresses the interconnectedness of independent variables (e.g., UV Fluence, respirator material) that require consideration when assessing UV light efficacy for disinfecting respirators. Through electron microscopy and Fourier-transform infrared (FTIR) spectroscopy, we characterized respirator filter layers and revealed that polymer type affects disinfection efficacy. Specifically, FFR layers made from polypropylene (PP) (hydrophobic in nature) resulted in higher disinfection efficiency than layers composed of polyethylene terephthalate (PET-P) (hygroscopic in nature). An analysis of elastic band materials on the respirators indicated that silicone rubber-based bands achieved higher disinfection efficiency than PET-P bands and have a woven, fabric-like texture. While there is a strong desire to repurpose respirators, through this work we demonstrated that the design of an appropriate UV system is essential and that only respirators meeting specific design criteria may be reasonable for repurposing via UV disinfection.
New insights on the Ife-Ilesha schist belt using integrated satellite, aeromagnetic and radiometric data
Authors: Salawu Naheem Banji , Fatoba Julius Ogunmola , Adebiyi Leke Sunday , Orosun Muyiwa Michael , Dada Silas Sunday 
Published: July 2021

AbstractThe present study combined analysis of satellite, aeromagnetic and radiometric data for evaluation of structural features within the Ife-Ilesha schist belt. Shuttle Radar Topographic Mission digital elevation data have been enhanced using hill-shading technique for the delineation of morphological features. The superposition of total gradient amplitude lineaments on the 3-D Euler deconvolution map revealed the trends and depth of structural features within the study region. The major trends are NE–SW, NNE–SSW, E–W and minor trends in the N–S direction, including the Ifewara shear zone that trends in the NNE–SSW. The estimated depths to the top of the sources within the shear zone varies from 90 to 200 m. Complementary analysis of the airborne radiometric data revealed that the Ifewara shear zone and adjacent regions are characterized by radiometric anomalies, indicating regional mineralization alteration zone. Generally, there is a good correlation between the satellite, radiometric, aeromagnetic maps which provides new insights and re-evaluation of structural features.
A theoretical approach for estimating the effect of water-jet quenching on low-carbon steel beams
Authors: Koo Bon Seung 
Published: July 2021

AbstractQuenching is an efficient manufacturing technique to improve the strength of steel after hot rolling. The benefit of this application is to enhance the mechanical properties of steel products while reducing strengthening alloying elements, e.g., C, Mn, V, Nb, and N. Quenching and self-tempering (QST) especially for H-beams is a unique material strengthening process that adopts intensive surface cooling and self-tempering. A methodological difficulty in estimating the quenching effect has been a long-standing concern in the QST application. The purpose of this study was therefore to specify quenching parameters, quantify quenching, analyze the effect, and verify the credibility of the results. Transient quenching was simulated in ANSYS to analyze heat transfer and phase transformations due to quenching. An individual concept, e.g., heat exchange, cumulative quenching infiltration, or recalescence phenomena, was merged and interpreted newly for the quenching simulation. Computational results based on theoretical approaches were well consistent with empirical studies.
A TLR4 agonist improves immune checkpoint blockade treatment by increasing the ratio of effector to regulatory cells within the tumor microenvironment
Authors: Farias A. , Soto A. , Puttur F. , Goldin C. J. , Sosa S. , Gil C. , Goldbaum F. A. , Berguer P. M. 
Published: July 2021

AbstractBrucella lumazine synthase (BLS) is a homodecameric protein that activates dendritic cells via toll like receptor 4, inducing the secretion of pro-inflammatory cytokines and chemokines. We have previously shown that BLS has a therapeutic effect in B16 melanoma-bearing mice only when administered at early stages of tumor growth. In this work, we study the mechanisms underlying the therapeutic effect of BLS, by analyzing the tumor microenvironment. Administration of BLS at early stages of tumor growth induces high levels of serum IFN-γ, as well as an increment of hematopoietic immune cells within the tumor. Moreover, BLS-treatment increases the ratio of effector to regulatory cells. However, all treated mice eventually succumb to the tumors. Therefore, we combined BLS administration with anti-PD-1 treatment. Combined treatment increases the outcome of both monotherapies. In conclusion, we show that the absence of the therapeutic effect at late stages of tumor growth correlates with low levels of serum IFN-γ and lower infiltration of immune cells in the tumor, both of which are essential to delay tumor growth. Furthermore, the combined treatment of BLS and PD-1 blockade shows that BLS could be exploited as an essential immunomodulator in combination therapy with an immune checkpoint blockade to treat skin cancer.
Vacancy tuned thermoelectric properties and high spin filtering performance in graphene/silicene heterostructures
Authors: Gholami Zainab , Khoeini Farhad 
Published: July 2021

AbstractThe main contribution of this paper is to study the spin caloritronic effects in defected graphene/silicene nanoribbon (GSNR) junctions. Each step-like GSNR is subjected to the ferromagnetic exchange and local external electric fields, and their responses are determined using the nonequilibrium Green’s function (NEGF) approach. To further study the thermoelectric (TE) properties of the GSNRs, three defect arrangements of divacancies (DVs) are also considered for a larger system, and their responses are re-evaluated. The results demonstrate that the defected GSNRs with the DVs can provide an almost perfect thermal spin filtering effect (SFE), and spin switching. A negative differential thermoelectric resistance (NDTR) effect and high spin polarization efficiency (SPE) larger than 99.99% are obtained. The system with the DV defects can show a large spin-dependent Seebeck coefficient, equal to Ss ⁓ 1.2 mV/K, which is relatively large and acceptable. Appropriate thermal and electronic properties of the GSNRs can also be obtained by tuning up the DV orientation in the device region. Accordingly, the step-like GSNRs can be employed to produce high efficiency spin caloritronic devices with various features in practical applications.
The effect of long-term poor sleep quality on risk of back-related disability and the modifying role of physical activity
Authors: Skarpsno Eivind Schjelderup , Nilsen Tom Ivar Lund , Mork Paul Jarle 
Published: July 2021

AbstractSleep problems and regular leisure time physical activity (LTPA) are interrelated and have contrasting effects on risk of back pain. However, no studies have investigated the influence of long-term poor sleep quality on risk of back-related disability, or if LTPA modifies this association. The study comprised data on 8601 people who participated in three consecutive surveys over ~ 22 years, and who reported no chronic back pain at the two first surveys. Adjusted risk ratios (RRs) for back-related disability were calculated at the last survey, associated with the joint effect of changes in sleep quality between the two first surveys and meeting physical activity guidelines at the second survey. Compared to people with long-term good sleep, people with long-term poor sleep had nearly twice the risk of back-related disability (RR 1.92, 95% CI 1.48–2.49). There was no statistical interaction between sleep and LTPA but people who reported long-term poor sleep and meeting the physical activity guidelines had 35% lower risk of back-related disability compared to people with same level of sleep problems, but who not met the guidelines. These findings suggest that long-term poor sleep quality contributes to a substantially increased risk of chronic and disabling back pain irrespective of LTPA.
IL-8 correlates with reduced baseline femoral neck bone mineral density in adults with cystic fibrosis: a single center retrospective study
Authors: Lam Grace Y. , Desai Sameer , Fu Joey , Hu Xun Yang , Jang Jiah , Goshtasebi Azita , Kalyan Shirin , Quon Bradley S. 
Published: July 2021

AbstractCystic fibrosis (CF) is a multi-system disease that is characterized by lung disease due to recurrent airway infection and inflammation. Endocrine complications, such as CF bone disease (CFBD), are increasingly identified as patients are living longer. The cause of CFBD is multifactorial with chronic systemic inflammation theorized to be a contributing factor. Thus, we attempted to identify inflammatory biomarkers that are associated with CFBD. We conducted a retrospective observational study of 56 adult patients with CF with an average percentage predictive forced expiratory volume in one second (ppFEV1) of 73.7% (standard deviation: 30.0) who underwent baseline serum analysis for osteoprotegerin (OPG) and pro-inflammatory biomarkers (IL-1β, IL-6, IL-8 and TNF-α), and had repeated dual-energy x-ray absorptiometry (DXA) scans separated by at least 2 years to examine correlations between serum biomarkers and bone mineral density (BMD) measurements. Univariate linear regression model analysis demonstrated that serum IL-1β and IL-8, but not other pro-inflammatory markers, were negatively correlated with baseline BMD results. However, after accounting for confounding variables, only the relationship between IL-8 and left femoral neck BMD remained statistically significant. Additionally, IL-8 level was associated with BMD decline over time. These results suggest that IL-8 might play a unique role in the pathophysiology of CFBD relative to other pro-inflammatory cytokines but further study is warranted before firm conclusions can be made.