bluuebunny/crossref_metadata_2025 huggingface dataset:
Advanced Molecular-Genetic Methods and Prospects for Their Application for the Indication and Identification of Yersinia pestis Strains
Authors: Nikiforov K. A.
Published: February 2023

The review provides an analysis of the literature data on the use of various modern molecular-genetic methods for the indication and identification of Yersinia pestis strains with different properties and degree of virulence, which is caused by the diverse natural conditions in which they circulate. The methods are also considered from the perspective of their promising application at three levels (territorial, regional and federal) of the system for laboratory diagnosis of infectious diseases at the premises of Rospotrebnadzor organizations to solve the problem of maintaining the sanitary and epidemiological well-being of the country’s population. The main groups of methods considered are as follows: based on the analysis of the lengths of restriction fragments (ribo- and IS-typing, pulse gel electrophoresis); based on the analysis of specific fragments (DFR typing, VNTR typing); based on sequencing (MLST, CRISPR analysis, SNP analysis); PCR methods (including IPCR, SPA); isothermal amplification methods (LAMP, HDA, RPA, SEA, PCA, SHERLOCK); DNA-microarray; methods using aptamer technology; bio- and nano-sensors; DNA origami; methods based on neural networks. We can conclude that the rapid development of molecular diagnostics and genetics is aimed at increasing efficiency, multi-factorial approaches and simplifying the application of techniques with no need for expensive equipment and highly qualified personnel for analysis. At all levels of the system for laboratory diagnosis of infectious diseases at the Rospotrebnadzor organizations, it is possible to use methods based on PCR, isothermal amplification, SHERLOCK, biosensors, and small-sized sequencing devices. At the territorial level, at plague control stations, the use of immuno-PCR and SPA for the indication of Y. pestis is viable. At the regional level, introduction of the technologies based on the use of aptamers and DNA chips looks promising. For the federal level, the use of DNA origami methods and new technologies of whole genome sequencing is a prospect within the framework of advanced identification, molecular typing and sequencing of the genomes of plague agent strains.
International Cooperation of Kazakhstan in the Prevention of Particularly Dangerous Infections
Authors: Erubaev T. K. , Kovaleva G. G. , Meka-Mechenko T. V. , Abdel Z. Zh. , Sutyagin V. V. , Kislitsyn Yu. V. , Belyaev A. I. , Kim I. B.
Published: February 2023

The dependence of the incidence of various nosologies on the epidemic situation in neighboring countries has been a feature of the epidemic process in recent years. In this regard, it is of particular importance to carry out joint anti-epidemic and preventive measures in border areas in order to prevent the importation of dangerous infections into the territory of neighboring states. The aim of the work was to analyze the results of international cooperation in the prevention of particularly dangerous infections. Presented are the areas of cooperation and outcomes of joint research activities. Measures for cooperation between the relevant institutions of the Ministry of Health of the Republic of Kazakhstan and the Rospotrebnadzor on the operational exchange of information in case of emergencies, joint research work on the monitoring of particularly dangerous and other natural-focal infectious diseases in the border areas, joint seminars, scientific and practical conferences on the introduction of modern methods of laboratory diagnostics into practice, internships on the exchange of experience in epizootiological survey in foci of particularly dangerous infections are described in the paper. Examples of Russian-Kazakh cooperation are provided. The results of a joint epizootiological survey of the territory of the Kazakh part of the Altai Mountains are presented. On a global scale, cases of plague and other particularly dangerous infections in any geographic region can constitute international public health emergencies and this type of threat requires international cooperation.
Long-Term Persistence of Yersinia pestis in Association with Acanthamoeba castellanii in Experiment
Authors: Makashova M. A. , Oglodin E. G. , Kukleva L. M. , Sharapova N. A. , Naryshkina E. A. , Germanchuk V. G. , Eroshenko G. A. , Kutyrev V. V.
Published: February 2023

The aim of the study was to test the feasibility of long-term survival and preservation of the properties of Yersinia pestis in association with soil amoeba Acanthamoeba castellanii. Materials and methods. Y. pestis strains and acanthamoeba isolated in the common area of the Gorno-Altai high-mountain plague focus were used for the study. The systematic affiliation of protozoa was determined through analyzing the 18S rRNA gene fragment sequencing data, followed by alignment with amoeba sequences from the NCBI GenBank database. A fluorescent Y. pestis strain was obtained by electroporation using the pTurboGFP-B plasmid. Co-cultivation was carried out in saline buffer in the absence of nutrients for the cells of plague pathogen. The influence of co-culturing with protozoa on Y. pestis properties was determined using microbiological, biological, and molecular-genetic methods. Results and discussion. The cell viability preservation for 22 months of the experiment in Y. pestis strain belonging to the main subspecies of the antique biovar, the 4.ANT phylogenetic line in co-culture with amoeba cells in the absence of additional nutrients has been established. Co-cultivation with amoebae did not lead to a change in the cultural, morphological, genetic and virulent properties of the plague pathogen strain. The data obtained confirm the possibility of using Acanthamoeba castellanii by the plague microbe to persist in soil biocenoses and open up the prospect of studying the mechanisms of plague pathogen surviving during extended inter-epizootic periods.
Selection Of Tomato Fruits by Color and Size Based on Arduino
Authors: Alamsah Faisal Baharudin , Syahrorini Syamsudduha
Published: February 2023

Human life relies heavily on agriculture. To fulfill the needs of human life every day, the process of planting, land, and harvest is fast. Short time and limited power are challenges that farmers should face. Similarly, the problem faced by tomato farmers is that they should be sorting tomatoes based on their level of maturity. The tomato farmers should be sorted by maturity level. The issue is a system of tomato partitioning based on maturity level. The purpose of this research is to design a tool to build the maturity of tomato fruit using Arduino. The tools used are color sensors TCS3200, HC-SR04 Ultrasonic, servo motors, and DC motors. The sorting system is designed using the principle of detecting red green blue (RGB) values of tomato fruit using color sensors. After that, the next system streams the tomatoes to the container according to the level of the decline by opening and closing the portal that is connected to the servo motor. The Portal leads to a ripe container if the fruit is ripe and vice versa if raw fruit leads to a raw container. Results obtained that the sorting tool is able to give a success rate of 90% in distinguishing ripe tomatoes ready to harvest (basil) from raw fruit (green).
Evaluation of Unmanned Aerial Vehicle (UAV) Control Range System using Lora-Based Communication System using Path Loss
Authors: Hariyadi Mokhammad Amin , Fadila Juniardi Nur
Published: February 2023

AbstractThis research aims to evaluate the communication system between the ground control system and the Unmanned Aerial Vehicle (UAV) using the Lora communication system based on its Path Loss data. Lora itself is a 433 MHz-based communication system used for very long-distance communication. As we know, today UAV market used a 2.4 GHz-based communication system because it is cheaper than using 433MHz. But, although it is cheaper than 433MHz, a lot of devices used the same frequency like WiFi systems and another wireless electrical components. That condition creates a lot of signal interference so communication between the ground control system and the UAV becomes shorter. 433MHz is not a new technology for a communication system, this frequency is usually used for radio news and long-range data logging. It is rarely used 433 MHz frequency for transmitting a big package of data because 433 MHz frequency has a slow data transfer rate but has a long data transfer distance. From testing, we got an improvement of control range more than twice with Lo-Ra 433 MHz compared to the 2.4 GHz module.Keywords: Control System, Lo-Ra, Long Range System, Radio Frequency, Transmission system, UAV Abstrak[Evaluasi Sistem Jarak Kendali Kendaraan Udara Tanpa Awak (UAV) Menggunakan Sistem Komunikasi Berbasis Lora Menggunakan Path Loss] Penelitian ini bertujuan untuk mengevaluasi sistem komunikasi antara ground control system dengan Unmanned Aerial Vehicle (UAV) menggunakan sistem komunikasi Lora berdasarkan data Path Loss-nya. Lora sendiri merupakan sistem komunikasi berbasis 433 MHz yang digunakan untuk komunikasi jarak jauh. Seperti yang kita ketahui, pasar UAV saat ini menggunakan sistem komunikasi berbasis 2,4 GHz karena lebih murah daripada menggunakan 433MHz. Tapi, meski lebih murah dari 433MHz, banyak perangkat yang menggunakan frekuensi yang sama seperti sistem WiFi dan komponen listrik nirkabel lainnya. Kondisi tersebut menimbulkan banyak gangguan sinyal sehingga komunikasi antara ground control system dan UAV menjadi lebih singkat. 433MHz bukanlah teknologi baru untuk sistem komunikasi, frekuensi ini biasanya digunakan untuk berita radio dan data logging jarak jauh. Frekuensi 433 MHz jarang digunakan untuk transmisi paket data yang besar karena frekuensi 433 MHz memiliki kecepatan transfer data yang lambat namun memiliki jarak transfer data yang jauh. Dari pengujian, kami mendapatkan peningkatan jangkauan kendali lebih dari dua kali lipat dengan Lo-Ra 433 MHz dibandingkan dengan modul 2,4 GHz.Kata Kunci: Sistem Kontrol, Lo-Ra, Sistem Jarak Jauh, Frekuensi Radio, Sistem Trnsmisi, UAV
A comparative study on the occurrence, risk factors, and genetic characteristics of Listeria species recovered from cattle farms, and beef abattoirs in Gauteng Province, South Africa
Authors: Gana James , Gcebe Nomakorinta , Moerane Rebone , Ngoshe Yusuf , Tshuma Takula , Moabelo Khomotso , Adesiyun Abiodun Adewale
Published: February 2023

These cross-sectional reported the occurrence, risk factors, and genetic characteristics of Listeria species recovered from cattle farms and beef abattoirs in Gauteng Province, South Africa. A total of 328 samples collected from 23 cattle farms and 262 samples from 8 beef abattoirs were processed using standard bacteriological and molecular methods to detect Listeria spp. The factors associated with the prevalence of Listeria spp. were investigated, and multiplex polymerase chain reaction (mPCR) was used to determine Listeria species, the pathogenic serogroups, and carriage of eight virulence-associated genes by Listeria monocytogenes. The overall prevalence of Listeria spp. in cattle farms was 14.6%, comprising Listeria innocua (11.3%), Listeria monocytogenes (3.4%), Listeria welshimeri (0.0%) compared with 11.1%, comprising Listeria innocua (5.7%), Listeria monocytogenes (4.6%), Listeria welshimeri (0.8%) for beef abattoirs. Of the three variables (area, type of farm/abattoir, and sample type) investigated, only the sample types at abattoirs had a significant (P < 0.001) effect on the prevalence of L. innocua and L. welshimeri. The frequency of distribution of the serogroups based on 11 L. monocytogenes isolated from farms was 72.7% and 27.3% for the serogroup 1/2a-3a and 4b-4d-4e, respectively, while for the 12 L. monocytogenes isolates recovered from abattoirs, it was 25%, 8.3%, 50% and 16.7% for the serogroup 1/2a-3a, 1/2b-3b, 1/2c-3c, and 4b-4d-4e respectively (P < 0.05). All (100.0%) isolates of L. monocytogenes from the farms and abattoirs were positive for seven virulence genes (hlyA, inlB, plcA, iap, inlA, inlC, and inlJ). The clinical and food safety significance of the findings cannot be ignored.
DLEU2 promotes proliferation and glycolysis of oral squamous cell carcinoma by regulating SIX1
Authors: CHEN DAN , XIANG LI
Published: February 2023

Objective
To look into the physiological functions of the lncRNA DLEU2 in the tumorigenesis of oral squamous cell carcinoma (OSCC), as well as whether it plays a role in the emergence and advancement of OSCC by governing SIX1.
Methods
The inhibitory role of DLEU2 on the proliferation of SCC-15 cells was examined by CCK8. Flow cytometry was used to study the influence of DLEU2 inhibitory activity on SCC-15 apoptotic cell death. In addition, trans-well assays were used to analyze the influence of DLEU2 suppression on SCC-15 cell differentiation and proliferation.
Results
The DLEU2 expression in OSCC cancerous specimens was considerably stronger than the corresponding healthy tissues; and DLEU2 was elevated in all four OSCC cells. The immunohistochemistry data also showed the level of DLEU2 was also greatly elevated in OSCC tissues than healthy specimens. After transfection of si-DLEU2, the viability of SCC-15 cells decreased significantly. Additionally, the number of apoptosis cells transfected with si-DLEU2 was significantly higher than controls. Using trans-well invasion assay, the data suggested the number of invasive cells formed by blocking DLEU2 of SCC-15 and SCC-25 cells was markerly lower than the controls. The results of ECAE and OCR also showed that DLEU2 could promote the glycolysis of OSCC cells while inhibit the oxidative phosphorylation progress of OSCC cells. Our subsequent analysis of the main enzymes affecting glycolysis, GLUT1 and HK2, showed that blocking expression of DLEU2 is able to obviously reduce the GLUT1 level, but not HK2. Subsequent ChIP experiments confirmed that SIX1 could bind to the promoter of GLUT1, and knocking down DLEU2 could reduce the binding ability of SIX1 to the promoter of GLUT1. Finally, we utilized luciferase assays to confirm that knockdown of DLEU2 expression could directly reduce GLUT1 transcript levels. The results of ECAR and OCR experiments also showed that overexpression of SIX1 could reverse the decreased glycolysis of OSCC cells brought down by knockdown of DLEU2.
Conclusion
DLEU2 is essential for OSCC tumorigenesis, migratory and glycogenolysis. The DLEU2/SIX1 role is implicated in OSCC cell invasion and aerobic glycolysis.
Residual stress superposition in milling process of thin-walled parts and comprehensive deformation control method
Authors: Shi Zhemin , Li Beizhi , Sun Zhihong
Published: February 2023

The processing deformation of thin-walled parts is difficult to control under the traditional process method because of the small rigidity of the parts and the large amount of removal. Simulation research of various process parameter combinations and engineering test are carried out for the typical thin-walled parts with 2mm wall thickness and diameter-thickness ratio more than 850 to solve the problem of deformation. Based on the umbrella-shaped special tool of YG8 tungsten steel, the influence of process parameters on the important indexes and distribution law of residual stress of thin-walled structure parts were studied. Residual stress superposition mechanism of process parameter combinations of semi-precision milling and fine milling are revealed. A process optimization method considering multiple deformation control objective of thin-walled parts is proposed, in order to improve residual stress and its distribution, reduce cutting deformation and the long-term stability of the thin-walled structure. The relative cross-section size, thickness, roundness and concentricity of thin-walled parts with conical surface were measured by roundness meter and CMM. Result reveals that the use of high-speed milling and the optimized combination of process parameters can effectively control residual stress and deformation.
Optimization on the Performance of Olea europaea (Olive Oil) Based Blended Esters with Butylated hydroxyanisole and Butylated hydroxytoluene using Response Surface Methodology - Central Composite Design: An Experimental Approach for Ecofriendly Biofuels
Authors: Thangaraj Hariharasudhan , David Prince Winston , Balachandran Gurukarthik Babu , Sivasekar Gowthama Kannan
Published: February 2023

In this paper, an effort is made to develop the alternate insulating liquid for the power transformer applications. With that aim, the edible natural esters such as refined Olea europaea (olive oil), rice bran oil, soya bean oil, sunflower oil and corn oil are investigated as the suitable replacement for the mineral oil (MO) used in the transformer. Also, the blended natural esters are made with olive oil and other natural esters for further analysis with the above aspiration for better insulating medium. The effect of antioxidants inclusion is also studied for analyzing the performance enrichment of blended natural esters. Butylated hydroxyanisole (BHA) and Butylated hydroxytoluene (BHT) were chosen as antioxidants for this work. In this study, we aim to investigate the role of key input factors [A-Speed, B-Time, and C-Temperature] on the output response [Y-Breakdown Voltage]. It was determined that the optimal condition for the [Y] is at [A] of 699.91 rpm, [B] of 49.95 min, and [C] of 88.75 ℃. In order to ensure natural esters are desirable, some critical properties are measured, such as Breakdown Voltage (BDV), viscosity, fire point (FeP), and flash point (FhP). In accordance with international standards such as American Society for Testing and Materials (ASTM) and International Electrotechnical Commission (IEC), measurements are conducted. From the results, it is observed that the natural esters and blended natural esters have the ability to use in the transformer as alternate insulating medium and also the antioxidants have the significant effect on the properties of natural ester combinations.
Providing a method for security analysis and evaluation of infrastructure services in cloud computing
Authors: Morshedi Roya , Matinkhah S Mojtaba
Published: February 2023

Today, cloud security is necessary to improve the service allocation, continuity of operations, storage management, information security and. In this way, analyzing the server in question and then defining a formal model by applying the security features is essential. In this paper, infrastructure services are described as services in cloud computing and each vulnerability is investigated. According to Petri's modeling tools, a new approach to assessing the security of infrastructure systems as a service is provided and analyzed. With the help of this method, the security of infrastructure systems as a service in cloud computing can be compared and evaluated. Consequently, using Petri's modeling tool, one of the most famous commercial systems of the infrastructure is modeled as a service called OpenStack, and the behavior of the attacks is evaluated. Applying this method to the OpenStack system demonstrates that our work is safe and that researchers, designers and cloud service providers are expected to make significant gains in delivering results.
LINC01137 facilitates pancreatic cancer stemness via the miR-7155-5p/KLF12/AKT axis
Authors: Peng Chenghong , Li Kexian , Feng Zengyu , Qin Kai , Luo Jiaxin , Ma Yang , Zhao Shiwei , Chen Peng , Lin Jiewei , Jiang Yongsheng , Han Lijie , Cao Yizhi , Shi Minmin , Chen Hao , Wang Jiancheng , Jiang L
Published: February 2023

Pancreatic cancer, of which pancreatic ductal adenocarcinoma (PDAC) is one of the most prevalent type, is one of the most malignant tumors, with a 5-year survival rate of about 10%. Pancreatic cancer stem cells play pivotal roles in chemoresistance and recurrence. Long non-coding RNAs (lncRNAs) have been identified as key regulators of the biological progression of various cancers. Recently, lncRNAs were found to be associated with cancer stem cells, which are related to chemoresistance. LINC01137 was predicted associated with pancreatic cancer stem cells, however, its function and underlying mechanisms in pancreatic cancer remain unclear. In this study, we found that LINC01137 was upregulated in pancreatic cancer tissues and cell lines. Its high expression correlated with advanced pathological stages and poor prognosis. Induction of LINC01137 expression boosted pancreatic cancer stemness, chemoresistance, and proliferation. Mechanistically, LINC01137 exerted its biological function by binding to miR-7155-5p to activate the KLF12/PI3K/AKT pathway. KLF12 also promoted LINC01137 expression. LINC01137 and KLF12 were involved in promoting PDAC tumorigenesis. Our results suggested that LINC01137 functions as an oncogene in pancreatic cancer and identified its post-transcriptional regulatory mechanisms, which may contribute to targeted therapy for pancreatic cancer.
Chiral Dirac fermion in a collinear antiferromagnet
Authors: Zhang Ao , Deng Ke , Sheng Jieming , Liu Pengfei , Kumar Shiv , Shimada Kenya , Jiang Zhicheng , Liu Zhengtai , Shen Dawei , Li Jiayu , Ren Jun , Wang Le , Zhou Liang , Ishikawa Yoshihisa , Zhang Qiang , McIntyre Garry , Yu Dehong , Liu Enke , Wu Liusuo , Chen Chaoyu , Liu Qihang
Published: February 2023

The Dirac equation combines the two cornerstones of modern physics—quantum mechanics and relativity. There are several manifestations of the Dirac equation in condensed matter systems, such as the quasiparticle dispersion in graphene1, topological insulators2-4, Dirac semimetals (DSMs)5-9, Weyl semimetals10-12, and d-wave high-temperature superconductors13. In a DSM, the massless Dirac fermion has zero chirality, leading to surface states connected adiabatically to a topologically trivial surface state as well as vanishing anomalous Hall effect (AHE). Recently, it is predicted that in the nonrelativistic limit of certain antiferromagnets, there exists a type of chiral “Dirac-like” fermion, whose dispersion manifests four-fold degenerate crossing points formed by doubly degenerate linear bands, with topologically protected Fermi arcs14. Such unconventional chiral fermion, protected by a hidden SU(2) symmetry in the hierarchy of an enhanced crystallographic group, namely spin space group15-17, is not experimentally verified yet. Here, by combining neutron diffraction, angle-resolved photoemission spectroscopy and first-principles calculations, we reveal the existence of the Fermi-arc surface states induced by chiral Dirac-like fermions in collinear antiferromagnet CoNb3S6, which caught great interest due to its surprisingly large AHE18-23. Our transport measurements and theoretical calculations provide a scenario that large Berry curvature embedded in the chiral fermions and weak symmetry breaking are responsible for the emergent AHE. Our work evidences the existence of chiral Dirac-like fermion in CoNb3S6, paving an avenue for exploring new emergent phenomena in quantum materials with unconventional quasiparticle excitations.
Dynamic model based adaptive sliding mode trajectory tracking control of pendulum-driven spherical mobile robot
Authors: Tian Xinyang , Xiang Hongwei , Yang Yanbo , Yan Meng , Zhan Qiang
Published: February 2023

Spherical mobile robot is a special non-chained nonholonomic system with underactuation and strong coupling, which make its trajectory tracking control very difficult and complex to realize. Precise trajectory tracking control depends on concise and accurate dynamic model. However, the current researches of trajectory tracking control rarely considered the influence of nonlinear factors and uncertain disturbances of spherical robot. In order to achieve strong robustness and anti-interference of trajectory tracking control of spherical robot, taking spherical mobile robot driven by a two-degrees of freedom pendulum as the research object, its complete dynamic model was established with Boltzmann-Hamel equation and simplified to obtain the one easy to control and with the key motion characteristics. Aiming at the modeling uncertainty of the spherical robot and the environment disturbances that may be encountered during movements, an adaptive sliding mode trajectory tracking control based on double power reaching law was proposed and proved to be stable by Lyapunov theorem. The effectiveness and robustness of the proposed control law are verified through simulations.
Telecom-band photodetection in MoS2/Au heterostructures via sub-band light absorption
Authors: Hong Chengyun , Oh Saejin , Dat Vu Khac , Low Tony , Oh Sang-Hyun , Kim Ji-Hee
Published: February 2023

Transition metal dichalcogenide (TMD) layered semiconductors possess immense potential in the design of photonic, electronic, optoelectronic, and sensor devices. However, sub-bandgap light absorption of TMD in the range from near-infrared (NIR) to short-wavelength infrared (SWIR) is insufficient for applications beyond the bandgap limit. Herein, we report that the sub-band photoresponse of MoS2 /Au heterostructures can be robustly modulated by the electrode fabrication method employed. We observed up to 60% sub-bandgap absorption in the MoS2 /Au heterostructure, which includes the hybridized interface, where the Au layer was applied via sputter deposition. The greatly enhanced absorption of sub-bandgap light is due to the planar cavity formed by MoS2 and Au; as such, the absorption spectrum can be tuned by altering the thickness of the MoS2 layer. Photocurrent in the SWIR wavelength range increases due to increased SWIR absorption, which means that broad wavelength detection from visible toward SWIR is possible. We also achieved rapid photoresponse (~ 164 µs) and high responsivity (17 mA W− 1) at an excitation wavelength of 1,550 nm. Our findings here demonstrate a facile method for optical property modulation using metal electrode engineering and for realizing SWIR photodetection in wide-bandgap 2D materials.
Malnutrition and visceral obesity predict adverse short-term and long-term outcomes in patients undergoing proctectomy for rectal cancer
Authors: Zhou Chong-Jun , Lin Yi , Liu Jie-Yu , Wang Zhong-Lin , Chen Xi-Yi , Zheng Chen-Guo
Published: February 2023

Background
There was no study explored the relationship of malnutrition and visceral obesity in rectal cancer patients following radical proctectomy. Therefore, we aimed to investigate the value of malnutrition and visceral obesity in patients with rectal cancer.
Methods
This study included patients with rectal cancer who underwent proctectomy. Malnutrition was defined by Global Leadership Initiative on Malnutrition (GLIM). Visceral obesity was measured by computed tomography (CT). Patients were classified into four groups according to the presence of malnutrition or visceral obesity. Univariate and multivariate logistic regression analyses were performed to evaluate the risk factors for postoperative complications. Univariate and multivariate cox regression analyses were performed to evaluate the risk factors for overall survival (OS). Kaplan-Meier survival curves and log-rank tests were performed by four groups in patients with rectal cancer.
Results
This study enrolled 624 patients. 204 (32.7%) patients in the well-nourished non-visceral obesity (WN) group, 264 (42.3%) patients in the well-nourished visceral obesity (WO) group, 114 (18.3%) patients in the malnourished non-visceral obesity (MN) group, and 42 (6.7%) patients in the malnourished visceral obesity (MO) group. In the multivariate cox regression analysis, Charlson comorbidity index (CCI), MN and MO were associated with postoperative complications. In the multivariate cox regression analysis, age, American Society of Anesthesiologists (ASA), tumor differentiation, tumor node metastasis (TNM), and MO were associated with worse OS.
Conclusion
This study demonstrated that the MO group had the higher postoperative complication and mortality rate and was a good indicator of poor prognosis in patients with rectal cancer.
Femtosecond conformational changes in a photolyase guide
long-range electron transfer as resolved by serial crystallography
Authors: Cellini Andrea , Shankar Madan Kumar , Nimmrich Amke , Mutisya Jennifer , Furrer Antonia , Beale Emma , Carrillo Melissa , Malla Tek Narsingh , Maj Piotr , Vrhovac Lidija , Dworkowskic Florian , Cirelli Claudio , Johnson Philip , Ozerov Dmitry , Bacellar Camila , Standfuss Jörg , Schmidt Marius , Weinert Tobias , Ihalainen Janne , Wahlgren Weixiao , Westenhoff Sebastian
Published: February 2023

Charge transfer reactions in proteins are fundamentally important for life, but it is currently not clear how protein structural dynamics control these electron transfer reactions. Photolyases/cryptochromes, which repair DNA and signal in all kingdoms of life, have a paradigm electron transfer cascade. Here, photoreduction of the flavin cofactor initiates charge transfer along a chain of four conserved tryptophans. We report femtosecond X-ray crystallographic snap-shots for the Drosophila melanogaster (6-4) photolyase, revealing protein structural changes while electron transfer occurs. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at key residue asparagine 403, at a conserved salt bridge, and by rearrangements of nearby water molecules. Along the tryptophan cascade, we detect charge-induced protein structural changes close to the second tryptophan from 1 ps to 20 ps, thereby identifying methionine 408 as an active participant in the redox chain, and from 300 ps around the fourth tryptophan. The data reveal that the protein undergoes highly directed and carefully timed adaptations of its structure to facilitate electron transfer. This suggests that evolution has optimized fast protein fluctuations for optimal function.
A case of primary osteosarcoma of the penis arising from Paget’s disease: a rare diagnosis
Authors: Lang A.J.
Published: February 2023

A 35-year-old male with primary penile osteosarcoma which was extraaxial is presented in
this case report and literature review. This very rare diagnosis is infrequently seen in the
literature and our case highlights a case which was deemed to have arisen from a Paget’s
disease lesion with histological and immunohistochemical findings and a scoping search of
the literature provided.
STAT3-CD163 crosstalk exhibits promising biomarkers for a progressive Ischemic cardiomyopathy; integrative computational and gene expression profiling based on GEO datasets
Authors: Mohareb Mina Wageh , Kariem Mohammed Abdelghaney , Tohamy Aly , Gamal Noha M. , Mosaad Rehab M. , Esmaiel Nora N. , Fayez Alaaeldin
Published: February 2023

Background:Ischemic heart diseaseis one of the heaviest health-related burdens worldwide.We aimed to identify the common hub mRNA and pathways that are involved in pathological progression of ischemic cardiomyopathy(ICM). Methods:To explore potential differentially expressed genes (DEGs) of all ischemic heart disease stages, we used chipster and GEO2R tools to analyze of retrieved eight high throughput RNA datasets obtained from GEO database. Gene Ontology functional annotation and Pathways enrichment analyses were used to obtain the common functional enriched DEGs which were visualized in protein–protein interactions (PPI) network to explore the hub mRNA according to the interaction scores. Validation qRT-PCR was carried out for blood and cardiac biopsies compared with controls to validate the determined four hub mRNAs and subsequently reviewed inside comprehensive published meta-analysis database. The validated mRNAs were visualized in two interaction modules. Finally screening of approved drugs was applied.
Results: 15 common DEGs with p value ≤ 0.01 were identified and carbohydrate &amino acids metabolism and inflammatory responses were significantly enriched. STAT3, CEBPD, GLUL and CD163 were hub enriched mRNAs with interaction score ≥ 0.50. Our qRT-PCR analysis showed increased expression of STAT3 over all patients groups and CD163 mainly in cardiac samples with remarked ascending manner. Interaction modules showed co-regulators supporting high STAT3-CD163 connectivity providing potential role of STAT3-CD163 crosstalk mediated inflammatory responses in ICM progression. We determined two reported drugs targeting STAT3.
Conclusion:Post analysis of the used GEO datasets and qRT-PCR data pointed that STAT3-CD163 crosstalk was potential biomarkers for ICM progression.
Clinical trial registration: www.clinicaltrials.gov, Identifier: NCT05508269
Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila
Authors: Singh Badri Nath , Tran Hiep , Kramer Joseph , Kirishenko Elmira , Changela Neha , Wang Fei , Feng Yaping , Kumar Dibyendu , Tu Min , Lan Jie , Bizet Martin , Fuks François , Steward Ruth
Published: February 2023

Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases enzymes catalyzing the transition of 5mC to 5hmC in DNA and have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila because Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by determining Tet DNA-binding sites throughout the genome and by mapping the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC-modified sites can be found along the entire transcript and are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are frequently involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and are sensitized to reduced levels of slit. Both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs, primarily in developing nerve cells.
Endometrial cancer PDX-derived organoids (PDXOs) and PDXs with FGFR2c isoform expression are sensitive to FGFR inhibition.
Authors: Sengal Asmerom , Bonazzi Vanessa , Smith Deborah , Moiola Cristian , Lourie Rohan , Rogers Rebecca , Colas Eva , Gil-Moreno Antonio , Frentzas Sophia , Chetty Naven , Perrin Lewis , Pollock Pamela
Published: February 2023

Endometrial cancer (EC) patients with metastatic/recurrent disease have limited treatment options and poor survival outcomes. Recently, we discovered the FGFR2c isoform is associated with poor prognosis in EC patients. Here we report the establishment of 14 EC patient-derived xenografts (PDX)-derived organoids (PDXOs) with or without FGFR2c expression. Treatment of 5 EC PDXOs with BGJ398 showed significant cell death in 3 models with FGFR2c expression. PDXs with FGFR2c+ showed significant tumour growth inhibition (TGI) following 21-day treatment with FGFR inhibitors (BGJ398 or pemigatinib) and significantly prolonged survival in 4/5 models. Pemigatinib + cisplatin combination therapy (n=5) resulted in significant TGI and prolonged survival in one of two p53abn PDXs. All five models treated with cisplatin alone showed de novo resistance and no survival benefit. Seven-day treatment with BGJ398 revealed a significant reduction in angiogenesis and CD206+ M2 macrophages. This data collectively supports the evaluation of FGFR inhibitors in a clinical trial.
A method for morphological feature extraction based on variational auto-encoder : an application to mandible shape
Authors: Furusawa Chikara , Tsustumi Masato , Koyabu Daisuke , Saito Nen
Published: February 2023

Shape measurements are crucial for evolutionary and developmental biology; however, they present difficulties in the objective and automatic quantification of arbitral shapes. Conventional approaches are based on anatomically prominent landmarks, which require manual annotations by experts. Here, we present morphological regulated variational AutoEncoder (Morpho-VAE), an image-based deep-learning framework, to conduct landmark-free shape analysis. The proposed architecture combines the unsupervised and supervised learning models to reduce dimensionality by focusing on morphological features that distinguish data with different labels. We applied the method to primate mandible image data. The extracted morphological features reflected the characteristics of the families to which the organisms belong, and then those features were visualized. Additionally, the reconstruction of the missing segments from incomplete images was demonstrated. The proposed method provides a flexible and promising tool for analyzing a wide variety of image data of biological shapes even those with missing segments.
baymobil: A Python package for detection of graft-mobile mRNA using exact Bayesian inference on RNA-Seq data
Authors: Hoerbst Franziska , Morris Richard J. , Tomkins Melissa
Published: February 2023

Background: A popular method for the detection of graft-mobile mRNA on a genomic scale in plants is to perform RNA-Seq on heterografts comprising different ecotypes, species, or cultivars (types). Transcripts from one plant type that are detected in the other type can be assumed to have been transported across the graft junction. A necessary step is the ability to differentiate between transcripts from each plant type, which can be achieved based on known single nucleotide polymorphisms (SNPs) between types. One current challenge is to differentiate between RNA-Seq reads associated with specific SNPs and RNA-Seq errors. Here, we present baymobil, a Python package that implements a Bayesian framework for determining between graft-mobile transcripts and sequencing errors.
Results: baymobil takes processed RNA-Seq data from homo- and heterografted plant samples as input and for each mRNA calculates a Bayes factor: the ratio of the evidence for transcripts having crossed the graft junction over the evidence for the data being a consequence of sequencing errors. These Bayes factors can be used to rank mRNAs based on the statistical support for their mobility. Furthermore, the package includes functions for the creation of simulated RNA-Seq datasets, which have been used to demonstrate that this approach outperforms existing mobility criteria and is a necessary step in the successful detection of graft-mobile mRNA.
Conclusion: The baymobil Python package improves the accuracy of pipelines for the detection of graft-mobile mRNA based on SNP differences between heterografted types. It is openly and freely available via GitHub, and is easily installed with pip and pypi. A detailed tutorial with test data and results for the statistics and simulation package baymobil can be found on github.com/mtomtom/baymobil.
The Thermal Error Modeling Approach of Feeding Axes for Horizontal CNC Lathes Based on Transfer Learning
Authors: Zhou Dan , Zeng Fuhong , Jia Shuyuan
Published: February 2023

Modeling the thermal error for each feeding axis of the CNC machine one by one will lead to an exponential increase in the thermal error compensation time. Th e feeding axes in the same CNC machine tool have similar thermal characteristics. The thermal error modeling approach based on transfer learning was proposed to improve the efficiency of thermal error modeling. The thermal error module was bulit for the X-axis of the horizontal lathe. Then, the thermal error module of the X-axis was transferred to the Z-axis of the same lathe by transfer learning based on domain adaptation. After verification, the prediction residual range of the Z-axis thermal error module based on transfer learning was only -3.2μm~1.4μm, which has proved that the method proposed in this paper is effective in thermal error modeling of the feeding axis. It will provide an effective means to effectively improve the efficiency of thermal error modeling for the feeding axes of CNC machine tools.
Clinical characteristics of autoimmune encephalitis with co-existence of multiple anti-neuronal antibodies
Authors: Zhou Yiyi , Chen Hao , Zhu Min , Li Menghua , Wang Lianqun , Xie Zunchun , Zhou Meihong , Wu Xiaomu , Hong Daojun
Published: February 2023

Background
Autoimmune encephalitis (AE) usually referred to a single anti-neuronal antibody-mediated encephalopathy syndrome. AE with co-existence of multiple anti-neuronal antibodies was reported in a few case reports or single-center retrospective studies. Further studies might be helpful to elucidate the uncertainties of clinical features, treatment and prognosis.
Methods
AE patients with two or more anti-neuronal antibodies were retrospectively recruited between August 2019 and February 2022 in our center. Clinical and laboratory data were collected. A total of 83 AE cases (9 cases in this study and 74 cases in the literatures) with multiple anti-neuronal antibodies were summarized and re-analyzed.
Results
Nine AE patients with co-existence of multiple anti-neuronal antibodies were identified from our 85 AE patients. The combination of anti-neuronal antibodies included NMDAR plus CASPR2 in 3 cases, NMDAR plus GABABR in 2 cases, AMPAR2 plus Hu in one, LGI1 plus IGLON5 in one, LGI1 plus CASPR2 in one, NMDAR plus GABABR and GAD65 in one. All 9 patients presented with encephalitis symptoms, clinically characterized by disturbance of consciousness, seizures, cognitive impairment, and psychiatric disorder. All 83 cases revealed that 73 cases had co-existence of two types of antibodies, 8 cases had three types, and 2 cases had four types. Thirty-nine cases (39/83, 46.9%) were confirmed or suspected to be accompanied with tumors, of which the most common was lung cancer (28/83, 33.7%). Partial or complete recovery was achieved in 57 cases (57/83, 68.6%), and 26 cases (26/83 31.3%) died during treatment or follow-up.
Conclusions
AE with co-existence of multiple anti-neuronal antibodies was a specific subgroup, which was increasingly recognized in the clinical practice. The co-existence of multiple anti-neuronal antibodies had complicated impacts on clinical features, disease progression, and prognosis.
The influence factors of clinical efficacy and prognosis of breast cancer patients treated with neoadjuvant chemotherapy
Authors: tang binbin , xiping Zhang
Published: February 2023

Objective
To investigate predictive indicators of clinical efficacy and prognosis of breast cancer patients treated with neoadjuvant chemotherapy.
Methods
290 female patients with breast cancer who treated with neoadjuvant chemotherapy were enrolled in this study. The collected data including tumor position, tumor size, cTNM staging, LNR, pathological molecular types(including ER, PR, Her-2, Ki-67 and so on), neoadjuvant chemotherapy regimens, pathological complete response rate, postoperative treatment and survival time.
Results
Neoadjuvant chemotherapy curative effect was related to pausimenia, T staging, N staging, ER/PR and Ki-67(P < 0.05), N staging (OR = 0.041, 95% CI = 0.012 ~ 0.134) and Ki-67 (OR = 9.340, 95% CI = 1.770 ~ 49.286) were independent risk factors of pCR. Recurrence of metastases was related to T staging, LNR, Ki-67, ET regimen, postoperative chemotherapy and postoperation radiotherapy(P < 0.05), T staging (OR = 1.731, 95%CI = 1.244 ~ 2.408), LNR (OR = 2.726, 95%CI = 1.430 ~ 5.197) and Ki-67 (OR = 3.107, 95%CI = 1.395 ~ 6.920) were independent risk factors of recurrence of metastases. Patients with low Ki-67 expression, low LNR, T1 staging and T2 staging and N0/N1/N2 staging had a better prognosis.
Conclusion
Clinical efficacy and prognosis of breast cancer patients treated with neoadjuvant chemotherapy were related to cTNM staging, LNR, ER/PR and Ki-67.
Mother’s perceptions and concerns over sharing sexual and reproductive health information with their adolescent daughters- A qualitative study among mothers of adolescent girls aged 14-19 years in the developing world, Sri Lanka
Authors: Mataraarachchi D , Pathirana T.E.A , Mahesh P.K Buddhika , Vithana P.V.S.C
Published: February 2023

Introduction Studies across the world have shown that parent-adolescent SRH communication can prevent unhealthy SRH practices among adolescents and promote their sexual and reproductive health. Parents’ ability to provide individualized sexuality education to suit the needs of their children, their family, and societal values, and the fact that children have more opportunities in the family, makes parent-based sexuality education of children a better approach to Sri Lankan context. Objective To explore mother’s perceptions and concerns over sharing sexual and reproductive health information with their daughters among Sinhalese mothers of adolescent girls aged 14–19 years in Sri Lanka Methodology Six Focus group discussions were carried out among mothers of adolescent girls aged 14–19 years. Each focus group discussion included 10–12 participants. A Focus Group Discussion guide developed after an extensive literature search and expert opinion was used to retrieve information from mothers. Data management and analysis mainly followed an inductive approach to thematic analysis principles. The analysis results were presented in narrative form using quotes in respondents’ own words that highlighted the theory. Results The mean age of the participants was 43.5 years while 62.4% (n = 40) were educated above the Ordinary level. Analysis of data identified eight main themes from the FGDs. Many mothers thought that sexual and reproductive information is important to adolescent girls. They tried to keep their girl adolescent informed about SRH issues that she may face during this time. They preferred abstinence-only education over abstinence-plus education. Lack of skills and lack of knowledge on adolescent SRH issues was a major challenge identified by the mothers to communicate SRH matters with their children. Conclusions and recommendations Although mothers perceived their role as primary sex educators to their children, they were not confident about their knowledge and skills in discussing SRH matters with children. Implementation of interventions to improve mothers’ attitudes and skills in communicating SRH matters with children is recommended.