bluuebunny/crossref_metadata_2025_split huggingface dataset:
An in silico Design, Expression and Purification of a Chimeric Protein as an Immunogen Candidate Consisting of IpaD, StxB, and TolC Proteins from Shigella spp
Authors: Fathi Javad , Nazarian Shahram , Kordbacheh Emad , Hadi Nahal 
Published: June 2022

Background: Shigella spp. is the cause of dysentery and is widespread worldwide. On the other hand, antibiotic resistance is increasing in this bacterium. Bioinformatics is a new approach to vaccine and drug design involving the selection of appropriate antigens. This study aimed to design a chimeric protein consisting of IpaD, StxB, and TolC proteins from Shigella through a bioinformatics approach as an immunogen candidate.
Methods: The sequences of ipaD, stxB, and tolC genes were obtained. Additionally, the immunogenic regions of the associated protein, physicochemical characteristics, protein structures, B and T cells epitopes, and molecular docking were determined using in silico servers. Besides, the chimeric gene was synthesized following sequence optimization by utilizing the codon usage of Escherichia coli (E. coli). The expression of the recombinant protein was confirmed via SDS-PAGE and Western blot technique.
Results: The residues 41-160 of IpaD, 21-89 of StxB, and 40-335 of TolC were selected. According to half-life, instability, and buried indices, IpaD-StxB-TolC was selected as the best arrangement. The Ramachandran plot showed that 97.077% of the amino acids were in the favored area. Linear and conformational epitopes were also present throughout the chimeric protein sequence. Moreover, the C-ImmSim server indicated that IgG and IgM titers could reach desirable values by the third injection. Furthermore, the stability of the mRNA-optimized gene was enhanced, increasing the Codon Adaptive Index (CAI) to 0.9. Finally, the chimeric gene was transferred to E. coli BL21, and the expression of the 60.6 kDa recombinant protein was confirmed.
Conclusion: The results indicated that the recombinant protein could act as a proper immunogen candidate against Shigella spp.
Neutrophil to Lymphocyte Ratio (NLR) and Derived NLR Combination: A Cost-effective Predictor of Moderate to Severe COVID-19 Progression
Authors: Kaboudanian Ardestani Sussan , Salehi Mohammad Reza , Attaran Bahareh , Hashemi Seyed Mahmoud , Sadeghi Somayeh , Ghaffarpour Sara , Tuserkani Fatemeh , Ghazanfari Tooba 
Published: June 2022

Inflammation is an essential contributor to Coronavirus disease 2019 (COVID-19). In this regard, finding a prognostic indicator is valuable because the treatment will be more effective if critical patients with high inflammation are diagnosed earlier. We aimed to evaluate some hematologic markers for COVID-19 and assess their association with the severity of the disease.
A total of 154 COVID-19 patients were laboratory-confirmed and admitted to Imam Khomeini Hospital Complex, Tehran, Iran, from February 12, 2020, to April 4, 2020, and 55 healthy individuals were enrolled in the study. The severity of the patients' illnesses was classified into three subgroups according to the types of oxygen therapies (moderate (61), severe (28), and critical (43)) and examined the different ratios of total white blood cell (WBC) count, neutrophil to lymphocyte ratio (NLR), platelet to monocyte ratio (PLR), macrophage to lymphocyte ratio (MLR), derived NLR ratio (dNLR), and some biochemical tests.
COVID-19 patients had higher levels of NLR, MLR, PLR, and dNLR than healthy subjects. receiver operating characteristic (ROC) analysis of the curve revealed that NLR and dNLR had a high diagnostic value to differentiate COVID-19 patients from healthy subjects (area under the curve [AUC]=0.923 and 0.910, respectively) and predict mortality (AUC=0.726 and 0.735, respectively).
NLR and dNLR may be reliable markers to evaluate the severity of COVID-19. NLR and dNLR had a high diagnostic value for differentiating COVID-19 patients from healthy subjects, and they could predict the severity and outcome of the disease.
Induced Pluripotent Stem-cells Inhibit Experimental Bleomycin-induced Pulmonary Fibrosis Through Regulation of the Insulin-like Growth Factor Signaling
Authors: Bayati Paria , Taherian Marjan , Assarehzadegan Mohammad-Ali , Soleimani Mansoureh , Poormoghim Hadi , Mojtabavi Nazanin 
Published: June 2022

Idiopathic pulmonary fibrosis (IPF) is among the illnesses with a high mortality rate, yet no specific cause has been identified; as a result, successful treatment has not been achieved. Among the novel approaches for treating such hard-to-cure diseases are induced pluripotent stem cells (IPSCs). Some studies have shown these cells’ potential in treating IPF. Therefore, we aimed to investigate the impact of IPSCs on insulin-like growth factor (Igf) signaling as a major contributor to IPF pathogenesis.
C57BL/6 mice were intratracheally instilled with Bleomycin (BLM) or phosphate-buffered saline; the next day, half of the bleomycin group received IPSCs through tail vein injection. Hydroxyproline assay and histologic examinations have been performed to assess lung fibrosis. The gene expression was evaluated using specific primers for Igf-1, Igf-2, and insulin receptor substrate 1 (Irs-1) genes and SYBR green qPCR master mix. The data have been analyzed using the 2-ΔΔCT method.
The mice that received Bleomycin showed histological characteristics of the fibrotic lung injury, which was significantly ameliorated after treatment with IPSCs comparable to the control group. Furthermore, gene expression analyses revealed that in the BLM group, Igf1, Igf2, and Irs1 genes were significantly upregulated, which were returned to near-normal levels after treatment with IPSCs.
IPSCs could modulate the bleomycin-induced upregulation of Igf1, Igf2, and Irs1 genes. This finding reveals a new aspect of the therapeutic impact of the IPSCs on IPF, which could be translated into other fibrotic disorders.
Clinical and Molecular Assessment of Iranian Families with Severe Congenital Neutropenia, Identification of HYOU1 and SHOC2 as Potential Novel Gene Defects
Authors: Arab Fatemeh , Rezaei Nima , Taheri Forough , Kouhpeikar Hamideh , Rayzan Elham , Mirbeyk Mona , Zare‐Abdollahi Davood , Ghadami Mohsen 
Published: June 2022

Neutropenia congenita grave (SCN) is a rare disease with a genetically and clinically heterogeneous nature, usually diagnosed in childhood, with an elevated risk of infections such as otitis, skin infections, pneumonia, deep abscesses, and septicemia. Patients with SCN also have an increased risk of leukemia, and mutations in the ELANE and the HAX1 genes have been observed in those patients.
This study was conducted to genetically screen six Iranian families with SCN who have at least one affected person. In the first step, all exons and intron boundaries of ELANE and HAX1 genes were sequenced in probands. Cases with no pathogenic mutations were tested through whole-exome sequencing (WES).
Analysis showed five different variants in ELANE (c.377 C>T), HAX1 (c.130_131 insA), HYOU1 (c.69 G>C and c.2744 G>A) and SHOC2 (c.4 A>G) genes in four families. We found that two out of six families had mutations in ELANE and HAX1 genes. Moreover, we found
two novel mutations at the HYOU1 gene that had not previously been reported, as well as a pathogenic mutation at SHOC2 with multiple phenotypes, that will contribute to determining the genetic basis for SCN.
Our study revealed that WES could help diagnose SCN, improve the classification of neutropenia, and rule out other immunodeficiencies such as autoimmune neutropenia, primary immunodeficiency diseases, and inherited bone marrow failure syndromes.
Wpływ wybranych dodatków lekkich na zmianę parametrów technologicznych zaczynu
Authors:   Instytut Nafty i Gazu – Państwowy Instytut Badawczy, Kremieniewski Marcin 
Published: June 2022

W celu obniżenia gęstości zaczynów przeznaczonych do uszczelniania kolumn rur okładzinowych w warunkach obniżonego ciśnienia złożowego czy w strefach skał słabo zwięzłych stosuje się lekkie dodatki, takie jak mikrosfera bądź perlit. Użycie tego rodzaju materiałów pozwala na zredukowanie wartości ciśnienia hydrostatycznego i tym samym zapobiega ucieczce cementu w strefy słabo zwięzłe. Dodatkowo zaczyny o obniżonej gęstości mogą być stosowane w przypadku konieczności tłoczenia cementu w przestrzeni pozarurowej na dużą wysokość. Jednak wykorzystanie dodatków redukujących gęstość zaczynu nie pozostaje bez znaczenia dla parametrów technologicznych zarówno świeżego, jak i stwardniałego zaczynu. W przypadku płynnego zaczynu obecność lekkich frakcji powoduje zmianę parametrów reologicznych zaczynu, wzrost wartości filtracji bądź też odstoju wody. Natomiast analizując parametry stwardniałego zaczynu cementowego, należy się spodziewać obniżenia wartości wytrzymałości na ściskanie, wytrzymałości na zginanie, przyczepności do rur stalowych itp. Z uwagi na konieczność stosowania w recepturach zaczynów lekkich dodatków redukujących gęstość w niniejszej publikacji omówiono to zagadnienie na podstawie przeprowadzonych prac badawczych. W artykule przedstawiono wyniki badań zaczynów zawierających 4 różne dodatki (mikrosferę glinokrzemianową dotychczas stosowaną, mikrosferę glinokrzemianową nowej generacji CSF K, mikrosferę szklaną oraz perlit filtracyjny E100F). Dodatki lekkie stosowano w ilości 15% w stosunku do masy cementu. Przeprowadzono badania dla zaczynu kontrolnego (bez dodatków lekkich). Zaczyn ten zawierał w swoim składzie środki niezbędne do kontrolowania parametrów decydujących o efektywności uszczelniania otworu wiertniczego. Następnie receptura kontrolna była modyfikowana dodatkiem lekkich frakcji. Przeprowadzono badania laboratoryjne parametrów technologicznych zarówno świeżych, jak i stwardniałych zaczynów cementowych. Na podstawie uzyskanych wyników określono wpływ badanych lekkich dodatków na parametry świeżych i stwardniałych zaczynów cementowych.
Ocena kosztów produkcji wodoru z wykorzystaniem energii pochodzącej z instalacji fotowoltaicznej wybudowanej w Polsce
Authors:   Instytut Nafty i Gazu – Państwowy Instytut Badawczy, Filar Bogdan , Miziołek Mariusz ,   Instytut Nafty i Gazu – Państwowy Instytut Badawczy, Kwilosz Tadeusz ,   Instytut Nafty i Gazu - Państwowy Instytut Badawczy
Published: June 2022

W 2020 r. Komisja Europejska (KE) ogłosiła strategię wodorową spójną z założeniami Europejskiego Zielonego Ładu. Strategia zakłada ograniczenie wykorzystania paliw kopalnych do produkcji energii i zastępowanie ich energią odnawialną (OZE), produkowaną głównie przez farmy wiatrowe oraz solarne. Sumaryczna moc uruchomionych instalacji fotowoltaicznych (PV) w Polsce w listopadzie 2021 r. osiągnęła wartość 7,1 GW. Obecnie największą elektrownią fotowoltaiczną w Polsce jest elektrownia o mocy 70 MW wybudowana przez ZE PAK w Brudzewie. Nadwyżki energii pochodzącej z OZE mogłyby zostać wykorzystane do produkcji tzw. zielonego wodoru. W publikacji przedstawiono wyniki analizy, której celem było określenie szacunkowych kosztów produkcji wodoru przez elektrolizer zasilany energią pochodzącą z farmy fotowoltaicznej (PV). W przeprowadzonej analizie założono, że wodór będzie produkowany przez elektrolizer PEM o mocy 2,5 MW. W związku z tym, że ilość produkowanej energii jest zmienna w czasie, to ilość produkowanego wodoru obliczono dla instalacji o mocy zmieniającej się w zakresie 7–11 MW. Zakres minimalny wielkości instalacji był tak dobrany, aby w czerwcu (najlepszym miesiącu dla fotowoltaiki w Polsce) elektrolizer mógł pracować z całą mocą. Natomiast górny zakres mocy instalacji, wynoszący 11 MW, został określony w taki sposób, aby elektrolizer pracował z maksymalną mocą od marca do października. Obliczenia wykazały, że instalacja o mocy 7 MW pozwoli wyprodukować około 1,34 mln mn3 wodoru, podczas gdy instalacja o mocy 11 MW może wyprodukować około 1,7 mln mn3 wodoru. W dalszej kolejności obliczono nakłady inwestycyjne dla wszystkich wariantów budowy instalacji fotowoltaicznej. Koszt budowy instalacji o mocy 7–11 MW zmieniał się w przedziale 34,4–44,7 mln zł. Natomiast roczne koszty operacyjne eksploatacji instalacji o mocy 7–11 MW zmieniały się w przedziale 1,19–1,4 mln zł. W dalszej kolejności obliczono koszt wyprodukowania 1 mn3 wodoru, zakładając eksploatację całej instalacji przez 20 lat. Koszt produkcji 1 mn3 wodoru uzyskano dzieląc sumę zdyskontowanych kosztów inwestycyjnych i operacyjnych, uzyskaną w okresie 20 lat, przez sumę zdyskontowanej ilości wyprodukowanego wodoru. Obliczenia wykazały, że optymalna instalacja PV dla elektrolizera o mocy 2,5 MW posiada moc 9 MW. Koszt produkcji wodoru obliczony dla instalacji PV o mocy 9 MW wyniósł 3,17 zł/n3
Why Does Doxycycline Pose a Relatively Low Risk for Promotion of Clostridioides difficile Infection?
Authors: Xu Dongyan , Mana Thriveen , Cadnum Jennifer , Deshpande Abhishek , Afsari Faezeh , Sangwan Naseer , Donskey Curtis 
Published: June 2022

Background: Clinical studies suggest that doxycycline poses a low risk for promotion of Clostridioides difficileinfection, but the microbiologic explanation for this finding is unclear.
Methods: Mice treated with oral doxycycline, oral azithromycin, subcutaneous ceftriaxone, doxycycline plus ceftriaxone, or azithromycin plus ceftriaxone were challenged with 104 colony-forming units of 2 different C. difficilestrains on day 2 of 5 of treatment. The concentration of C. difficile was measured in stool 2 and 5 days after challenge. The impact of the treatments on the microbiota was assessed by sequencing.
Results: Doxycycline and azithromycin treatment did not promote colonization by either C. difficile strain in comparison to saline controls. Doxycycline treatment significantly reduced ceftriaxone-induced overgrowth of a C. difficile strain with doxycycline minimum-inhibitory concentration (MIC) of 0.06 µg/mL (P<0.01) but not a strain with doxycycline MIC of 48 µg/mL (P>0.05); azithromycin treatment did not reduce ceftriaxone-induced overgrowth of either strain. 16S rRNA amplicon sequencing revealed significantly lower bacterial diversity in the stool of ceftriaxone-treated mice, in comparison to doxycycline-treated and azithromycin-treated mice.
Conclusions: These findings suggest that doxycycline may have a low propensity to promote C. difficile colonization because it causes relatively limited alteration of the indigenous microbiota that provide colonization resistance and because it provides inhibitory activity against some C. difficile strains.
Autonomous Sensing Microsystem with H2S Compatible Package and Enhanced Buoyancy for Downhole Monitoring
Authors: Vellaluru Neeharika , Dutta Partha , Benken Alexander , Boero-Rollo Jean-Gregoire , Ordonez-Varela John-Richard , Gianchandani Yogesh 
Published: June 2022

Summary
We report an autonomous microsystem intended for deployment in harsh fluid environments. The microsystem incorporates pressure, temperature, and inertial sensors and Bluetooth Low Energy (BLE) communication electronics; power is supplied via secondary battery, recharged using Qi wireless power transfer. Sensors and electronics are incorporated within a circuit board measuring ø26.7 × 1.5 mm3 which is embedded in a package with volume &lt;25 cm3 and density &lt;1200 kg/m3. The small size and density permit enhanced buoyancy control and deployment through narrow apertures. The package is comprised of a fluorocarbon elastomer VitonTM shell, which provides the necessary mechanical and chemical protection, and is filled with low bulk density cenospheres, which reduce the overall density while still allowing pressure to be transferred to the board-mounted sensor. This integration approach allows reclamation and repackaging of the electronics for rapid evaluation in a variety of harsh environments. Microsystems were tested in laboratory conditions at pressures up to 41.5 MPa and temperatures up to the battery limit of 85°C while successfully recording data for &gt;96 hours. The VitonTM packaging was tested in H2S, diesel fuel, and 15% brine. Microsystems were then successfully evaluated in field deployment conditions in an oilwell to a depth of 1290 m, recording pressure, temperature, and inertial data.
Elevated circulating levels of phenylacetylglutamine in stroke patients with T2D are linked to specific gut microbiota
Authors: Wei Minping , Huang Qin , Yu Fang , Ying Yuanlin , Luo Yunfang , Feng Xianjing , Liao Di , Zhao Tingting , Huang Qing , Feng Jie , xia jian 
Published: June 2022

Abstract
Objective
Type 2 diabetes (T2D) aggravates the injury of ischemic stroke (IS). The alterations of gut microbiota and its metabolite phenylacetylglutamine (PAGln) levels in stroke patients with T2D remain unclear. Therefore, our study aimed to explore the differences in gut microbiota and its metabolite PAGln between IS patients with and without T2D.
Methods
In our study, 35 IS with T2D (IS-T2D group), 50 IS patients without T2D (IS-NT2D group), and 29 healthy controls (HC group) were recruited. Fecal samples were collected and analyzed using high-throughput sequencing of 16S rRNA genes, and plasma samples were subjected to targeted metabolomics to detect metabolite PAGln. Plasma PAGln levels of rats with transplantation of fecal microbes from patients were assessed.
Results
Our results showed that the plasma PAGln levels in IS-T2D patients were significantly higher than those in IS-NT2D patients. Correlation analysis showed that plasma PAGln levels were significantly correlated with the relative abundance of Enterobacteriaceae, Verrucomicrobiota, and Klebsiella, which were enriched in IS-T2D patients. Further studies demonstrated that plasma PAGln levels were positively correlated with the concentration of neutrophil extracellular traps (NETs), and NETs levels were increased in a dose-dependent manner according to PAGln levels. Moreover, the rats transplanted with fecal microbes from IS-T2D patients developed more severe brain injury and higher plasma PAGln levels compared to the rats transplanted with fecal microbes from IS-NT2D patients.
Conclusions
Our results suggest that T2D may contribute to aggravation in stroke patients via NETs, mediated in part by gut microbiota and its metabolite PAGln.
Multi-UAV Factor Graph Co-location Algorithm
Authors: Zhang Yuexia , Jia Pengfei 
Published: June 2022

Abstract
To tackle the difficulty and high cost of UAV positioning in a disaster environment, this study proposes a multi-UAV coordinated positioning algorithm based on a factor graph (MUAV-FGC). A factor graph model is designed for coordinated positioning of the master-slave UAVs. In the positioning process, the influence of the speed and heading errors of the UAV on the positioning accuracy was analyzed, and the expected and variance values of the variables were used as the information transmitted between the factors. The error of the cooperative positioning algorithm was derived based on the factor graph. The coordinated positioning of multiple drones and the positioning accuracy improved. The simulation results show that, compared with the traditional extended Kalman filter (EKF) algorithm, the proposed MUAV-FGC positioning algorithm reduces the mean positioning and root mean square error by approximately 18.86% and 17.54%, respectively, thus proving its effectiveness.
Gamification for behavior change: a scientometric review
Authors: Bassanelli Simone , Vasta Nicola , Bucchiarone Antonio , Marconi Annapaola 
Published: June 2022

Abstract
Gamification, which refers to the use of game design elements in non-game contexts, provides similar experiences and motivations as games do; this makes gamification a useful approach to promote positive behaviors. As a useful tool for keeping users motivated, engaged and active, there is a wide interest in adopting gamification solutions for supporting and promoting positive behaviors and behavior change (e.g. quit smoking, ecological behaviors, food choices, civic engagement, mental healthcare, sustainability, etc.). In this study, we use the CiteSpace software to examine 984 publications and their 46,609 unique references on gamification applied for behavior change. The corpus of studies was downloaded from the Scopus database and refers to studies published between 2011 and the beginning of 2022. Several methods were used to analyze these data: (1) document co-citation analysis (DCA) was performed to identify the pivotal researches and the research areas; (2) author co-citation analysis (ACA) was performed to identify the main authors; (3) and keyword analysis was performed to detect the most influential keywords and their change over time. The results of the analysis provide an overview of the influential documents, authors and keywords that have given shape to the literature of the field, and how it has evolved, showing an initial interest in motivational and persuasion techniques, and in the gamification design, and subsequently in the development of more rigorous methodologies for both design and use. As the first scientometric review of gamification applied to behavior change, this study will be of interest to junior and senior researchers, graduate students, and professors seeking to identify research trends, topics, major publications, and influential scholars.
Integrating Vernier Spectrum With Fano Resonance for High Sensitivity of All-optical Sensor
Authors: Aman Mohammad Amirul Hairol , Noorden Ahmad Fakhrurrazi Ahmad , Fajri Faris Azim Ahmad , Kadir Muhammad Zamzuri Abdul , Bahari Iskandar , Danial Wan Hazman , Daud Suzairi , Bahadoran Mahdi 
Published: June 2022

Abstract
Vernier and Fano resonances are promising approaches for enhancing the sensitivity of an alloptical sensor. A theoretical analysis was performed to integrate a Fano-like resonance shape with a Vernier resonance by considering the presence of partial reflective end facets at a double microring resonator waveguide. The system was developed based on scattering matrix and optical transfer function. The double and all-pass racetrack microring configurations were compared with and without the end facet at the waveguide to analyze the dynamic change of the output resonance spectrum. The spectrum were analyzed based on the free spectral range and resonance pattern. The resonator systems were applied to refractive index-based sensing protocol, which was operated by a shift of resonance wavelength with a change of refractive index. The sensitivity was optimized by varying the configuration parameters such as the radius of the ring, the distance between end facet, and the coupling coefficients. Integrating Vernier spectrum with Fano resonance improved the sensitivity for all-pass racetrack configuration by 5.16% and the sensitivity for double racetrack configuration by 6.31%. The recorded limit of detection (LOD) of double racetrack was 3.30 × 10 -5 .
Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides
Authors: Maranha Ana , Costa Mafalda , Ripoll-Rozada Jorge , Manso Jose , Miranda Vanessa , Mendes Vera , Manadas Bruno , Macedo-Ribeiro Sandra , Ventura Rita , Pereira Pedro José Barbosa , Empadinhas Nuno 
Published: June 2022

Abstract
The steep increase in nontuberculous mycobacteria (NTM) infections makes understanding their unique physiology an urgent health priority. NTM synthesize two polysaccharides proposed to modulate fatty acid metabolism: the ubiquitous 6-O-methylglucose lipopolysaccharide, and the 3-O-methylmannose polysaccharide (MMP) only detected in rapidly growing mycobacteria. The recent identification of a unique MMP methyltransferase implicated the adjacent genes in MMP biosynthesis. We report a wide distribution of this gene cluster in NTM, including slowly growing mycobacteria, which we reveal to produce MMP. Using a combination of MMP purification and chemoenzymatic syntheses of intermediates, we identified the biosynthetic mechanism of MMP, relying on two enzymes that we characterized biochemically and structurally: a unique α–endomannosidade that hydrolyses MMP into defined-sized mannoligosaccharides that prime the elongation of new daughter MMP chains by a rare α-(1>4)-mannosyltransferase. Therefore, MMP biogenesis occurs through a partially conservative replication mechanism, and disruption of the mechanism affected mycobacterial growth rate at low temperature.