bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation, characterization, anti-MRSA evaluation, and in-silico multi-target anti-microbial validations of actinomycin X2 and actinomycin D produced by novel Streptomyces smyrnaeus UKAQ_23
Authors: Qureshi Kamal A. , Bholay Avinash D. , Rai Pankaj K. , Mohammed Hamdoon A. , Khan Riaz A. , Azam Faizul , Jaremko Mariusz , Emwas Abdul-Hamid , Stefanowicz Piotr , Waliczek Mateusz , Kijewska Monika , Ragab Ehab A. , Rehan Medhat , Elhassan Gamal O. , Anwar Md Jamir , Prajapati Dinesh K. 
Published: July 2021

AbstractStreptomyces smyrnaeus UKAQ_23, isolated from the mangrove-sediment, collected from Jubail,Saudi Arabia, exhibited substantial antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), including non-MRSA Gram-positive test bacteria. The novel isolate, under laboratory-scale conditions, produced the highest yield (561.3 ± 0.3 mg/kg fermented agar) of antimicrobial compounds in modified ISP-4 agar at pH 6.5, temperature 35 °C, inoculum 5% v/w, agar 1.5% w/v, and an incubation period of 7 days. The two major compounds, K1 and K2, were isolated from fermented medium and identified as Actinomycin X2 and Actinomycin D, respectively, based on their structural analysis. The antimicrobial screening showed that Actinomycin X2 had the highest antimicrobial activity compared to Actinomycin D, and the actinomycins-mixture (X2:D, 1:1, w/w) against MRSA and non-MRSA Gram-positive test bacteria, at 5 µg/disc concentrations. The MIC of Actinomycin X2 ranged from 1.56–12.5 µg/ml for non-MRSA and 3.125–12.5 µg/ml for MRSA test bacteria. An in-silico molecular docking demonstrated isoleucyl tRNA synthetase as the most-favored antimicrobial protein target for both actinomycins, X2 and D, while the penicillin-binding protein-1a, was the least-favorable target-protein. In conclusion, Streptomyces smyrnaeus UKAQ_23 emerged as a promising source of Actinomycin X2 with the potential to be scaled up for industrial production, which could benefit the pharmaceutical industry.
Collagen and elastic fibres in acute and chronic liver injury
Authors: Hall Andrew , Cotoi Corina , Luong Tu Vinh , Watkins Jennifer , Bhathal Prithi , Quaglia Alberto 
Published: July 2021

AbstractThe histological distinction between acute and chronic liver injury is a challenging aspect of liver histopathology. It is traditionally based on the interpretation of morphological changes to the extracellular matrix (ECM) at sites of hepatocyte loss using histochemical stains. Our aim was to investigate whether immunohistochemistry and multiplexing for collagen type (I & III) and elastic fibres and a modified Victoria blue method could be helpful. We studied 43 livers removed at transplantation for acute liver failure (ALF, 20 cases) or cirrhosis (23) plus 8 normal controls. In ALF the periportal ECM was normal in 2 cases, contained mainly collagen I associated with a ductular reaction in 6 cases, and delicate elastic strands in 11 cases. Periportal deposition of mainly collagen I and mature elastic fibres was observed in cirrhosis. In ALF the perisinusoidal ECM was intact in 4 cases, collapsed or condensed but of normal composition (predominantly collagen III) in 2 cases, and collapsed and condensed containing mostly collagen I in 17 cases (7 including delicate immature elastic strands). In contrast, bridging fibrous septa of cirrhosis contained abundant collagen 1 and bundles of mature elastin. We propose the use of a scale and the use of immunohistochemistry and multiplexing in additional to histochemical stains to characterise the ECM changes in acute and chronic liver injury.
Notch signaling represses cone photoreceptor formation through the regulation of retinal progenitor cell states
Authors: Chen Xueqing , Emerson Mark M. 
Published: July 2021

AbstractNotch signaling is required to repress the formation of vertebrate cone photoreceptors and to maintain the proliferative potential of multipotent retinal progenitor cells. However, the mechanism by which Notch signaling controls these processes is unknown. Recently, restricted retinal progenitor cells with limited proliferation capacity and that preferentially generate cone photoreceptors have been identified. Thus, there are several potential steps during cone genesis that Notch signaling could act. Here we use cell type specific cis-regulatory elements to localize the primary role of Notch signaling in cone genesis to the formation of restricted retinal progenitor cells from multipotent retinal progenitor cells. Localized inhibition of Notch signaling in restricted progenitor cells does not alter the number of cones derived from these cells. Cell cycle promotion is not a primary effect of Notch signaling but an indirect effect on progenitor cell state transitions that leads to depletion of the multipotent progenitor cell population. Taken together, this suggests that the role of Notch signaling in cone photoreceptor formation and proliferation are both mediated by a localized function of Notch in multipotent retinal progenitor cells to repress the formation of restricted progenitor cells.
A fuzzy rank-based ensemble of CNN models for classification of cervical cytology
Authors: Manna Ankur , Kundu Rohit , Kaplun Dmitrii , Sinitca Aleksandr , Sarkar Ram 
Published: July 2021

AbstractCervical cancer affects more than 0.5 million women annually causing more than 0.3 million deaths. Detection of cancer in its early stages is of prime importance for eradicating the disease from the patient’s body. However, regular population-wise screening of cancer is limited by its expensive and labour intensive detection process, where clinicians need to classify individual cells from a stained slide consisting of more than 100,000 cervical cells, for malignancy detection. Thus, Computer-Aided Diagnosis (CAD) systems are used as a viable alternative for easy and fast detection of cancer. In this paper, we develop such a method where we form an ensemble-based classification model using three Convolutional Neural Network (CNN) architectures, namely Inception v3, Xception and DenseNet-169 pre-trained on ImageNet dataset for Pap stained single cell and whole-slide image classification. The proposed ensemble scheme uses a fuzzy rank-based fusion of classifiers by considering two non-linear functions on the decision scores generated by said base learners. Unlike the simple fusion schemes that exist in the literature, the proposed ensemble technique makes the final predictions on the test samples by taking into consideration the confidence in the predictions of the base classifiers. The proposed model has been evaluated on two publicly available benchmark datasets, namely, the SIPaKMeD Pap Smear dataset and the Mendeley Liquid Based Cytology (LBC) dataset, using a 5-fold cross-validation scheme. On the SIPaKMeD Pap Smear dataset, the proposed framework achieves a classification accuracy of 98.55% and sensitivity of 98.52% in its 2-class setting, and 95.43% accuracy and 98.52% sensitivity in its 5-class setting. On the Mendeley LBC dataset, the accuracy achieved is 99.23% and sensitivity of 99.23%. The results obtained outperform many of the state-of-the-art models, thereby justifying the effectiveness of the same. The relevant codes of this proposed model are publicly available on GitHub.
A new charophyte habitat with a stabilized good ecological potential of mine water
Authors: Napiórkowska-Krzebietke Agnieszka , Skrzypczak Andrzej Robert 
Published: July 2021

AbstractEach newly-created pond which is supplied with mine water gives the opportunity to study a unique ecosystem in context of possible conditions for biotic live. Therefore, this research aimed to assess a phytoplankton-based ecological potential against the trophic conditions and the risk of contamination with trace elements, and demonstrate the possibility to stabilize at least good water quality of a clarification pond. The gradual decrease in turbidity-related variables (including suspended solids and iron) and nutrients, on the one hand, and an increase in phytoplankton-related indicators, on the other hand, were the most evident. Besides, relative stability in trace elements (the best water quality class), trophic level (slightly eutrophic level) and ecological potential (maximum potential), and relative instability in sulfates and calcium were also recorded. The final stabilization of water habitat resulted in abundant growth of charophyte Nitella mucronata. This all suggested a new ecological opportunity for settlement of a rare species and important for biodiversity enhancement. Furthermore, the study revealed that a clarification pond did not pose any toxic risk from the elevated content of trace elements or the growth of toxic or potentially toxic cyanobacteria which is essential for proper functioning and management of water ecosystems.
The association between serum selenium concentration and prognosis in patients with heart failure in a Chinese population
Authors: Zhang Zhiliang , Chang Chao , Zhang Yuxin , Chai Zhiyong , Li Jinbei , Qiu Chunguang 
Published: July 2021

AbstractWhether Selenium (Se) deficiency relates with adverse prognosis in Chinese patients with heart failure (HF) is still unknown. This study aimed to investigate the association of serum Se level and the outcomes of patients with HF in a Chinese population. Patients with HF and serum Se examination were retrospectively included. Baseline information were collected at patient’s first admission. The primary and secondary outcomes were all-cause mortality and rehospitalization for HF during follow-up, respectively. The study participants were divided into quartiles according to their serum Se concentrations. The Cox proportional hazard models were adopted to estimate the association of serum Se levels with observed outcomes. A total of 411 patients with HF with a mean age of 62.5 years were included. The mean serum level of Se was 68.3 ± 27.7 µg/L. There was nonsignificant difference of baseline characterizes between the four quartile groups. In comparison with patients in the highest quartile, those with the lowest quartile (17.40–44.35 µg/L) were associated with increased risk of all-cause mortality [adjusted hazard ratios (95% CI) 2.32 (1.43–3.77); Ptrend = 0.001]. Our study suggested that a lower serum Se level was significantly associated with increased risk of all-cause mortality in patients with HF.
Type 1 diabetes patients increase CXCR4+ and CXCR7+ haematopoietic and endothelial progenitor cells with exercise, but the response is attenuated
Authors: Taylor Guy S. , Shaw Andy , Smith Kieran , Capper Tess E. , Scragg Jadine H. , Cronin Michael , Bashir Ayat , Flatt Anneliese , Campbell Matthew D. , Stevenson Emma J. , Shaw James A. , Ross Mark , West Daniel J. 
Published: July 2021

AbstractExercise mobilizes angiogenic cells, which stimulate vascular repair. However, limited research suggests exercise-induced increase of endothelial progenitor cell (EPCs) is completely lacking in type 1 diabetes (T1D). Clarification, along with investigating how T1D influences exercise-induced increases of other angiogenic cells (hematopoietic progenitor cells; HPCs) and cell surface expression of chemokine receptor 4 (CXCR4) and 7 (CXCR7), is needed. Thirty T1D patients and 30 matched non-diabetes controls completed 45 min of incline walking. Circulating HPCs (CD34+, CD34+CD45dim) and EPCs (CD34+VEGFR2+, CD34+CD45dimVEGFR2+), and subsequent expression of CXCR4 and CXCR7, were enumerated by flow cytometry at rest and post-exercise. Counts of HPCs, EPCs and expression of CXCR4 and CXCR7 were significantly lower at rest in the T1D group. In both groups, exercise increased circulating angiogenic cells. However, increases was largely attenuated in the T1D group, up to 55% lower, with CD34+(331 ± 437 Δcells/mL vs. 734 ± 876 Δcells/mLp = 0.048), CD34+VEGFR2+(171 ± 342 Δcells/mL vs. 303 ± 267 Δcells/mL,p = 0.006) and CD34+VEGFR2+CXCR4+(126 ± 242 Δcells/mL vs. 218 ± 217 Δcells/mL,p = 0.040) significantly lower. Exercise-induced increases of angiogenic cells is possible in T1D patients, albeit attenuated compared to controls. Decreased mobilization likely results in reduced migration to, and repair of, vascular damage, potentially limiting the cardiovascular benefits of exercise.Trial registration: ISRCTN63739203.
Plastome evolution and organisation in the Hoya group (Apocynaceae)
Authors: Rodda Michele , Niissalo Matti A. 
Published: July 2021

AbstractThe genus Hoya is highly diverse and many of its species are popular ornamental plants. However, the relationships between Hoya and related genera (the Hoya group) are not fully resolved. In this study, we report 20 newly sequenced plastomes of species in the Hoya group. The complete plastomes vary in length from 175,405 to 178,525 bp while the LSCs vary from 90,248 to 92,364 bp and the complete SSCs vary from 2,285 to 2,304 bp, making the SSC in the Hoya group one of the shortest known in the angiosperms. The plastome structure in the Hoya group is characterised by a massive increase in the size of the inverted repeats as compared to the outgroups. In all ingroup species, the IR/SSC boundary moved from ycf1 to ndhF while this was not observed in outgroup taxa, making it a synapomorphy for the Hoya group. We have also assembled the mitogenome of Hoya lithophytica, which, at 718,734 bp, is the longest reported in the family. The phylogenetic analysis using exons from 42 taxa in the Hoya group and three outgoups confirms that the earliest divergent genus in the Hoya group is Papuahoya, followed by Dischidia. The relationship between Dischidia and the clade which includes all Hoya and Oreosparte taxa, is not fully supported. Oreosparte is nested in Hoya making it paraphyletic unless Clemensiella is recognised as a separate genus.
Detection and analysis of photo-acoustic emission in Direct Laser Interference Patterning
Authors: Steege Tobias , Alamri Sabri , Lasagni Andrés Fabián , Kunze Tim 
Published: July 2021

AbstractFunctional laser texturing by means of Direct Laser Interference Patterning is one of the most efficient approaches to fabricate well-defined micro textures which mimic natural surfaces, such as the lotus effect for self-cleaning properties or shark skin for reduced friction. While numerous technical and theoretical improvements have been demonstrated, strategies for process monitoring are yet to be implemented in DLIP, for instance aiming to treat complex and non-plane surfaces. Over the last 35 years, it has been shown that the sound pressure generated by a laser beam hitting a surface and producing ablation can be detected and analysed using simple and commercially available transducers and microphones. This work describes the detection and analysis of photo-acoustic signals acquired from airborne acoustic emission during DLIP as a direct result of the laser–material interaction. The study includes the characterization of the acoustic emission during the fabrication of line-like micro textures with different spatial periods and depths, the interpretation the spectral signatures deriving from single spot and interference ablation, as well as a detailed investigation of the vertical extent of the interference effect based on the ablated area and its variation with the interference period. The results show the possibility to develop an autofocusing system using only the signals from the acoustic emission for 3D processing, as well as the possibility to predict deviations in the DLIP processing parameters.
Predictability of COVID-19-related morbidity and mortality based on model estimations to establish proactive protocols of countermeasures
Authors: Svensson Göran , Rodriguez Rocio , Padin Carmen 
Published: July 2021

AbstractThe COVID-19 pandemic (SARS-CoV-2) has revealed the need for proactive protocols to react and act, imposing preventive and restrictive countermeasures on time in any society. The extent to which confirmed cases can predict the morbidity and mortality in a society remains an unresolved issue. The research objective is therefore to test a generic model’s predictability through time, based on percentage of confirmed cases on hospitalized patients, ICU patients and deceased. This study reports the explanatory and predictive ability of COVID-19-related healthcare data, such as whether there is a spread of a contagious and virulent virus in a society, and if so, whether the morbidity and mortality can be estimated in advance in the population. The model estimations stress the implementation of a pandemic strategy containing a proactive protocol entailing what, when, where, who and how countermeasures should be in place when a virulent virus (e.g. SARS-CoV-1, SARS-CoV-2 and MERS) or pandemic strikes next time. Several lessons for the future can be learnt from the reported model estimations. One lesson is that COVID-19-related morbidity and mortality in a population is indeed predictable. Another lesson is to have a proactive protocol of countermeasures in place.
Salt-tolerance screening in Limonium sinuatum varieties with different flower colors
Authors: Xu Xiaojing , Zhou Yingli , Mi Ping , Wang Baoshan , Yuan Fang 
Published: July 2021

AbstractLimonium sinuatum, a member of Plumbaginaceae commonly known as sea lavender, is widely used as dried flower. Five L. sinuatum varieties with different flower colors (White, Blue, Pink, Yellow, and Purple) are found in saline regions and are widely cultivated in gardens. In the current study, we evaluated the salt tolerance of these varieties under 250 mmol/L NaCl (salt-tolerance threshold) treatment to identify the optimal variety suitable for planting in saline lands. After the measurement of the fresh weight (FW), dry weight (DW), contents of Na+, K+, Ca2+, Cl−, malondialdehyde (MDA), proline, soluble sugars, hydrogen peroxide (H2O2), relative water content, chlorophyll contents, net photosynthetic rate, and osmotic potential of whole plants, the salt-tolerance ability from strongest to weakest is identified as Pink, Yellow, Purple, White, and Blue. Photosynthetic rate was the most reliable and positive indicator of salt tolerance. The density of salt glands showed the greatest increase in Pink under NaCl treatment, indicating that Pink adapts to high-salt levels by enhancing salt gland formation. These results provide a theoretical basis for the large-scale planting of L. sinuatum in saline soils in the future.
Oncological and functional outcomes of supratotal resection of IDH1 wild-type glioblastoma based on 11C-methionine PET: a retrospective, single-center study
Authors: Hirono Seiichiro , Ozaki Ko , Kobayashi Masayoshi , Hara Ayaka , Yamaki Tomohiro , Matsutani Tomoo , Iwadate Yasuo 
Published: July 2021

AbstractThe oncological and functional outcomes in glioblastoma (GBM) patients following supratotal resection (SupTR), involving complete resection of contrast-enhancing enhanced (CE) tumors and areas of methionine (Met) uptake on 11C-met positron emission tomography (Met-PET), are unknown. We conducted a retrospective review in newly diagnosed, IDH1 wild-type GBM patients, comparing SupTR with gross total resection (GTR), in which only CE tumor tissue was resected. All patients underwent standard radiotherapy and temozolomide treatment, and were followed for tumor recurrence and overall survival (OS). Among the 30 patients included in this study, 7 underwent SupTR and 23 underwent GTR. Awake craniotomy with cortical and subcortical mapping was more frequently performed in the SupTR group than in the GTR group. During the follow-up period, significantly different patterns of disease progression were observed between groups. Although more than 80% of recurrences were local in the GTR group, all recurrences in the SupTR group were distant. Median OS in the GTR and SupTR groups was 18.5 months (95% confidence interval [CI] 14.2–35.1) and not reached (95% CI 30.5-not estimable), respectively; this difference was statistically significant (p = 0.03 by log-rank test). No postoperative neurocognitive decline was evident in patients who underwent SupTR. Compared to GTR alone, aggressive resection of both CE tumors and areas with Met uptake (SupTR) under awake craniotomy with functional mapping results in a survival benefit associated with better local control and neurocognitive preservation.
Polarization-insensitive GaN metalenses at visible wavelengths
Authors: Chen Meng-Hsin , Yen Cheng-Wei , Guo Chia-Chun , Su Vin-Cent , Kuan Chieh-Hsiung , Lin Hoang Yan 
Published: July 2021

AbstractThe growth of wide-bandgap materials on patterned substrates has revolutionized the means with which we can improve the light output power of gallium nitride (GaN) light-emitting diodes (LEDs). Conventional patterned structure inspection usually relies on an expensive vacuum-system-required scanning electron microscope (SEM) or optical microscope (OM) with bulky objectives. On the other hand, ultra-thin metasurfaces have been widely used in widespread applications, especially for converging lenses. In this study, we propose newly developed, highly efficient hexagon-resonated elements (HREs) combined with gingerly selected subwavelength periods of the elements for the construction of polarization-insensitive metalenses of high performance. Also, the well-developed fabrication techniques have been employed to realize the high-aspect-ratio metalenses working at three distinct wavelengths of 405, 532, and 633 nm with respective diffraction-limited focusing efficiencies of 93%, 86%, and 92%. The 1951 United States Air Force (USAF) test chart has been chosen to characterize the imaging capability. All of the images formed by the 405-nm-designed metalens show exceptional clear line features, and the smallest resolvable features are lines with widths of 870 nm. To perform the inspection capacity for patterned substrates, for the proof of concept, a commercially available patterned sapphire substrate (PSS) for the growth of the GaN LEDs has been opted and carefully examined by the high-resolution SEM system. With the appropriately chosen metalenses at the desired wavelength, the summits of structures in the PSS can be clearly observed in the images. The PSS imaging qualities taken by the ultra-thin and light-weight metalenses with a numerical aperture (NA) of 0.3 are comparable to those seen by an objective with the NA of 0.4. This work can pioneer semiconductor manufacturing to choose the polarization-insensitive GaN metalenses to inspect the patterned structures instead of using the SEM or the bulky and heavy conventional objectives.
Salient region growing based on Gaussian pyramid
Authors: Jiao Jianjun , Wang Xiaopeng , Zhang Jungping , Wang Qingsheng 
Published: July 2021

AbstractFor region growing image segmentation, seed selection and image noise are two major concerns causing negative segmentation performance. This paper proposes a regional growth algorithm based on the Gaussian pyramid (GPRG), which automatically selects seed points and optimizes the growth path. To achieve automatic seed selection, Gaussian difference pyramid generated by the Gaussian pyramid is required. The growing seed of the salient target in an image is acquired by searching for extremums in each image of the Gaussian difference pyramid. For growing path optimization, edge changing direction is updated according to different Gaussian difference pyramid images with sizes from small to large. The edge of region growing is determined by the edge of the salient target in an image. Segmentation experiments show that this algorithm is able to automatically select seeds and accurately segment the salient target in an image with and without image noise. Performances in terms of segmentation accuracy (SA), mean intersection‐over‐union (mIoU) and E‐measure are superior compared with other methods.