bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression and functional analysis of ace1 and ace2 reveal their differential roles in larval growth and insecticide sensitivity in Spodoptera frugiperda
Authors: Gao Jie , Gong Li-Feng , Wang Huan-Huan , Zhao Rui , Xiao Xing , Tian Xin-Yao , Li Bo , Liang Pei , Gao Xi-Wu , Gu Shao-Hua
Published: January 2023

Acetylcholinesterase (AChE, EC3.1.1.7) is a key enzyme in neuronal signal transduction that hydrolyzes the neurotransmitter acetylcholine (ACh). The toxicological and physiological functions of AChEs in the destructive pest Spodoptera frugiperda, however, are still exclusive. In the present study, two acetylcholinesterase genes, ace1 and ace2, were characterized from S. frugiperda transcriptome and genome. Spatial−temporal expression analysis indicated that both Sfruace1 and Sfruace2 had an enriched expression in the heads among all larval tissues, and in 3rd instar larvae among all developmental stages. Notably, the expression level of Sfruace1 is much higher than Sfruace2 in all tested tissues and developmental stages. The RNA interference (RNAi) with specific designed small interfering RNA (siRNA) significantly reduced the expression of Sfruace1 to 30%, and Sfruace2 to 39%. The knockdown of Sfruace1 expression resulted in mortality of 37.6%, which is significantly higher than 17.06% in the siSfruace2-treated group. Furthermore, the RNAi of Sfruace1 and Sfruace2 expressions reduced the AChE enzymatic activity to 32.81% and 65.77%, respectively, compared with those of the untreated group, 24 h after injection of 70 ng siRNA per insect. The survivors after the siRNA treatments showed an apparent motor retardation to the artificial diet, and an apparent growth inhibition in F0 generation larvae. There was no significant inhibition effect on the growth of F0 and F1 generation pupae and the fecundity of female adult. Insecticide bioassay showed that the siSfruace1-treated larvae were more susceptible to acephate than the siSfruace2-treated and untreated larvae. Our study suggests that Sfruace1 plays a more important role in larval survivorship and susceptibility to acephate than Sfruace2 did in S. frugiperda, and both ace genes may have differential roles in regulating larvae growth, motor ability and insecticidal sensitivity in S. frugiperda.
Proteomic analysis of N-glycosylation of the human placenta between preeclampsia and normal pregnancies
Authors: Qu Guangjin , Luo Qiqi , Hu Pan pan , Huang Kun , Hu Fei fei , Huang Ming li , Luo Shanshun , Li Yue
Published: January 2023

Protein N-glycosylation plays critical roles in modulating placental function, but little is known about N-glycoproteins in the human placenta and modifications in preeclampsia (PE). Here, we show a large, site-specific N-glycoproteome profiling study of PE and normal placenta using quantitative N-glycoproteomics based on mass spectrometry. The study identified disease signatures of altered N-glycoproteins and N-glycosylation site occupancy in PE and provided a system-level view of human placental N-glycoproteins and in vivo N-glycosylation sites. The study led to the discovery of a roster of glycoproteins with aberrant N-glycosylation levels associated with PE, including CD34, ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase family member 1), insulin-like growth factor binding protein (IGFBP3), and HYOU1 (hypoxia up-regulated 1). An emerging phenomenon that N-glycosylation is involved in several PE pathways, including cell adhesion molecules, PI3K-Akt signaling, pyrimidine metabolism, and metabolic pathways was revealed by pathway analysis of PE-associated aberrant glycoproteins. After enzymolysis, the proteins in each group were enriched with N-glycosylated peptides by lectin, the glycochain was excised by peptide N-glycosidase F (PNGase F) in H218O, and the glycosylated sites were analyzed by LC-MS/MS to achieve large-scale qualitative and quantitative analysis of N-glycosylated proteins. Our findings highlight the role of N-glycosylation in the pathogenesis of PE and provide new molecular and system-level insights for understanding and treating this disease.
Synthesis, antitumor evaluation and computational study of thiazolidinone derivatives of dehydroabietic acid-based B ring-fused-thiazole
Authors: Chen Nai-Yuan , Li Cui-Ping , Huang Hong-Fei
Published: January 2023

In an attempt to search for new natural product-based antitumor agents, a series of novel thiazolidinone derivatives of dehydroabietic acid-based B ring-fused-thiazole were designed and synthesized. The primary antitumor tests showed that compounds 5m exhibited almost the best inhibitory activity against the tested cancer cells. The computational study suggested NOTCH1, IGF1R, TLR4, and KDR were the core targets of the title compounds, and the IC50 of SCC9 and Cal27 is strong correlation with the binding ability of TLR4 and compounds.
Bat Mortality in Wind Farms of Southern Europe: Temporal Patterns and Implications in the Current Context of Climate Change
Authors: Salguero María del Mar , Cruz Andrés De la , Gallego Antonio Román Muñoz , Arroyo Gonzalo Muñoz
Published: January 2023

The expansion of renewable energy production, especially wind power, is one of the cornerstones of our strategy for mitigating climate change. However, there is growing concern about the impacts of this energy source on biodiversity, and a need to develop tools to adequately assess this impact and mitigate its effects. In particular, very little is known about the impact on groups of fauna such as bats, which are especially sensitive to environmental changes. We investigated the temporal patterns of bat fatalities in wind farms in the province of Cádiz, in the south of the Iberian Peninsula. An eleven-year data set (2009–2019) from a surveillance program of bird and bat mortality in wind farms was analysed. A total of 2,858 fatalities concerning 10 bat genera were reported, although more than 90% of the affected animals were individuals of the genera Pipistrellus, Eptesicus and Nyctalus. Bat mortality occurred throughout the year, including all winter months in the case of the genus Pipistrellus. Nonetheless, the majority of fatalities of bats with wind turbines in the province of Cádiz occurred during summer and autumn, especially during August. The probability of mortality was positively correlated with the maximum daily temperature. According to the model prediction, the probability of fatality begins to increase slightly from 20°C and then rises sharply when the temperature exceeds 30°C. According to the regional projections of global climate models, an increase in maximum temperatures and the arrival of milder winters may lead to an increase in the annual mortality of bats in wind farms in the coming decades.
Variation in Tree Density, Biomass and Carbon Stock across an Altitudinal Gradient under Large Cardamom Agroforestry System of Darjeeling Himalaya
Authors: . Vineeta , Sarkar B. C. , Tamang M. , Shukla Gopal , N Shahina N , Nath Arun Jyoti , Chakravarty Sumit
Published: January 2023

It has been reported that the large cardamom-based traditional agroforestry systems in the Darjeeling Himalaya of West Bengal, India represents a sustainable land use system with a high potential to store and sequester biomass carbon. Therefore, the present study was undertaken to evaluate the changes in biomass stock and carbon accumulation of this indigenous system along an altitudinal gradient. The study area was classified into three altitude classes as low (700–1200 m asl), mid (1200–1700 m asl) and high (> 1700 m asl). The biomass and carbon storage for low-, mid- and high-altitude classes was estimated at 630.17 and 296.18 Mg ha− 1, 397.05 and 186.61 Mg ha− 1 and 315.78 and 148.42 Mg ha− 1, respectively. Schima wallichi, Cryptomeria japonica and Cupressus cashmeriana were the most dominant species in the low-, mid-, and high altitudinal classes, respectively. The IVI and total biomass of the five dominant species in low-, mid- and high altitudes ranged from 17.34–26.04, 18.15–37.56, 27.13–42.43 and 9.05-133.75 Mgha− 1, 1.38–37.43 Mgha− 1 and 19.0-72.1 Mgha− 1 respectively. Schima wallichi occurred in all the altitudinal classes among the top five dominant species. Across all the altitudinal gradients, the average ecosystem carbon storage was estimated at 295.02 Mg ha− 1. The contribution of SOC to the ecosystem carbon stock increased with the increasing altitude. In contrast, the contribution of biomass carbon to the ecosystem carbon stock decreased with the increase in altitude. The ecosystem carbon stock estimated for the low-altitude class was 36.43% and 45.30% higher than the mid- and high-altitude agroforestry systems. The large cardamom-based agroforestry systems in the Darjeeling Himalayas are thus a prospective carbon sink, both in vegetation and soil due to higher tree densities and natural resource conservation-based traditional farming practices.
Face validity and reliability test of the Danish version of the Compliance Questionnaire Rheumatology
Authors: Knudsen Line Raunsbæk , de Thurah Annette
Published: January 2023

Background Supporting adherence to medication
is an essential part of the treatment and care of patients with
rheumatic and musculoskeletal diseases. The Compliance
Questionnaire Rheumatology (CQR) measures adherence in rheumatic
diseases through 19 items covering drug-taking behaviour to
identify the reasons for adhering to treatment and the factors that
contribute to suboptimal adherence. The objective of this study was
to present the translation of the CQR into Danish and the face
validity and reliability test.

Methods The CQR was translated into Danish according to international guidelines, followed by a face validity test among 10 patients with rheumatoid arthritis. The test–retest reliability of the Danish CQR was evaluated in 49 patients with rheumatoid arthritis using the standard error of the measurement (SEM) converted into the minimally detectable change (MDC) and the intraclass correlation coefficient (ICC). Questionnaires were administered with a minimum of 10 days between assessments.
Results The participants in the reliability test had a mean age of 57.4 years (SD 16.1) and a mean disease duration of 1.13 years (range 2 months–2 years). The mean CQR score in the test and retest was 62.69 (confidence interval (CI) 58.76; 66.63) and 62.51 (CI 58.91; 66.12), respectively, with a SEM of 8.59 (7.16; 10.73) and an MDC of 16.83. A satisfactory test–retest reliability was confirmed by an ICC value of 0.79 (CI 0.68; 0.89).
Conclusion The Danish CQR has satisfactory test–retest reliability in patients newly diagnosed with rheumatoid arthritis and is considered a reliable tool to measure adherence in this group.
The increase in cardiac output induced by a decrease in positive end-expiratory pressure reliably detects volume responsiveness: the PEEP-test study
Authors: Lai Christopher , Shi Rui , Beurton Alexandra , Moretto Francesca , Ayed Soufia , Fage Nicolas , Gavelli Francesco , Pavot Arthur , Dres Martin , Teboul Jean-Louis , Monnet Xavier
Published: January 2023

Background: In patients on mechanical ventilation, positive end-expiratory pressure (PEEP) can decrease cardiac output through a decrease in cardiac preload and/or an increase in right ventricular afterload. Increase in central blood volume by fluid administration or passive leg raising (PLR) may reverse these phenomena through an increase in cardiac preload and/or a reopening of closed lung microvessels. We hypothesized that a transient decrease in PEEP (PEEP-test) may be used as a test to detect volume responsiveness.
Methods: Mechanically ventilated patients with PEEP ≥10 cmH2O (“high level”) and without spontaneous breathing were prospectively included. Volume responsiveness was assessed by a positive PLR test, defined as an increase in pulse-contour-derived cardiac index (CI) during PLR ≥10%. The PEEP-test consisted in reducing PEEP from the high level to 5 cmH2O for one minute. Pulse-contour-derived CI (PiCCO2) was monitored during PLR and the PEEP-test.
Results: We enrolled 64 patients among whom 31 were volume responsive. The median increase in CI during PLR was 14% (11%-16%). The median PEEP at baseline was 12 (10-15) cmH2O and the PEEP-test resulted in a median decrease in PEEP of 7 (5-10) cmH2O, without difference between volume responsive and unresponsive patients. Among volume responsive patients, the PEEP-test induced a significant increase in CI of 16% (12%-20%) (from 2.4±0.7 to 2.9±0.9 L/min/m2, p<0.0001) in comparison with volume unresponsive patients. In volume unresponsive patients, PLR and the PEEP-test increased CI by 2% (1%-5%) and 6% (3%-8%), respectively. Volume responsiveness was predicted by an increase in CI >8.6% during the PEEP-test with a sensitivity of 96.8% (95% confidence interval (95%CI): 83.3%-99.9%) and a specificity of 84.9% (95%CI: 68.1%-94.9%). The area under the receiver operating characteristic curve of the PEEP-test for detecting volume responsiveness was 0.94 (95%CI: 0.85-0.98) (p<0.0001 vs. 0.5). Spearman’s correlation coefficient between the changes in CI induced by PLR and the PEEP-test was 0.76 (95%CI: 0.63-0.85, p<0.0001).
Conclusions: A CI increase >8.6% during a PEEP-test, which consists in reducing PEEP to 5 cmH2O, reliably detects volume responsiveness in mechanically ventilated patients with a PEEP ≥10 cmH2O.
Trial registration
ClinicalTrial.gov (NCT 04023786). Registered July 18, 2019.
Ethics Committee approval CPP Est III (N° 2018-A01599-46)
Recurrent Cushing’s Disease in Adults: Predictors and Long-term Follow-up
Authors: Ünal Mustafa , Selek Alev , Gezer Emre , Canturk Zeynep , Cetinarslan Berrin , Çabuk Burak , Anık İhsan , Ceylan Savaş , koksalan damla , sozen mehmet
Published: January 2023

Purpose
Cushing’s disease (CD) is characterized by endogenous hypercortisolism that is associated with increased mortality and morbidity. Due to high recurrence rates in CD, determination of high-risk patients is of paramount important. In this study, we aimed to determine recurrence rates and clinical, laboratory and histological predictors of recurrence in a high volume single-center.
Methods
This retrospective study included 273 CD patients operated in a single pituitary center between 1997 and 2020. The patients with early postoperative remission were further grouped according to recurrence status (recurrent and sustained remission groups). Demographic, radiologic, laboratory, pathologic and follow-up clinical data of the patients were analyzed and compared between groups.
Results
The recurrence rate was 9.6% in the first 5 years; however, overall recurrence rate was 14.2% in this study. Higher preoperative basal ACTH levels were significantly correlated with CD recurrence even with ACTH levels adjusted for tumor size, Ki-67 levels and tumoral invasion. Recurrence rates were significantly higher in patients with ACTH levels higher than 55 pg/mL, tumor diameter > 9.5 mm, and if adrenal axis recovery was before 6 months. The severity of hypercortisolism, morbidities and demographic factors except age were not predictive factors of recurrence.
Conclusion
Based on our study data, younger age at diagnosis, a diagnosis of osteoporosis, higher preoperative ACTH levels, larger tumor size, invasive behavior, higher Ki 67 index and early recovery of adrenal axis during the postoperative period attracted attention as potential predictors of recurrent disease.
Changes in the equine facial repertoire during different orthopedic pain intensities
Authors: Ask Katrina , Rhodin Marie , Rashid-Engström Maheen , Hernlund Elin , Andersen Pia Haubro
Published: January 2023

A number of facial expressions are associated with pain in horses, however, the entire display of facial activities during orthopedic pain have yet to be described. The aim of the present study was to exhaustively map changes in facial activities in eight resting horses during a progression from sound to mild and moderate degree of orthopedic pain, induced by lipopolysaccharides (LPS) administered in the tarsocrural joint. Lameness progression and regression was measured by objective gait analysis during movement, and facial activities were described by EquiFACS in video sequences (n = 348, total length 892.5 minutes) of the horses obtained when resting in their box stalls. Predictive modeling identified 16 action units and action descriptors, related to ears, eyes, and lower face. Lower lip depressor (AU16), lips part (AU25), half blink (AU47), single ear forward (SEAD101) and single ear rotator (SEAD104) were selected as co-occurring significantly more in horses with pain than in horses without pain. The major change in co-occurring facial activities occurred in the transition from no pain to mild pain. In conclusion, resting horses with induced orthopedic pain showed a dynamic upper and lower facial repertoire and the relationship between level of pain intensity and facial activity appears complex.
Can a powered knee-ankle prosthesis improve weight-bearing symmetry during stand-to-sit transitions in individuals with above-knee amputations?
Authors: Hunt Grace R. , Hood Sarah , Gabert Lukas , Lenzi Tommaso
Published: January 2023

Background: After above-knee amputation, the missing biological knee and ankle are replaced with passive prosthetic devices which are able to dissipate limited amounts of energy using resistive damper systems during “negative energy” tasks like sit-down. However, passive prosthetic knees are not able to provide high levels of resistance at the end of the sit-down movement when the knee is flexed and users need the most support. Consequently, users are forced to over-compensate with their upper body, residual hip, and intact leg, and/or sit down with a ballistic and uncontrolled movement. Powered prostheses have the potential to solve this problem by controlling the joints using motors, which can produce higher levels of resistance at a larger range of joint positions than passive damper systems. Therefore, powered prostheses have the potential to make sitting down more controlled and less difficult for above-knee amputees, improving their functional mobility.
Methods: Ten individuals with above-knee amputations sat down using their prescribed passive prosthesis and a research powered knee-ankle prosthesis. Subjects performed three sit-downs with each prosthesis while we recorded joint angles, forces, and muscle activity from the intact quadricep muscle. Our main outcome measures were weight-bearing symmetry and muscle effort of the intact quadricep muscle. We performed paired t-tests on these outcome measures to test for significant differences between passive and powered prostheses.
Results: We found that the average weight-bearing symmetry improved by 42.1% when subjects sat down with the powered prosthesis compared to their passive prostheses. This difference was significant (p = 0.0012) and every subject’s weight-bearing symmetry improved when using the powered prosthesis. Although the intact quadricep muscle contraction differed in shape, neither the integral nor the peak of the signal was significantly different between conditions (p > 0.01).
Conclusions: In this study, we found that a powered knee-ankle prosthesis significantly improved weight-bearing symmetry during sit-down compared to passive prostheses. However, we did not observe a corresponding decrease in intact-limb muscle effort. These results indicate that powered prosthetic devices have the potential to improve balance during sit-down for individuals with above-knee amputation and provide insight for future development of powered prosthetics.
Hoeflea algicola sp. nov. and Hoeflea ulvae sp. nov., isolated from phycosphere of marine algae
Authors: Kristyanto Sylvia , Kim Jeong Min , Han Dong Min , Jeon Che Ok
Published: January 2023

Two Gram-negative, moderately halophilic, and motile rod bacteria, strains G2-23T and J2-29T, showing catalase- and oxidase-positive activities were isolated from marine algae. Both strains optimally grew at 30°C, pH 7.0, and 2% (w/v) NaCl. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. As major cellular fatty acids and polar lipids, strain G2-23T contained summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and summed feature 3 (iso-C15:0 2-OH and/or C16:1 ω7c/ω6c) and phosphatidylethanolamine (PE), phosphatidyl-N-monomethylethanolamine (PME), phosphatidylglycerol (PG), diphosphatidylglycerol, sulfoquinovosyl diacylglycerol (SQDG), and an unidentified phospholipid (PL), respectively, while strain J2-29T contained summed feature 8, C18:1 ω7c 11-methyl, and C16:0 and PE, PME, PG, SQDG, and PL, respectively. The genomic DNA G + C contents of strains G2-23T and J2-29T were 59.5 and 62.2 mol%, respectively. Both strains shared 97.9% 16S rRNA gene sequence similarity, 79.8% average nucleotide identity (ANI), and 22.8% digital DNA-DNA hybridisation (DDH) value, indicating that they are different species. Phylogenetic and phylogenomic analyses by 16S rRNA gene and genome sequences, respectively, revealed that strains G2-23T and J2-29T formed different phylogenic lineages within the genus Hoeflea. ANI and digital DDH values between strains G2-23T and J2-29T and other Hoeflea type strains were less than 79.0 and 22.1% and 80.5 and 23.3%, respectively, representing that they are novel species of the genus Hoeflea. Based on the phenotypic, chemotaxonomic, and molecular properties, strains G2-23T and J2-29T represent two different novel species of the genus Hoeflea, for which the names Hoeflea algicola sp. nov. (G2-23T = KACC 22714T = JCM 35548T) and Hoeflea ulvae sp. nov. (J2-29T = KACC 22715T = JCM 35549T), respectively, are proposed.
Effects of Various Copper Sources and Concentrations on Performance, Skeletal Growth, and Mineral Content of Excreta in Broiler Chickens
Authors: Deo Chandra , Biswas Avishek , Sharma Divya , Tiwari Ashok Kumar
Published: January 2023

The experiment was designed to study the effect of supplemental sources and concentrations of copper on the performance and development and mineralization of tibia bones in broiler chickens. 42-day feeding trial using three copper sources i.e., copper sulphate (CuS), copper chloride (CuCl), and copper propionate (CuP) each with four copper levels i.e., 8, 100, 150, and 200 mg/kg was taken. During 4–6 wk of age, the body weight gain was significantly higher at 200 mg Cu/kg diet. There was no significant difference on body weight gain due to interaction between Cu sources and levels. The feed intake during different growth phases did not differ significantly due to either main effect or interaction between copper sources and levels. The feed conversion ratio during 4–6 and 0–6 wk was significantly (P < 0.05) better in CuP supplemented diet (200 mg/kg diet). A total of 72 tibia bones, six per treatment, were collected at the end of experiment. Metabolic trial was conducted to look into mineral retention in broiler chickens on the final three days of the trial (40-42d). 8mg Cu/kg diet with Cu chloride, 100mg Cu/kg diet with Cu propionate, 8mg Cu/kg diet with Cu sulphate, and 8mg/kg diet with Cu propionate supplemented diet resulted in significantly (P < 0.05) increased tibia bone zinc (Zn) levels. Significantly (P < 0.01) lower tibia Zn content was recorded at higher levels of Cu (150 and 200 mg/kg diet). Higher (P < 0.01) tibia Cu content was recorded at 8 mg Cu/kg diet with Cu sulphate treated group. Excreta Zn content was higher (P < 0.01) in Cu sulphate supplemented diet than Cu chloride supplemented diet and lowest excreta Zn content was recorded in Cu propionate supplemented diet. Higher excreta Fe content (P < 0.05) was observed in Cu sulphate and Cu chloride supplemented diet than that recorded in Cu propionate supplemented diet. With the exception of a decrease in the zinc content of the tibia, feeding dietary Cu concentrations up to 200 mg Cu/kg diet, regardless of the different sources, showed no adverse impact on bone morphometry and mineralization parameters.
Robust Speaker Recognition Utilizing Lexical, MFCC Feature Extraction and Classification Technique
Authors: Singh Mahesh K.
Published: January 2023

The authors have requested that this preprint be removed from Research Square.
Fusion data of digital olfation devises for the evaluation of the quality of fresh coffee beans
Authors: Cascos Gema , Lozano Jesús , Arroyo Patricia , Ruiz-Canales Antonio , Oates Martin John , Martín-Vertedor Daniel
Published: January 2023

The aim of this work is to discriminate the volatile organic compounds (VOCs) that are characteristic of different qualities of fresh coffee beans, with two electronic devises that allows one to classify the fresh product. Coffea arabica at red stage of ripeness were harvested in the Choluteca region (Honduras). Sensory analysis classification, volatile compound profile and electronic nose analysis were done. Samples were classiffied as high, medium and low-quality coffee. The tasting panel could discriminate samples based on their pleasant or unpleasant attributes. The high-quality coffee presented the highest values of the positive attributes with the highest scores in the fruity, herbal and sweet attribute. Low-quality samples showed negative attributes related to roasted, smokey and abnormal fermentation. Alcohols and aromatic compounds were highest in high-quality samples, while carboxylic acids, pyrazines and pyridines in low-quality ones. The VOC with positive attribute were phenylethyl alcohol, nonanal and 2-methyl-propanoic acid, octyl ester, while the compounds with negative attribute were pyridine, octanoic acid and dimethyl sulfide. The aroma of fresh coffee beans qualities were also discriminated by the E-nose instruments. PLS-DA model obtained from the E-nose data was able to classify the different qualities of fresh coffee beans and explained 96.9% of the total variance. A PLS chemometric approach was assed for quantifying the fruity aroma of the fresh coffee beans, obtaining an RP2 of 0.88. Thus, the E-nose is concluded to be an acurate, inexpensive and non-destrutive device for discriminating between different coffee qualities during the processing.
Model Selection for Deep Learning with Gradient Norms: An Empirical Study
Authors: Xiong Haoyi , An Haozhe , Li Xuhong , Li Xingjian , Zhu Zhanxing , Ma Yingying , Sun Zeyi
Published: January 2023

Recent theoretical works [1–3] propose to exploit the loss gradient norm averaged across training samples as a measure of overfitting and generalization performance of DNNs, to investigate the upper bound of generalization error of deep neural networks (DNNs). However, the extremely high computational cost makes such gradient norms infeasible to obtain in practice. In this work, we carry out empirical studies by proposing a formulated mean empirical gradient norms (MEGAN), where we use a fast implementation of Fully-Connected (FC) Layer gradient norms [4] to compute MEGAN. Our empirical studies find that the sum of MEGAN over the optimization path of deep learning (i.e. epochs) could accurately predict the generalization performance of DNNs. Our empirical studies also include extensive experiments to demonstrate the potential of MEGAN for model selection of DNNs in hyper-parameter search settings. Our in-depth analyses interpret the behavior of MEGAN during training epochs and confirm MEGAN as an efficient and effective way to measuring the generalization performance of DNN with the training set only.
PhyloBench: a Benchmark for Evaluating Phylogenetic Programs
Authors: Spirin Sergey , Sigorskikh Andrey , Efremov Aleksei , Penzar Dmitry , Karyagina Anna
Published: January 2023

Motivation. Phylogenetic inference based on protein sequence alignment is a widely used procedure. Numerous phylogenetic algorithms have been developed, most of which have many parameters and options.Choosing a program, options, and parameters can be a nontrivial task.No benchmark for comparison of phylogenetic programs on real protein sequences is publicly available.
Results. We have developed PhyloBench, a benchmark for evaluating the quality of phylogenetic inference, and used it to test a number of popular phylogenetic programs. PhyloBench is based on natural, not simulated, protein sequences of orthologous evolutionary domains. The measure of accuracy of an inferred tree is its distance to the corresponding species tree. A number of tree-to-tree distance measures were tested. The most reliable results were obtained using the Robinson–Foulds distance. Our results confirmed recent findings that distance methods are more accurate than maximum likelihood and maximum parsimony. We tested the bayesian program MrBayes on natural protein sequences and found that it is superior to maximum likelihood, but inferior to distance methods. Of the methods we tested, the Balanced Minimum Evolution method implemented in FastME yielded the best results.
Availability. Benchmark alignments and reference trees are available at https://mouse.belozersky.msu.ru/tools/phylobench/ together with a web-interface that allows for a semi-automatic comparison of a user's method with a number of popular programs.
Clinical Application of the Global Leadership Initiative on Malnutrition Using a Combination of Different Muscle Mass Indices in Patients with Gastric Cancer: A Multicenter, Cross-Sectional, Observational Cohort Study
Authors: Zheng Jingxian , Wang Xiaojie , Yu Jiami , Hu Qiaoting , Zhan Zhouwei , Zhou Sijing , Xu Jingjie , Li Qifei , Wang Chang , Zhao Qingchuan , Xu Hongxia , Shi Hanping , Guo Zengqing
Published: January 2023

Background: Malnutrition is associated with poor prognosis and prevalent in gastric cancer patients. However, there is no standardized method for evaluating malnutrition; the Global Leadership Initiative on Malnutrition (GLIM) aimed to establish a standard criteria for evaluating malnutrition. However, the cutoff point for muscle reduction remains unclear, and its clinical value has not yet been verified. Hence, we aimed to examine the relationship between combinations of different muscle measurement indices and the survival of gastric cancer patients to determine the accurate method for diagnosing sarcopenia, establish the standard GLIM criteria, and explore its clinical value.
Methods: This multicenter and observational cohort study included 1,406 gastric cancer patients. The accurate prediction combination was determined using the cutoff point for muscle loss by predicting the survival risk according to the GLIM criteria established using a combination of muscle mass indicators. Least absolute shrinkage and selection operator regression analysis was used to screen the independent risk factors for survival with the construction of a Cox regression model. The R software was used to establish the nomogram of individual survival prediction and to verify the clinical significance of malnutrition diagnosed based on the GLIM criteria.
Results: The risk ratio of patients with malnutrition based on the leg circumference and weight-corrected grip strength was the highest (hazard ratio [HR]=2.159, 95% confidence interval [CI]=1.800, 2.588 in severely malnourished patients). Malnutrition occurred in 54.5% of patients diagnosed with gastric cancer based on the GLIM criteria. Malnutrition is an independent risk factor for unfavorable survival in gastric cancer patients; its nomogram model can accurately predict the survival of gastric cancer.
Conclusion: Muscle loss is one of the components of the GLIM criteria and is determined by measuring the leg circumference and weight-corrected grip strength. The GLIM criteria are effective in diagnosing malnutrition and predicting the survival in gastric cancer patients.
Differences in molecular characteristics and overall survival between incidental and symptomatic lower grade gliomas
Authors: Demetz Matthias , Krigers Aleksandrs , Moser Patrizia , Kerschbaumer Johannes , Thomé Claudius , Freyschlag Christian F.
Published: January 2023

Purpose:
Data on differences in overall survival and molecular characteristics between incidental (iLGG) and symptomatic lower grade Glioma (sLGG) are limited. The aim of this study was to investigate differences between patients with iLGG and sLGG.
Methods:
All adult patients with a histologically proven diffuse (WHO°II) or anaplastic (WHO°III) glioma who underwent their first surgery at the authors’ institution between 2010 and 2019 were retrospectively included. Tumor volume on pre- and postoperative MRI scans was determined. Clinical and routine neuropathological data were gained from patients’ charts.
Results:
Out of 161 patients included, 23 (14%) were diagnosed as incidental findings. Main reasons for obtaining MRI were: headache(n=12), trauma(n=2), MRI indicated by other departments(n=7), staging examination for cancer(n=1), volunteering for MRI sequence testing(n=1).
The asymptomatic patients were significantly younger with a median age of 38 years (IqR28-48) vs. 50 years (IqR38-61), p=0.011. Incidental LGG showed significantly lower preoperative tumor volumes in T1 CE (p=0.008), FLAIR (p=0.038) and DWI (p=0.028).
Incidental LGG demonstrated significantly lower anaplasia levels (p=0.004) and lower expression of MIB-1 (p=0.008) compared to sLGG. IDH1-mutation was significantly more common in iLGG (p=0.024).
Incidental LGG showed a significantly longer OS (mean 212 vs 70 months, p=0.005) and PFS (mean 201 vs 61 months, p=0.001) compared to sLGG.
Conclusion:
Our study is the first to depict a significant difference in molecular characteristics between iLGG and sLGG. The findings of this study confirmed and extended the results of previous studies showing a better outcome and more favorable radiological, volumetric and neuropathological features of iLGG.
Compressive and Tensile Strength Anisotropy of Friable Sandstone and Thin-bed Shale of the Pleistocene Erin Formation – Insights for safe operating mud weight windows for vertical and horizontal wells
Authors: Harrypersad-Daniel A. M. , Blake O. O. , Ramsook R.
Published: January 2023

The compressive and tensile strengths are essential parameters used for determining the safe mud weight window (SMWW) during borehole drilling, especially in friable rocks where the SMWW tends to be narrow and therefore, the margin for wellbore instability issues is high. However, these parameters are seldomly reported for friable rocks due to the difficulties and challenges faced while recovering and preparing friable cores and outcrop samples for strength testing. This study evaluates the compressive and tensile strengths of friable rocks under dry and saturated conditions, and investigates how strength anisotropy affect the SMWW. Unconfined compressive strength, confined compressive strength (up to 130 MPa effective pressure), and Brazilian (tensile strength) measurements were made perpendicular and parallel to the outcrop bedding of the friable sandstone and thin-bed shale lithofacies of the Erin Formation, Southern Trinidad. In spite of this Formation being one of the main petroleum reservoirs, there are no published data on the rock strength. The results show that strength anisotropy exist, which is larger under saturated conditions. Under confinement, the friable rocks accumulated large strain (an average of 20% strain) and experienced significant strain hardening causing the strength to be high. The ratio of the yield strength to failure strength is less than 0.2, under dry conditions. Thin section analysis of tested specimens shows intragranular fracturing across quartz grains, which led to grain crushing and pore collapse. Catalastic flow within the specimens and no stress drop after the peak stress suggest the friable rocks failed in a ductile manner. The effect of the strength anisotropy on the SMWW for the sandstone and thin-bed shale was determined for wells that are orientated in the principal stress directions (Sv, Shnmi and SHmax), of a normal faulting stress regime, at depths of 3400 to 6900 ft. The upper mud weight limit of the SMWW is not influenced by the tensile strength anisotropy. However, the lower mud weight of the SMWW was influenced by the compressive strength anisotropy, predominantly for Sv and Shnmi aligned wells that are penetrating through the saturated friable sandstone. Since the rocks are friable, drilling outside of the SMWW by 5% to 8%, if forecasted using the strongest compressive strength, can result in wellbore instability.
An intelligent radiation frost forecasting and warning system for agricultural environments
Authors: Bagheri Nikrooz , bagheri meisam , Sepahvand Movahed
Published: January 2023

Every year, radiation frost causes the loss of a large number of agricultural products. Currently, there is numerous equipment to protect plants against frost. Turning on the equipment late causes inefficiency in raising the air temperature in time, and turning them on early increases energy consumption and costs. Therefore, accurately forecasting frost is very important for turning on the equipment in time. Therefore, in this research, an intelligent radiation frost forecasting and warning system was designed and constructed. This system is composed of a wireless sensor, computing and intelligent forecasting based on deep learning methods and warning announcements to the farmer by the SMS. Intelligent forecasting is based on forecasting dew point temperature for the next three hours according to the in-situ measurement of temperature and relative humidity of the air. The meteorological data of the studied regain from 2011–2021 were used to train the network. The Performance evaluation of the IFFS was carried out. Based on the obtained results, the system accuracy in measuring temperature and relative humidity of the air was 99% and 98%, respectively. The F-score of the IFFS obtained 96%, and the system accuracy in the announcement of the warning obtained 100%. Due to the high accuracy of the IFFS for forecasting radiation frost, the application of this system is recommended for better protection of plants.
Effect of argon to oxygen ratio on the properties of tungsten oxide films prepared by DC magnetron sputtering
Authors: 史 泽 , Li Yuechan , Xie An , Sun Dongya
Published: January 2023

In this paper, tungsten oxide films were deposited on ITO-coated glass by DC magnetron sputtering at different argon to oxygen ratio (30:10, 40:10, 50:10, 60:10, 70:10, 80:10). The microstructure was analyzed by means of XRD and SEM. The electro-chromic properties were analyzed by UV-Vis and electrochemical workstation. The results show that the electrochromic properties of tungsten oxide films can be con-trolled by changing the ratio of argon to oxygen. When the ratio of argon to oxygen is 50:10, the electrochromic property is the best. The optical modulation amplitude of the films prepared under this process reached 56.92%, the response time from the colored state to the bleached state was the shortest (tc=5.8s, tb=3.4s), and there was a maximum coloring efficiency (CE=52.5 cm2/C). After 600 cycles, the attenuation degree of cyclic voltammetry curve is the smallest, indicating that its cyclic stability effect is the best. This work offers an important reference value for the development of high-performance electrochromic films via magnetron sputtering engineering techniques.
Metabolomic analysis for the unique profile and novel biomarkers of neuropsychiatric systemic lupus erythematosus
Authors: Li Xue , Guo Yixue , Lu Huaqing , Pei Wenwen , Wang Yifan , He Jing , Sun Xiaolin
Published: January 2023

Background: Neuropsychiatric systemic lupus erythematosus (NPSLE) is a common manifestation of systemic lupus erythematosus (SLE), with high mortality and disability rate. The lack of effective diagnostic methods, such as biomarkers, makes it difficult to diagnose and treat NPSLE. Metabolomics studies in autoimmune diseases shed new light on the identification of biomarkers beyond autoantibodies and cytokine profiling. This research aimed to explore the unique metabolomic profile, and discover novel molecular biomarkers and pathways for NPSLE.
Methods: Cerebrospinal fluid samples from 26 NPSLE patients, 9 SLE controls, 7 connective tissue disease (CTD) controls and 9 nervous system disorder (NSD) controls were analysed to identify metabolomic signatures, significant pathways and biomarkers in the discovery cohort, using ultra performance liquid chromatography–tandem mass spectrometry (UPLC–MS). Next, the potential biomarkers were verified in an independent validation cohort including 22 NPSLE patients, 11 SLE controls and 4 NSD controls.
Results: The metabolite profiles of cerebrospinal fluid (CSF) samples allowed significant differentiation of NPSLE patients from other disease controls. β-alanine metabolism and inositol phosphate metabolism pathways were significantly perturbed in NPSLE group. In the discovery cohort, 44 CSF metabolites with variable importance in projection (VIP) scores >1.5 and p < 0.05 were considered as the most differential metabolic biomarkers, including β-alanine amino acid and inositol. The diagnostic value of inositol was verified in the validation cohort, with the greatest specificity of 95.45% and the sensitivity of 60.00% for NPSLE. The CSF inositol level was higher in NPSLE patients with neuropsychiatric damage, cranial neuropathy and cerebrovascular disease.
Conclusion: CSF metabolomic profile of NPSLE patients is unique from other disease controls. The pathway perturbations are involved in β-alanine metabolism and inositol phosphate metabolism. Inositol is a promising biomarker for the diagnosis and neuropsychiatric damage evaluation of NPSLE, and has potential relationships with specific NPSLE manifestations.
Validate your white matter tractography algorithms with a reappraised ISMRM 2015 Tractography Challenge scoring system
Authors: Renauld Emmanuelle , Théberge Antoine , Petit Laurent , Houde Jean-Christophe , Descoteaux Maxime
Published: January 2023

Since 2015, research groups seek to produce the nec-plus-ultra tractography algorithms using the ISMRM 2015 Tractography Challenge as evaluation. In particular, since 2017, machine learning has made its entrance into the tractography world. The ISMRM 2015 Tractography Challenge is the most used phantom during tractography validation, although it contains limitations. We offer, here, a new Tractometer scoring system for this phantom, where segmentation of the bundles is now based on manually-defined regions of interest rather than on bundle recognition. Bundles are now more reliably segmented, offering more stable metrics with higher precision for future users. New code is available online. Scores of the initial 96 submissions to the challenge are updated. Overall, conclusions from the 2015 challenge are confirmed with the new scoring, but individual tractograms scores have changed, and the data is much improved at the bundle- and streamline-level. This work also led to the production of a ground truth tractogram with less noisy streamlines and an example of processed data, all available on the Tractometer website. This enhanced Tractometer scoring system and new data should continue to help researchers develop and evaluate the next generation of tractography techniques.
Utility of monocyte distribution width for diagnosing colonic diverticulitis in the emergency department: a retrospective cohort study
Authors: Chang Chang-Yuan , Hsu Tai-Yi , He Guan-Yi , Shih Hong-Mo , Wu Shih-Hao , Huang Fen-Wei , Chen Pei-Chun , Tsai Wen-Chen
Published: January 2023

Background
Colonic diverticulitis is a leading cause of abdominal pain. The monocyte distribution width (MDW) is a novel inflammatory biomarker with prognostic significance for coronavirus disease and pancreatitis; however, no study has assessed its correlation with the severity of colonic diverticulitis.
Methods
This single-center retrospective cohort study included patients older than 18 years who presented to the emergency department between November 1, 2020, and May 31, 2021, and received a diagnosis of acute colonic diverticulitis after abdominal computed tomography. The characteristics and laboratory parameters of patients with simple versus complicated diverticulitis were compared. The significance of categorical data was assessed using the chi-square or Fisher’s exact test. The Mann–Whitney U test was used for continuous variables. Multivariate regression analysis was performed to identify predictors of complicated colonic diverticulitis. Receiver operator characteristic (ROC) curves were used to test the efficacy of inflammatory biomarkers in distinguishing simple from complicated cases.
Results
Of the 160 patients enrolled, 21 (13.125%) had complicated diverticulitis. Although right-sided was more prevalent than left-sided colonic diverticulitis (70% versus 30%), complicated diverticulitis was more common in those with left-sided colonic diverticulitis (61.905%, p = 0.001). Age, white blood cell (WBC) count, neutrophil count, C-reactive protein (CRP) level, neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and MDW were significantly higher in the complicated diverticulitis group (p < 0.05). Logistic regression analysis indicated that the left-sided location and the MDW were significant and independent predictors of complicated diverticulitis. The area under the ROC curve (AUC) was as follows: MDW, 0.870 (95% confidence interval [CI], 0.784–0.956); CRP, 0.800 (95% CI, 0.707–0.892); NLR, 0.724 (95% CI, 0.616–0.832); PLR, 0.662 (95% CI, 0.525–0.798); and WBC, 0.679 (95% CI, 0.563–0.795). The MDW had the largest AUC for diagnosing complicated diverticulitis; when the MDW cutoff was 20.38, the sensitivity and specificity were maximized to 90.5% and 80.6%, respectively.
Conclusions
Patients with complicated diverticulitis were significantly older and predominantly had left-sided colonic diverticulitis. A large MDW was a significant and independent predictor of complicated diverticulitis. The MDW may aid in planning antibiotic therapy for patients with colonic diverticulitis in the emergency department.
Surface Water Quality Trends in the Tarkwa Mining Area: 1993 – 2013
Authors: Seshie Vivian Isabella , Kuma Jerry Samuel Yao , Lasidzi Nikao Adziman
Published: January 2023

Tarkwa is characterised by a tropical and humid climate, as well as Birimian quartzites, sandstones, schists, phyllites, and conglomerates. The mining area is located in the Ankobra River Basin, bounded to the west, north, and south by the Ankobra, Huni, and Bonsa Rivers. Huni and Bonsa tributaries include Ahumabru, Teberebie, Bediabewu, Achofe, Awonabeng, Abekoase, Esumang, and Subri. This study presents 1993, 2002 and 2013 data. From 1993–2013, pH, conductivity, TDS, Alk, Ca, Mg, Na, K, Cl, SO₄², NO₃, Fe, Cu, Hg, Pb, Cr, Al, and Mn were studied. This paper compares early 1990s baseline data from Ghana Australian Gold (GAG), now AngloGold Ashanti Iduapriem Limited (AAIL), and Gold Fields Ghana Limited (GF), to recent data from the Tarkwa Nsuaem Municipality (TNM) mining area. Descriptive statistics and paired t-tests were used to calculate K-values and 20-year trends. For 20 years, pH, TDS, Cl, Mg, Na, SO₄², and NO₃ did not change significantly; Cu, Pb, and Conductivity did. Between 1993 and 2002, Fe, Ca, K, Alkalinity, and Mn increased, but not between 2002 and 2013. From 1993–2013, the pH, Cond, TDS, Cl, SO₄², NO₃, Ca, Al, Na, Fe, Cu, and Pb were all lower than the EPA's maximum mine effluent discharge limit.