bluuebunny/crossref_metadata_2025_split huggingface dataset:
Process optimization and kinetic study of biodegradation of dimethyl phthalate by KS2, a novel strain of Micrococcus sp.
Authors: Patil Sangram Shamrao , Jena Hara Mohan 
Published: March 2023

AbstractThe present study elucidates identification and characterization of dimethyl phthalate (DMP) degrading novel bacterial strain, Micrococcus sp. KS2, isolated from soil contaminated with municipal wastewater. Statistical designs were exercised to achieve optimum values of process parameters for DMP degradation by Micrococcus sp. KS2. The screening of the ten important parameters was performed by applying Plackett–Burman design, and it delivered three significant factors (pH, temperature, and DMP concentration). Further, response surface methodology involving central composite design (CCD) was implemented to examine mutual interactions among variables and achieve their optimal response. The predicted response indicated that maximum DMP degradation (99.67%) could be attained at pH 7.05, temperature 31.5 °C and DMP 289.19 mg/l. The strain KS2 was capable of degrading up to 1250 mg/l of DMP in batch mode and it was observed that oxygen was limiting factor in the DMP degradation. Kinetic modeling of DMP biodegradation indicated that Haldane model fitted well with the experimental data. During DMP degradation, monomethyl phthalate (MMP) and phthalic acid (PA) were identified as degradation metabolites. This study provides insight into DMP biodegradation process and proposes that Micrococcus sp. KS2 is a potential bacterial candidate to treat effluent containing DMP.
An automatic entropy method to efficiently mask histology whole-slide images
Authors: Song Yipei , Cisternino Francesco , Mekke Joost M. , de Borst Gert J. , de Kleijn Dominique P. V. , Pasterkamp Gerard , Vink Aryan , Glastonbury Craig A. , van der Laan Sander W. , Miller Clint L. 
Published: March 2023

AbstractTissue segmentation of histology whole-slide images (WSI) remains a critical task in automated digital pathology workflows for both accurate disease diagnosis and deep phenotyping for research purposes. This is especially challenging when the tissue structure of biospecimens is relatively porous and heterogeneous, such as for atherosclerotic plaques. In this study, we developed a unique approach called ‘EntropyMasker’ based on image entropy to tackle the fore- and background segmentation (masking) task in histology WSI. We evaluated our method on 97 high-resolution WSI of human carotid atherosclerotic plaques in the Athero-Express Biobank Study, constituting hematoxylin and eosin and 8 other staining types. Using multiple benchmarking metrics, we compared our method with four widely used segmentation methods: Otsu’s method, Adaptive mean, Adaptive Gaussian and slideMask and observed that our method had the highest sensitivity and Jaccard similarity index. We envision EntropyMasker to fill an important gap in WSI preprocessing, machine learning image analysis pipelines, and enable disease phenotyping beyond the field of atherosclerosis.
Genetic diversity between local landraces and current breeding lines of pepper in China
Authors: Guo Guangjun , Pan Baogui , Yi Xixi , Khan Abid , Zhu Xuemei , Ge Wei , Liu Jinbing , Diao Weiping , Wang Shubin 
Published: March 2023

AbstractBased on 22 qualitative traits, 13 quantitative traits, and 27 molecular markers (26 SSR and 1 InDel), in the current study we compared the diversity and population structure of 94 local landraces and 85 current breeding lines of pepper in China. The results showed that the Shannon Diversity indices of 9 qualitative traits and 8 quantitative traits in current breeding lines were greater than those of landraces, of which 11 were fruit organ-related traits. Compared with current breeding lines, the mean values of Gene Diversity index and Polymorphism Information content of local landraces were higher by 0.08 and 0.09, respectively. Population structure and phylogenetic tree analysis showed that the 179 germplasm resources could be divided into two taxa, dominated by local landraces and current breeding lines, respectively. The above results indicated that the diversity of quantitative traits of current breeding lines were higher than that of local landraces, especially traits related to fruit organs, but the genetic diversity based on molecular markers was lower than that of local landraces. Therefore, in the future breeding process, we should not only focus on the selection of target traits, but also strengthen the background selection based on molecular markers. Moreover, the genetic information of other domesticated species and wild species will be transferred to the breeding lines through interspecific crosses to expand the genetic background of the breeding material.
Deduction of the operable design space of RP-HPLC technique for the simultaneous estimation of metformin, pioglitazone, and glimepiride
Authors: Marie Aya A. , Hammad Sherin F. , Salim Mohamed M. , Elkhodary Mahmoud M. , Kamal Amira H. 
Published: March 2023

AbstractA reversed-phase RP-HPLC method was developed for the simultaneous determination of metformin hydrochloride (MET), pioglitazone (PIO), and glimepiride (GLM) in their combined dosage forms and spiked human plasma. Quality risk management principles for determining the critical method parameters (CMPs) and fractional factorial design were made to screen CMPs and subsequently, the Box–Behnken design was employed. The analytical Quality by Design (AQbD) paradigm was used to establish the method operable design region (MODR) for the developed method depended on understanding the quality target product profile (QTPP), analytical target profile (ATP), and risk assessment for different factors that affect the method performance to develop an accurate, precise, cost-effective, and environmentally benign method. The separation was carried out using a mobile phase composed of methanol: 0.05 M potassium dihydrogen phosphate buffer pH 3.7 with 0.05% TEA (78:22, v/v). The flow rate was 1.2 mL/min. DAD detector was set at 227 nm. Linagliptin (LIN) was used as an internal standard. The proposed method was validated according to The International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH). The assay results obtained by using the developed method were statistically compared to those obtained by the reported HPLC method, and a satisfying agreement was observed.
Exact Gaussian processes for massive datasets via non-stationary sparsity-discovering kernels
Authors: Noack Marcus M. , Krishnan Harinarayan , Risser Mark D. , Reyes Kristofer G. 
Published: March 2023

AbstractA Gaussian Process (GP) is a prominent mathematical framework for stochastic function approximation in science and engineering applications. Its success is largely attributed to the GP’s analytical tractability, robustness, and natural inclusion of uncertainty quantification. Unfortunately, the use of exact GPs is prohibitively expensive for large datasets due to their unfavorable numerical complexity of$$O(N^3)$$O(N3)in computation and$$O(N^2)$$O(N2)in storage. All existing methods addressing this issue utilize some form of approximation—usually considering subsets of the full dataset or finding representative pseudo-points that render the covariance matrix well-structured and sparse. These approximate methods can lead to inaccuracies in function approximations and often limit the user’s flexibility in designing expressive kernels. Instead of inducing sparsity via data-point geometry and structure, we propose to take advantage of naturally-occurring sparsity by allowing the kernel to discover—instead of induce—sparse structure. The premise of this paper is that the data sets and physical processes modeled by GPs often exhibit natural or implicit sparsities, but commonly-used kernels do not allow us to exploit such sparsity. The core concept of exact, and at the same time sparse GPs relies on kernel definitions that provide enough flexibility to learn and encode not only non-zero but also zero covariances. This principle of ultra-flexible, compactly-supported, and non-stationary kernels, combined with HPC and constrained optimization, lets us scale exact GPs well beyond 5 million data points.
Characteristics of the Northern Hemisphere cold regions changes from 1901 to 2019
Authors: Huang Yutao , Zhang Lijuan , Li Yongsheng , Ren Chong , Pan Tao , Zhang Wenshuai , Zhang Fan , Li Chunyang , Gu Jiakai , Liu Jie 
Published: March 2023

AbstractThe accurate delineation of the spatial extent of cold regions provides the basis for the study of global environmental change. However, attention has been lacking on the temperature-sensitive spatial changes in the cold regions of the Earth in the context of climate warming. In this study, the mean temperature in the coldest month lower than − 3 °C, no more than 5 months over 10 °C, and an annual mean temperature no higher than 5 °C were selected to define cold regions. Based on the Climate Research Unit land surface air temperature (CRUTEM) of monthly mean surface climate elements, the spatiotemporal distribution and variation characteristics of the Northern Hemisphere (NH) continental cold regions from 1901 to 2019 are analyzed in this study, by adopting time trend and correlation analyses. The results show: (1) In the past 119 years, the cold regions of the NH covered on average about 4.074 × 107 km2, accounting for 37.82% of the total land area of the NH. The cold regions can be divided into the Mid-to-High latitude cold regions and the Qinghai-Tibetan Plateau cold regions, with spatial extents of 3.755 × 107 km2 and 3.127 × 106 km2, respectively. The Mid-to-High latitude cold regions in the NH are mainly distributed in northern North America, most of Iceland, the Alps, northern Eurasia, and the Great Caucasus with a mean southern boundary of 49.48° N. Except for the southwest, the entire region of the Qinghai-Tibetan Plateau, northern Pakistan, and most of Kyrgyzstan are cold regions. (2) In the past 119 years, the rates of change in the spatial extent of the cold regions in the NH, the Mid-to-High latitude, and the Qinghai-Tibetan Plateau were − 0.030 × 107 km2/10 a, − 0.028 × 107 km2/10 a, and − 0.013 × 106 km2/10 a, respectively, showing an extremely significant decreasing trend. In the past 119 years, the mean southern boundary of the Mid-to-High latitude cold regions has been retreating northward at all longitudes. For instance, the mean southern boundary of the Eurasian cold regions moved 1.82° to the north and that of North America moved 0.98° to the north. The main contribution of the study lies in the accurate definition of the cold regions and documentation of the spatial variation of the cold regions in the NH, revealing the response trends of the cold regions to climate warming, and deepening the study of global change from a new perspective.
MR-guided ultrasound-stimulated microbubble therapy enhances radiation-induced tumor response
Authors: McNabb Evan , Sharma Deepa , Sannachi Lakshmanan , Giles Anoja , Yang Wenyi , Czarnota Gregory J. 
Published: March 2023

AbstractHigh intensity focused ultrasound (HIFU) systems have been approved for therapeutic ultrasound delivery to cause tissue ablation or induced hyperthermia. Microbubble agents have also been used in combination with sonication exposures. These require temperature feedback and monitoring to prevent unstable cavitation and prevent excess tissue heating. Previous work has utilized lower power and pressure to oscillate microbubbles and transfer energy to endothelial cells in the absence of thermally induced damage that can radiosensitize tumors. This work investigated whether reduced acoustic power and pressure on a commercial available MR-integrated HIFU system could result in enhanced radiation-induced tumor response after exposure to ultrasound-stimulated microbubbles (USMB) therapy. A commercially available MR-integrated HIFU system was used with a hyperthermia system calibration provided by the manufacturer. The ultrasound transducer was calibrated to reach a peak negative pressure of − 750 kPa. Thirty male New Zealand white rabbits bearing human derived PC3 tumors were grouped to receive no treatment, 14 min of USMB, 8 Gy of radiation in a separate irradiation cabinet, or combined treatments. In vivo temperature changes were collected using MR thermometry at the tumor center and far-field muscle region. Tissues specimens were collected 24 h post radiation therapy. Tumor cell death was measured and compared to untreated controls through hematoxylin and eosin staining and immunohistochemical analysis. The desired peak negative pressure of − 750 kPa used for previous USMB occurred at approximately an input power of 5 W. Temperature changes were limited to under 4 °C in ten of twelve rabbits monitored. The median temperature in the far-field muscle region of the leg was 2.50 °C for groups receiving USMB alone or in combination with radiation. Finally, statistically significant tumor cell death was demonstrated using immunohistochemical analysis in the combined therapy group compared to untreated controls. A commercial MR-guided therapy HIFU system was able to effectively treat PC3 tumors in a rabbit model using USMB therapy in combination with radiation exposures. Future work could find the use of reduced power and pressure levels in a commercial MR-guided therapy system to mechanically stimulate microbubbles and damage endothelial cells without requiring high thermal doses to elicit an antitumor response.
Interpreting random forest analysis of ecological models to move from prediction to explanation
Authors: Simon Sophia M. , Glaum Paul , Valdovinos Fernanda S. 
Published: March 2023

AbstractAs modeling tools and approaches become more advanced, ecological models are becoming more complex. Traditional sensitivity analyses can struggle to identify the nonlinearities and interactions emergent from such complexity, especially across broad swaths of parameter space. This limits understanding of the ecological mechanisms underlying model behavior. Machine learning approaches are a potential answer to this issue, given their predictive ability when applied to complex large datasets. While perceptions that machine learning is a “black box” linger, we seek to illuminate its interpretive potential in ecological modeling. To do so, we detail our process of applying random forests to complex model dynamics to produce both high predictive accuracy and elucidate the ecological mechanisms driving our predictions. Specifically, we employ an empirically rooted ontogenetically stage-structured consumer-resource simulation model. Using simulation parameters as feature inputs and simulation output as dependent variables in our random forests, we extended feature analyses into a simple graphical analysis from which we reduced model behavior to three core ecological mechanisms. These ecological mechanisms reveal the complex interactions between internal plant demography and trophic allocation driving community dynamics while preserving the predictive accuracy achieved by our random forests.
Interannual variability in early life phenology is driven by climate and oceanic processes in two NE Atlantic flatfishes
Authors: Vaz Ana , Primo Ana Lígia , Crespo Daniel , Pardal Miguel , Martinho Filipe 
Published: March 2023

AbstractEarly life phenology is a crucial factor for population dynamics in a climate change scenario. As such, understanding how the early life cycle of marine fishes is influenced by key oceanic and climate drivers is of chief importance for sustainable fisheries. This study documents interannual changes in early life phenology of two commercial flatfishes: European flounder (Platichthys flesus) and common sole (Solea solea) from 2010 to 2015 based on otolith microstructure. Using GAMs, we looked for correlations of the North Atlantic Oscillation (NAO), Eastern Atlantic pattern (EA), sea surface temperature (SST), chlorophyl a concentration (Chla) and upwelling (Ui) variation with the onset of hatch, metamorphosis, and benthic settlement day. We concluded that higher SST, more intensive upwelling, and EA were coincident with a later the onset of each stage, while increasing NAO induces an earlier onset of each stage. Although similar to S. solea, P. flesus showed a more complex interaction with the environmental drivers, most possibly because it is at its southern limit of its distribution. Our results highlight the complexity of the relationship between climate conditions and fish early life history, particularly those with complex life cycles that include migrations between coastal areas and estuaries.
Characterization of phyto-components with antimicrobial traits in supercritical carbon dioxide and soxhlet Prosopis juliflora leaves extract using GC-MS
Authors: Naik Nagaraj M. , Krishnaveni M. , Mahadevswamy M. , Bheemanna M. , Nidoni Udaykumar , Kumar Vasant , Tejashri K. 
Published: March 2023

AbstractThis study aimed to screen the bioactive compounds from Prosopis juliflora leaf supercritical fluid extract and to assess its antimicrobial properties. Supercritical carbon dioxide and Soxhlet methods were used for extraction. The extract was subjected to Gas Chromatography-Mass Spectrometer (GC-MS) and Fourier Transform Infrared for the characterization of the phyto-components. When compared to soxhlet extraction, more components (35) were eluted by supercritical fluid extraction (SFE), according to GC-MS screening. Rhizoctonia bataticola, Alternaria alternata, and Colletotrichum gloeosporioides were all successfully inhibited by P. juliflora leaf SFE extract, which demonstrated strong antifungal properties with mycelium percent inhibition of 94.07%, 93.15%, and 92.43%, respectively, compared to extract from Soxhlet, which registered 55.31%, 75.63% and 45.13% mycelium inhibition respectively. Also, SFE P. juliflora extracts registered higher zone of inhibition 13.90 mm, 14.47 mm and 14.53 mm against all three test food-borne bacterial pathogens viz Escherichia coli, Salmonella enterica and Staphylococcus aureus respectively. Results obtained from GC-MS screening revealed that SFE is more efficient than soxhlet extraction in recovering the phyto-components. P. juliflora may provide antimicrobial agents, a novel natural inhibitory metabolite.
Lrig1-expressing epidermal progenitors require SCD1 to maintain the dermal papilla niche
Authors: Lim Sophia Beng Hui , Wei Shang , Tan Andy Hee-Meng , van Steensel Maurice A. M. , Lim Xinhong 
Published: March 2023

AbstractNiche cells are widely known to regulate stem/progenitor cells in many mammalian tissues. In the hair, dermal papilla niche cells are well accepted to regulate hair stem/progenitor cells. However, how niche cells themselves are maintained is largely unknown. We present evidence implicating hair matrix progenitors and the lipid modifying enzyme, Stearoyl CoA Desaturase 1, in the regulation of the dermal papilla niche during the anagen-catagen transition of the mouse hair cycle. Our data suggest that this takes place via autocrine Wnt signalling and paracrine Hedgehog signalling. To our knowledge, this is the first report demonstrating a potential role for matrix progenitor cells in maintaining the dermal papilla niche.
Short term results in a population based study indicate advantage for laparoscopic colon cancer surgery versus open
Authors: Petersson Josefin , Matthiessen Peter , Jadid Kaveh Dehlaghi , Bock David , Angenete Eva 
Published: March 2023

AbstractThe aim of this study was to compare LAP with OPEN regarding short-term mortality, morbidity and completeness of the cancer resection for colon cancer in a routine health care setting using population based register data. All 13,683 patients who were diagnosed 2012–2018 and underwent elective surgery for right-sided or sigmoid colon cancer were included from the Swedish Colorectal Cancer Registry and the National Patient Registry. Primary outcome was 30-day mortality. Secondary outcomes were 90-day mortality, length of hospital stay, reoperation, readmission and positive resection margin (R1). Weighted and unweighted multi regression analyses were performed. There were no difference in 30-day mortality: LAP (0.9%) and OPEN (1.3%) (OR 0.89, 95% CI 0.62–1.29, P = 0.545). The weighted analyses showed an increased 90-day mortality following OPEN, P < 0.001. Re-operations and re-admission were more frequent after OPEN and length of hospital stay was 2.9 days shorter following LAP (P < 0.001). R1 resections were significantly more common in the OPEN group in the unweighted and weighted analysis with P = 0.004 and P < 0.001 respectively. Therefore, the favourable short-term outcomes following elective LAP versus OPEN resection for colon cancer in routine health care indicate an advantage of laparoscopic surgery.
Zinc and iron dynamics in human islet amyloid polypeptide-induced diabetes mouse model
Authors: Fukunaka Ayako , Shimura Mari , Ichinose Takayuki , Pereye Ofejiro B. , Nakagawa Yuko , Tamura Yasuko , Mizutani Wakana , Inoue Ryota , Inoue Takato , Tanaka Yuto , Sato Takashi , Saitoh Tatsuya , Fukada Toshiyuki , Nishida Yuya , Miyatsuka Takeshi , Shirakawa Jun , Watada Hirotaka , Matsuyama Satoshi , Fujitani Yoshio 
Published: March 2023

AbstractMetal homeostasis is tightly regulated in cells and organisms, and its disturbance is frequently observed in some diseases such as neurodegenerative diseases and metabolic disorders. Previous studies suggest that zinc and iron are necessary for the normal functions of pancreatic β cells. However, the distribution of elements in normal conditions and the pathophysiological significance of dysregulated elements in the islet in diabetic conditions have remained unclear. In this study, to investigate the dynamics of elements in the pancreatic islets of a diabetic mouse model expressing human islet amyloid polypeptide (hIAPP): hIAPP transgenic (hIAPP-Tg) mice, we performed imaging analysis of elements using synchrotron scanning X-ray fluorescence microscopy and quantitative analysis of elements using inductively coupled plasma mass spectrometry. We found that in the islets, zinc significantly decreased in the early stage of diabetes, while iron gradually decreased concurrently with the increase in blood glucose levels of hIAPP-Tg mice. Notably, when zinc and/or iron were decreased in the islets of hIAPP-Tg mice, dysregulation of glucose-stimulated mitochondrial respiration was observed. Our findings may contribute to clarifying the roles of zinc and iron in islet functions under pathophysiological diabetic conditions.