bluuebunny/crossref_metadata_2025 huggingface dataset:
An eco-friendly method of extracting alizarin from Rubia tinctorum roots under supercritical carbon dioxide and its application to wool dyeing
Authors: Abou Elmaaty Tarek , Sayed-Ahmed Khaled , Magdi Mai , Elsisi Hanan
Published: January 2023

Because of its low critical temperature and pressure levels, supercritical carbon dioxide (scCO2) is the most widely used supercritical fluid in the supercritical fluid extraction (SFE) technique. Alizarin was extracted from madder roots (Rubia tinctorum) using scCO2 under different conditions of co-solvent ratio (0–50%), temperature (45–95 °C), pressure (150–250 bar), extraction time (15–120 min), and flow rate (5–9 mL/min). Based on alizarin recovery and minimization of environmental risk, the optimum conditions were determined. SFE was optimum at 90% CO2:10% methanol (Me), 65 °C, 250 bar, 45 min, and 9 mL/min. The alizarin recovery, and its content in R. tinctorum extract (RE) under the optimum conditions were 1.34 g/kg roots, and 6.42%, respectively. Using conventional dyeing methods, wool fabrics were dyed with RE at different concentrations (2–6%). Various types of mordants were also used in the dyeing process, including chemical and bio-mordants. Color and fastness properties of dyed wool fabrics were evaluated based on RE concentration and mordant type. A higher RE concentration and the use of mordants, specifically Punica granatum (P. granatum) peels, increased the color characteristics. RE and dyed fabrics exhibited good antibacterial activity against the tested bacterial strains, especially Pseudomonas aeruginosa and Escherichia coli.
Cancer bioimaging using dual mode luminescence of graphene/FA-ZnO nanocomposite based on novel green technique
Authors: Wanas Wessam , Abd El-Kaream Samir Ali , Ebrahim Shaker , Soliman Moataz , Karim Marwa
Published: January 2023

Graphene based nanomaterials are explored in the field of cancer bioimaging and biomedical science and engineering. The luminescent nanostructures with a low toxicity and high photostability can be used as probes in bioimaging applications. This work is aimed to prepare graphene/folic acid-zinc oxide (GN/FA-ZnO) nanocomposite with dual-mode emissions (down-conversion and up-conversion) to be used in cancer bioimaging. The dual mode emissions offer long luminescence lifetime, multicolor emissions detected by the naked eyes after excitation and narrow band absorption and emission spectra. ZnO nanospheres and nanorods structures were prepared using co-precipitation technique and were conjugated with FA to separate the bulk graphite layers electrostatically into GN. The optical, morphological, surface charge and structural properties of the prepared nanostructures were investigated and discussed using different characterization techniques such as UV–visible spectroscopy, photoluminescence (PL) spectroscopy, scanning electron microscope (SEM), high resolution transmission electron microscope (HRTEM), Zeta potential, Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), X-ray powder diffraction (XRD), and Fourier transform infrared (FTIR). GN/FA-ZnO nanocomposites were injected into Swiss albino mice implanted with Ehrlich Tumor and the bioimaging was investigated using photon imager and digital camera. The results showed clear fluorescence and confirmed that the green design of GN/FA-ZnO nanocomposite with targeting behavior was capable of selective bioimaging of the tumor. This study presented a novel dual mode emission nanocomposite for tumor targeting and is a promising strategy for the fabrication of a new design of spectral encoding.
Comparison of long-term outcomes in simultaneous pancreas-kidney transplant versus simultaneous deceased donor pancreas and living donor kidney transplant
Authors: Kim Jin-Myung , Ko Youngmin , Choi Minha , Kwon Hye Eun , Lee Jae Jun , Jung Joo Hee , Kwon Hyunwook , Kim Young Hoon , Shin Sung
Published: January 2023

Simultaneous deceased donor pancreas and living donor kidney transplant (SPLK) has certain advantages over conventional simultaneous pancreas-kidney transplant (SPK) and may be beneficial for overcoming the paucity of organs needed for diabetic patients requiring transplant. We compared the clinical outcomes of patients who underwent either SPK (n = 149) or SPLK (n = 46) in terms of pre- and post-transplantation variables, development of de novo DSA, occurrence of biopsy-proven acute rejection (BPAR), and graft survival rates. There were no significant differences in the baseline characteristics between the SPK and SPLK groups except for the shorter cold ischemic time of kidney grafts, shorter duration of diabetes, older age of pancreas graft-donors, and younger age of kidney graft-donors in the SPLK group. Our results showed that the death-censored pancreas graft survival rate was lower in the SPLK group. In addition, the incidence of BPAR of the pancreas graft was higher in the SPLK group. There was no significant difference in the presence of de novo DSA and the rates of kidney graft failure, kidney BPAR, and mortality. Our results show that SPLK can be considered an alternative option for SPK although higher incidences of BPAR and graft failure of pancreas after SPLK need to be overcome.
White matter alterations in MR-negative temporal and frontal lobe epilepsy using fixel-based analysis
Authors: Bartoňová Michaela , Tournier Jacques-Donald , Bartoň Marek , Říha Pavel , Vojtíšek Lubomír , Mareček Radek , Doležalová Irena , Rektor Ivan
Published: January 2023

This study focuses on white matter alterations in pharmacoresistant epilepsy patients with no visible lesions in the temporal and frontal lobes on clinical MRI (i.e. MR-negative) with lesions confirmed by resective surgery. The aim of the study was to extend the knowledge about group-specific neuropathology in MR-negative epilepsy. We used the fixel-based analysis (FBA) that overcomes the limitations of traditional diffusion tensor image analysis, mainly within-voxel averaging of multiple crossing fibres. Group-wise comparisons of fixel parameters between healthy controls (N = 100) and: (1) frontal lobe epilepsy (FLE) patients (N = 9); (2) temporal lobe epilepsy (TLE) patients (N = 13) were performed. A significant decrease of the cross-section area of the fixels in the superior longitudinal fasciculus was observed in the FLE. Results in TLE reflected widespread atrophy of limbic, thalamic, and cortico-striatal connections and tracts directly connected to the temporal lobe (such as the anterior commissure, inferior fronto-occipital fasciculus, uncinate fasciculus, splenium of corpus callosum, and cingulum bundle). Alterations were also observed in extratemporal connections (brainstem connection, commissural fibres, and parts of the superior longitudinal fasciculus). To our knowledge, this is the first study to use an advanced FBA method not only on the datasets of MR-negative TLE patients, but also MR-negative FLE patients, uncovering new common tract-specific alterations on the group level.
A new dataset for mongolian online handwritten recognition
Authors: Pan Yuecai , Fan Daoerji , Wu Huijuan , Teng Da
Published: January 2023

This paper introduces a new traditional Mongolian word-level online handwriting dataset, MOLHW. The dataset consists of handwritten Mongolian words, including 164,631 samples written by 200 writers and covering 40,605 Mongolian common words. These words were selected from a large Mongolian corpus. The coordinate points of words were collected by volunteers, who wrote the corresponding words on the dedicated application for their mobile phones. Latin transliteration of Mongolian was used to annotate the coordinates of each word. At the same time, the writer’s identification number and mobile phone screen information were recorded in the dataset. Using this dataset, we propose an encoder–decoder Mongolian online handwriting recognition model with a deep bidirectional gated recurrent unit and attention mechanism as the baseline evaluation model. Under this model, the optimal performance of the word error rate (WER) on the test set was 24.281%. Furthermore, we present the experimental results of different Mongolian online handwriting recognition models. The experimental results show that compared with other models, the model based on Transformer could learn the corresponding character sequences from the coordinate data of the dataset more effectively, with a 16.969% WER on the test set. The dataset is now freely available to researchers worldwide. The dataset can be applied to handwritten text recognition as well as handwritten text generation, handwriting identification, and signature recognition.
Formation of the North Atlantic Warming Hole by reducing anthropogenic sulphate aerosols
Authors: Kusakabe Yuki , Takemura Toshihiko
Published: January 2023

The North Atlantic Warming Hole (NAWH) has been observed and predicted due to the increase in carbon dioxide (CO2) concentration. If sulphate aerosols, which have a cooling effect on the atmosphere, are reduced by air pollution control, the NAWH may form as it would if CO2 concentrations increased. In this study, sensitivity experiments using a coupled atmosphere–ocean-aerosol model were conducted by varying the amount of sulphur dioxide (SO2) emissions, a precursor of sulphate which is the primary anthropogenic aerosol in the atmosphere, to analyse the changes in the ocean temperature, salinity, and density. The results showed that although the spatial patterns of the NAWH due to the changes in SO2 emissions was similar to that due to the changes in the CO2 concentrations, the magnitude of the shifts in the ocean parameters due to the changes in SO2 emissions is larger even when changes in global mean temperature are comparable. This can be due to the spatial concentration of sulphate aerosols in the mid-latitudes of the Northern Hemisphere, resulting larger changes in the heat transport from the south on the Gulf Stream and the North Atlantic Current along with changes in freshwater inflow from the Arctic through the Labrador Sea.
Computational method of the cardiovascular diseases classification based on a generalized nonlinear canonical decomposition of random sequences
Authors: Atamanyuk Igor , Kondratenko Yuriy , Havrysh Valerii , Volosyuk Yuriy
Published: January 2023

Decision support systems can seriously help medical doctors in the diagnosis of different diseases, especially in complicated cases. This article is devoted to recognizing and diagnosing heart disease based on automatic computer processing of the electrocardiograms (ECG) of patients. In the general case, the change of the ECG parameters can be presented as a random sequence of the signals under processing. Developing new computational methods for such signal processing is an important research problem in creating efficient medical decision support systems. Authors consider the possibility of increasing the diagnostic accuracy of cardiovascular diseases by implementing of the new proposed computational method of information processing. This method is based on the generalized nonlinear canonical decomposition of a random sequence of the change of cardiogram parameters. The use of a nonlinear canonical model makes it possible to significantly simplify the maximum likelihood criterion for classifying diseases. This simplification is provided by the transition from a multi-dimensional distribution density of cardiogram parameters to a product of one-dimensional distribution densities of independent random coefficients of a nonlinear canonical decomposition. The absence of any restrictions on the class of random sequences under study makes it possible to achieve maximum accuracy in diagnosing cardiovascular diseases. Functional diagrams for implementing the proposed method reflecting the features of its application are presented. The quantitative parameters of the core of the computational diagnostic procedure can be determined in advance based on the preliminary statistical data of the ECGs for different heart diseases. That is why the developed method is quite simple in terms of computation (computing complexity, accuracy, computing time, etc.) and can be implemented in medical computer decision systems for monitoring cardiovascular diseases and for their diagnosis in real time. The results of the numerical experiment confirm the high accuracy of the developed method for classifying cardiovascular diseases.
A nomogram risk assessment model to predict the possibility of type II endoleak-related re-intervention after endovascular aneurysm repair (EVAR)
Authors: Liu Zongwei , Chen Yonghui , Qin Yafei , Bi Jiaxue , Wang Jiaxin , Niu Fang , Dai Xiangchen
Published: January 2023

This study aimed to develop and validate a novel nomogram risk assessment model to predict the possibility of type II endoleak (T2EL)-related re-intervention. The data of 455 patients with abdominal aortic aneurysms who underwent elective endovascular aneurysm repair (EVAR) procedures between January 2018 and December 2021 at our single center were retrospectively reviewed. Following the implementation of exclusion criteria, 283 patients were finally included and divided into T2EL-related re-intervention (n = 42) and non-T2EL (n = 241) groups. The overall T2EL-related re-intervention rate for 283 patients was 14.8% (42/283). Using multivariate analysis, significant risk factors for re-intervention included age (OR, 1.172; 95% CI, 1.051–1.307; P = 0.004), smoking (OR, 13.418; 95% CI, 2.362–76.215; P = 0.003), diameter of inferior mesenteric artery (IMA) (OR, 21.380; 95% CI, 3.060–149.390; P = 0.002), and number of patent lumbar arteries (OR, 9.736; 95% CI, 3.175–29.857; P < 0.001). The discrimination ability of this risk-predictive model was reasonable (concordance index [C-index] = 0.921; 95% CI, 0.878–0.964). The Hosmer–Lemeshow goodness of fit test was performed on the model, and the chi-square value was 3.210 (P = 0.920), presenting an excellent agreement between the model-predicted and observed values. The receiver operating characteristic (ROC) curve identified that the risk thresholds of re-intervention were a diameter of > 2.77 mm for the diameter of the inferior mesenteric artery and a proportion of < 45.5% for thrombus volume in the aneurysm sac. This novel nomogram risk assessment model for predicting the possibility of patients’ T2EL-related re-interventions after EVAR should be helpful in discriminating high-risk patients. Two novel risk thresholds may imply a higher possibility of T2EL-related re-intervention after EVAR.
The analysis of per- and polyfluoroalkyl substances in wastewater sludges and biosolids: which adsorbents should be used for the cleanup of extracts?
Authors: Ozelcaglayan Ali Can , Parker Wayne J. , Pham Anh Le-Tuan
Published: January 2023

The analysis of PFAS in a variety of municipal biosolids was enhanced through optimizing adsorbent use in sample cleanup.
Soy yoghurts produced with efficient GABA (γ-aminobutyric acid)-producing Lactiplantibacillus plantarum ameliorate hyperglycaemia and re-establish gut microbiota in streptozotocin (STZ)-induced diabetic mice
Authors: Weng Brian Bor-Chun , Yuan Hung-De , Chen Lih-Geeng , Chu Chishih , Hsieh Chia-Wen
Published: January 2023

Soy yogurt has been gaining popularity as a vegan food produced simply by soymilk fermentation with proper microbial manipulation.
Effects of MOF linker rotation and functionalization on methane uptake and diffusion
Authors: Yue Shuwen , Oh Changhwan , Nandy Aditya , Terrones Gianmarco G. , Kulik Heather J.
Published: January 2023

Neglecting linker rotation in molecular simulations of methane in UiO-66 can have a significant impact on methane diffusion and moderate impact on methane uptake.
Novel electronic and magnetic features in XC (X = Si and Ge) monolayers induced by doping with group-VA atoms
Authors: Ha Chu Viet , Nguyen Duy Khanh , Anh Dang Tuan , Guerrero-Sanchez J. , Hoat D. M.
Published: January 2023

Spin density in the XC (X = Si and Ge) monolayers doped with group-VA (N, P, and As) atom.
Nanoarchitectonics in fully printed perovskite solar cells with carbon-based electrodes
Authors: Bogachuk Dmitry , Girard Jessica , Tilala Siddharth , Martineau David , Narbey Stéphanie , Verma Anand , Hinsch Andreas , Kohlstädt Markus , Wagner Lukas
Published: January 2023

In this work, we demonstrate a novel nanoarchitectonic approach to tailor perovskite crystal growth leading to the enhancement of the opto-electronic properties and power conversion efficiency of perovskite solar cells.
Electrospun polymer nanocomposites for thermal management: a review
Authors: Han Wei-Hua , Wang Qing-Yu , Kang Yuan-Yi , Zhou Xin , Hao Chun-Cheng
Published: January 2023

This review addresses the applications of electrospinning in the thermal management of polymer matrix composites, mainly involving enhanced thermal conductivity, thermal insulation, and passive daytime radiative cooling.
Synthesis of cyano-substituted γ-lactams through a copper-catalyzed cascade cyclization/cyanation reaction
Authors: Liu Wen , Wang Liang , Mu Haiping , Zhang Qian , Fang Zeguo , Li Dong
Published: January 2023

A copper-catalyzed cascade cyclization/cyanation of N-aryl-4-pentenamides with TMSCN was developed. The reaction proceeded in water under simple conditions to generate a series of cyano-substituted γ-lactam derivatives.
All-small-molecule efficient ternary organic solar cells employing a coumarin donor and two fullerene-free acceptors
Authors: Sharma Ganesh D. , Pradhan Rashmirekha , Khandelwal Kanupriya , Singhal Rahul , Liu Wenrui , Zhu Xiaozhang , Mishra Amaresh
Published: January 2023

A ternary organic solar cell composed of two fullerene-free acceptors and a coumarin donor attained appropriate nano-scale phase separation, achieving a PCE of 15.54%.
Efficacy and safety of repeated endoscopic radial incision and cutting procedure for benign esophageal stricture
Authors: Kano Yuki , Kadota Tomohiro , Inaba Atsushi , Sunakawa Hironori , Takashima Kenji , Nakajo Keiichiro , Murano Tatsuro , Shinmura Kensuke , Yoda Yusuke , Ikematsu Hiroaki , Akimoto Tetsuo , Yano Tomonori
Published: January 2023

Background and study aims: Radial incision and cutting (RIC) is indicated for refractory benign esophageal strictures after curative treatment for esophageal cancer and has shown favorable short-term outcomes. However, re-stricture after RIC may occur in the long term, and RIC is performed repeatedly in such cases, but the efficacy and safety of repeated RIC are unclear. Therefore, we aimed to demonstrate the efficacy and safety of the repeated RIC for refractory benign esophageal strictures after surgical and non-surgical treatment.

Patients and methods: Between April 2008 and September 2019, we enrolled patients who were treated with the first RIC for benign esophageal strictures. The RIC was indicated for the refractory stricture and repeatedly performed for re-refractory esophageal stricture after RIC. We retrospectively evaluated the 6-month refractory stricture-free rate, and adverse events (AEs) in the first RIC and repeated RICs.

Results: Forty-six patients (39 men, 7 women; median age, 71 years, range 49–85) were included. RIC was performed once in 24 patients (non-repeated RIC group) and two or more times in 22 patients (repeated RIC group). In all patients, the 6-month refractory stricture-free rate after the first RIC were 42.3 %. In the repeated RIC group, the 6-month refractory stricture-free rate after the first and repeated RICs were 18.2 % vs 18.2 %, respectively. No AEs were noted.

Conclusions: Repeated RIC could be effective in the short-term and safe even for patients with refractory benign esophageal stricture after the first RIC. However, it cannot be considered curative treatment for refractory stricture because of poor long-term results.
Gender Parity in Healthcare: A Chronicle of Escalating Success Rate of Female Radiation Oncologists in India
Authors: Sarkar Biplab , Pradhan Anirudh
Published: January 2023

Objectives This editorial describes the growth pattern of female radiation oncologists (FRO) in India and the prediction of gender equality through a mathematical formulation.

Materials and Methods Among the countries in South Asia, India has the largest population of radiation oncologists (RO), a total of 3,763: 1,286 female and 2,477 male radiation oncologists (MROs), and they are registered with the Association of Radiation Oncologists of India (AROI). The data were analyzed to find the differential and cumulative growth pattern of the FROs and MROs and predict gender equality in radiation oncology. The cumulative growth rate indicates the total number of FROs and MROs by end of every year. Differential growth rate indicates the differential increase in the number of FROs and MROs for a particular year. Annual cumulative and differential growth patterns were plotted as a function of the time, and an analytical functional form was fitted to predict the future growth pattern and achievement of gender equality.

Results AROI registration of FROs and MROs for 2013–2020 were as follows: FRO: MRO 2013-54: 102, 2014-99: 162, 2015-77: 148; 2016-86: 143, 2017-110: 110, 2018-116: 151, 2019-121: 152, 2020 (October)-129: 110. Differential growth pattern between 2013 and 2020 with the average incremental growth rate for FROs and MROs were 12.7 ± 14.8% and 2.1 ± 32.0%. Differential growth rate FRO fits in a power-law exponent 58.6 ×(Power0.3695), where MRO growth pattern showed a saturation [4.7ln(×) + 128.5] . Gender parity among Indian radiation oncologists is likely to be achieved by end of 2027.

Conclusions The present density of FRO in India 34.1% is high compared to developed countries such as the United States (≈26%). It is a big leap for the Indian radiation oncology society tending toward gender parity.
Rare Case of Extracranial Metastases in a Patient with IDH-Mutant Glioblastoma
Authors: Thimma Sudarsan Rishan , Ramanujan Vishnu , Rajendran Adhithyan , Shafi Sadiya , Patil Sushma , Ghosh Siddhartha , Jalali Rakesh
Published: January 2023

Glioblastoma are known for its aggressive intracranial course of disease, where the overall survival is less than 18 months. Of late, the World Health Organization has reclassified and renamed secondary glioblastomas as isocitrate dehydrogenase (IDH)-mutant grade 4 astrocytomas, which is relatively better than its IDH wild-type counterpart; however, overall survival remains poor. In such tumors, metastases outside the craniospinal neuraxis is very rare, and does sometimes present with symptoms which create a diagnostic dilemma and arriving at such diagnosis is still challenging even for the best of the clinicians worldwide. Here we present such a rare case scenario, where a grade 4 astrocytoma that has transformed from a low-grade glioma, presenting with bone metastases, its workup, treatment, and various possible mechanisms underlying such a rare event, and the need of such clinical scenario especially long-term survivors to be wary of distant metastases.
Patellar Proximo-Distal Displacement following Modified Maquet Technique Is Not Predictive of Patellar Luxation
Authors: Giansetto Thomas Elie , Pierrot Emilie , Picavet Pierre P. , Lefebvre Michael , Rives Albane , Farnir Frédéric , Claeys Stéphanie , Balligand Marc
Published: January 2023

Objective The aim of this study was to test the low sensitivity of the Allberg and Miles index to the stifle opening angle, evaluate the displacement of the patella after a Modified Maquet Technique using this index and assess the incidence of patellar luxation post-Modified Maquet Technique in dogs.

Study Design Medical records were reviewed from 2012 to 2017. Allberg Miles index were determined for each stifle pre- and postoperatively, as well as the stifle joint opening of each case. Occurrence of patellar luxation was recorded.

Results 137 stifles on 116 dogs were reviewed. The stifle opening angle did not influence the Allberg Miles index. Pre- and postoperative index showed a distal displacement of the patella after a Modified Maquet Procedure, especially at 135° of stifle opening angle. Only 1/137 cases demonstrated patellar luxation after the surgery.

Conclusion Based on our statistical analysis, we were able to conclude that within the maximum stifle opening angle range recorded in our series of cases; the Allberg Miles index variation was not significant. While patellar baja is clearly induced by the Modified Maquet Technique, the latter did not seem to predispose patients to post-operative patellar luxation in our study population.
Venous Thromboembolism Associated with Assisted Reproductive Technology: A Systematic Review and Meta-analysis
Authors: Goualou Marianne , Noumegni Steve , de Moreuil Claire , Le Guillou Mathilde , De Coninck Gabrielle , Hoffmann Clément , Robin Sara , Morcel Karine , Le Moigne Emmanuelle , Tremouilhac Christophe , Merviel Philippe , Le Mao Raphael , Leroyer Christophe , Bouée Sarah , Couturaud Francis , Tromeur Cécile
Published: January 2023

Background Hormonal exposure leads to an increased risk of venous thromboembolism (VTE) but the risk of VTE associated with assisted reproductive technology (ART) is not clearly determined.

Methods We searched in PubMed, EMBASE, Web of Science, and the Cochrane Library databases and identified all relevant articles published up to February 1, 2021. The primary objective was to determine the frequency of VTE associated with ART. Secondary objectives were to determine (1) the risk of VTE associated with ART as compared to pregnancy without ART; (2) the risk of VTE associated with ovarian hyperstimulation syndrome (OHSS); and (3) to determine potential risk factors of VTE related to ART.

Results Fourteen studies were included. The overall frequency of VTE associated with ART was 0.23% (95% confidence interval [CI]: 0.07–0.46). Women undergoing ART had a two- to threefold increased risk of VTE as compared to spontaneous pregnancy (relative risk [RR]: 2.66; 95% CI: 1.60–4.43). The overall frequency of VTE specifically related to OHSS was <0.001%. The risk of VTE after ART complicated by OHSS, as compared to ART without OHSS, was higher but not statistically significant (RR: 14.83; 95% CI: 0.86–255.62). Risk factors of VTE associated with ART were in vitro fertilization procedure (RR, odds ratio [OR], and hazard ratio varying from 1.77, 95% CI: 1.41–2.23 to 4.99, 95% CI: 1.24–20.05), hyperhomocysteinemia (OR: 15.2; 95% CI: 2.0–115.0), polycystic ovarian syndrome (PCOS) (RR: 4.8; 95% CI: 1.7–13.4), successful ART leading to pregnancy (OR: 13.94; 95% CI: 1.41–137.45).

Conclusion Further large prospective studies on risk factors of VTE in women undergoing ART are needed in order to optimize thromboprophylaxis in this context.
Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye
Authors: Barclay Matthew S. , Chowdhury Azhad U. , Biaggne Austin , Huff Jonathan S. , Wright Nicholas D. , Davis Paul H. , Li Lan , Knowlton William B. , Yurke Bernard , Pensack Ryan D. , Turner Daniel B.
Published: January 2023

DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA–Cy5 complex. These insights will support future studies on DNA’s structural heterogeneity.
Correlated Dirac–Coulomb–Breit multiconfigurational self-consistent-field methods
Authors: Hoyer Chad E. , Lu Lixin , Hu Hang , Shumilov Kirill D. , Sun Shichao , Knecht Stefan , Li Xiaosong
Published: January 2023

The fully correlated frequency-independent Dirac–Coulomb–Breit Hamiltonian provides the most accurate description of electron–electron interaction before going to a genuine relativistic quantum electrodynamics theory of many-electron systems. In this work, we introduce a correlated Dirac–Coulomb–Breit multiconfigurational self-consistent-field method within the frameworks of complete active space and density matrix renormalization group. In this approach, the Dirac–Coulomb–Breit Hamiltonian is included variationally in both the mean-field and correlated electron treatment. We also analyze the importance of the Breit operator in electron correlation and the rotation between the positive- and negative-orbital space in the no-virtual-pair approximation. Atomic fine-structure splittings and lanthanide contraction in diatomic fluorides are used as benchmark studies to understand the contribution from the Breit correlation.
Inverse condensation of adsorbed molecules with two conformations
Authors: Picard Joël A. K. L. , Speck Thomas
Published: January 2023

Conventional gas–liquid phase transitions feature a coexistence line that has a monotonic and positive slope in line with our intuition that cooling always leads to condensation. Here, we study the inverse phenomenon, condensation of adsorbed organic molecules into dense domains upon heating. Our considerations are motivated by recent experiments [Aeschlimann et al., Angew. Chem., Int. Ed. 60, 19117–19122 (2021)], which demonstrate the partial dissolution of an ordered molecular monolayer and the mobilization of molecules upon cooling. We introduce a simple lattice model in which each site can have three states corresponding to unoccupied and two discernible molecular conformations. We investigate this model through Monte Carlo simulations, mean-field theory, and exact results based on the analytical solution of the Ising model in two dimensions. Our results should be broadly applicable to molecules with distinct conformations that have sufficiently different entropies or heat capacities.
Inference of 3D genome architecture by modeling overdispersion of Hi-C data
Authors: Varoquaux Nelle , Noble William S , Vert Jean-Philippe
Published: January 2023

Motivation

We address the challenge of inferring a consensus 3D model of genome architecture from Hi-C data. Existing approaches most often rely on a two-step algorithm: first, convert the contact counts into distances, then optimize an objective function akin to multidimensional scaling (MDS) to infer a 3D model. Other approaches use a maximum likelihood approach, modeling the contact counts between two loci as a Poisson random variable whose intensity is a decreasing function of the distance between them. However, a Poisson model of contact counts implies that the variance of the data is equal to the mean, a relationship that is often too restrictive to properly model count data.

Results

We first confirm the presence of overdispersion in several real Hi-C datasets, and we show that the overdispersion arises even in simulated datasets. We then propose a new model, called Pastis-NB, where we replace the Poisson model of contact counts by a negative binomial one, which is parametrized by a mean and a separate dispersion parameter. The dispersion parameter allows the variance to be adjusted independently from the mean, thus better modeling overdispersed data. We compare the results of Pastis-NB to those of several previously published algorithms, both MDS-based and statistical methods. We show that the negative binomial inference yields more accurate structures on simulated data, and more robust structures than other models across real Hi-C replicates and across different resolutions.

Availability and implementation

A Python implementation of Pastis-NB is available at https://github.com/hiclib/pastis under the BSD license.

Supplementary information

Supplementary data are available at Bioinformatics online.
The PRALINE database: protein and Rna humAn singLe nucleotIde variaNts in condEnsates
Authors: Vandelli Andrea , Arnal Segura Magdalena , Monti Michele , Fiorentino Jonathan , Broglia Laura , Colantoni Alessio , Sanchez de Groot Natalia , Torrent Burgas Marc , Armaos Alexandros , Tartaglia Gian Gaetano
Published: January 2023

Biological condensates are membraneless organelles with different material properties. Proteins and RNAs are the main components, but most of their interactions are still unknown. Here, we introduce PRALINE, a database for the interrogation of proteins and RNAs contained in stress granules, processing bodies and other assemblies including droplets and amyloids. PRALINE provides information about the predicted and experimentally validated protein–protein, protein–RNA and RNA–RNA interactions. For proteins, it reports the liquid–liquid phase separation and liquid–solid phase separation propensities. For RNAs, it provides information on predicted secondary structure content. PRALINE shows detailed information on human single-nucleotide variants, their clinical significance and presence in protein and RNA binding sites, and how they can affect condensates’ physical properties.

Availability and implementation

PRALINE is freely accessible on the web at http://praline.tartaglialab.com.
Brain microdialysate tau dynamics predict functional and neurocognitive recovery after poor-grade subarachnoid haemorrhage
Authors: Heilig Marina , Rass Verena , Lindner Anna , Kofler Mario , Ianosi Bogdan-Andrei , Gaasch Maxime , Putnina Lauma , Humpel Christian , Scherfler Christoph , Zamarian Laura , Bodner Thomas , Djamshidian Atbin , Schiefecker Alois , Thomé Claudius , Beer Ronny , Pfausler Bettina , Helbok Raimund
Published: January 2023

Subarachnoid haemorrhage is a devastating disease that results in neurocognitive deficits and a poor functional outcome in a considerable proportion of patients. In this study, we investigated the prognostic value of microtubule-associated tau protein measured in the cerebral microdialysate for long-term functional and neuropsychological outcomes in poor-grade subarachnoid haemorrhage patients. We recruited 55 consecutive non-traumatic subarachnoid haemorrhage patients who underwent multimodal neuromonitoring, including cerebral microdialysis. Mitochondrial dysfunction was defined as lactate-to-pyruvate ratio >30 together with pyruvate >70 mmol/L and metabolic distress as lactate-to-pyruvate ratio >40. The multidimensional 12-month outcome was assessed by means of the modified Rankin scale (poor outcome: modified Rankin scale ≥4) and a standardized neuropsychological test battery. We used multivariable generalized estimating equation models to assess associations between total microdialysate-tau levels of the first 10 days after admission and hospital complications and outcomes. Patients were 56 ± 12 years old and presented with a median Hunt & Hess score of 5 (interquartile range: 3–5). Overall mean total microdialysate-tau concentrations were highest within the first 24 h (5585 ± 6291 pg/mL), decreased to a minimum of 2347 ± 4175 pg/mL on Day 4 (P < 0.001) and remained stable thereafter (P = 0.613). Higher total microdialysate-tau levels were associated with the occurrence of delayed cerebral ischaemia (P = 0.001), episodes of metabolic distress (P = 0.002) and mitochondrial dysfunction (P = 0.034). Patients with higher tau levels had higher odds for a poor 12-month functional outcome (adjusted odds ratio: 2.61; 95% confidence interval: 1.32–5.17; P = 0.006) and impaired results in the trail making test-B (adjusted odds ratio: 3.35; 95% confidence interval: 1.16–9.68; P = 0.026) indicative of cognitive flexibility. Total microdialysate-tau levels significantly decreased over the first 10 days (P < 0.05) in patients without delayed cerebral ischaemia or good functional outcomes and remained high in those with delayed cerebral ischaemia and poor 12-month outcomes, respectively. Dynamic changes of total tau in the cerebral microdialysate may be a useful biomarker for axonal damage associated with functional and neurocognitive recovery in poor-grade subarachnoid haemorrhage patients. In contrast, ongoing axonal damage beyond Day 3 after bleeding indicates a higher risk for delayed cerebral ischaemia as well as a poor functional outcome.
Unemployment persistence among second-generation immigrants
Authors: Aradhya Siddartha , Grotti Raffaele , Härkönen Juho
Published: January 2023

Many immigrant groups disproportionately experience unemployment and this disadvantage often extends to their children—the second generation. This paper contributes to this stream of research by studying unemployment dynamics of the ancestral population and second-generation immigrants in Sweden. In particular, we ask: does unemployment persistence differ between ancestral Swedes and 10 second-generation immigrant groups? We answer this question using correlated dynamic random-effects logit models to study the effect of past on current unemployment—also known as genuine state dependence. We use Swedish register data to follow individuals over their early working careers. The results indicate that although past unemployment has a similar relative effect on current unemployment across the ancestry groups, past unemployment increases the probability of current unemployment (absolute effect) more among second-generation Middle-Eastern, Turkish, and Southern European immigrants. Because of higher baseline levels of unemployment, the labour market consequences of similar relative effects are more pronounced among the second generation as compared to ancestral Swedes. The paper concludes by elaborating on the reasons behind these contrasting results while highlighting the importance of examining heterogeneous effects on both the relative and absolute scales.
Members ofEnsiferandRhizobiumgenera are new bacterial endosymbionts nodulatingPisum sativum(L.)
Authors: Mahdhi A , Mars M , Rejili M
Published: January 2023

A total of 84 Pisum sativum legume nodulating bacteria (LNB) were isolated from seven geographical sites from southern Tunisia. Phylogenetic analyses based on partial sequences of 16S rRNA gene and the housekeeping genes glnII, and recA grouped strains into six clusters, four of which belonged to the genus Rhizobium and two to the Ensifer genus. Among Rhizobium clusters, 41 strains were affiliated to Rhizobium leguminosarum, two strains to R. pisi, two strains to R. etli, and interestingly two strains belonged to previously undescribed Rhizobium species. The remaining two strains were closely related to Ensifer medicae (two strains) and Ensifer meliloti (two strains). A symbiotic nodC gene-based phylogeny and host specificity test showed that all Rhizobium strains nodulating pea belonged to the symbiovar viciae, whereas the Ensifer strains were associated with the symbiovar meliloti never described to date. All strains under investigation differed in the number of induced root nodules and the effectiveness of atmospheric nitrogen fixation. The R. leguminosarum PsZA23, R. leguminosarum PsGBL42, and E. medicae PsTA22a, forming the most effective symbiosis with the plant host, are potential candidates for inoculation programs.
The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes
Authors: Fletcher Kyle , Martin Frank , Isakeit Thomas , Cavanaugh Keri , Magill Clint , Michelmore Richard
Published: January 2023

Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.
From Trans-Atlantic Order to Afro-Eur-Asian Worlds? Reimagining International Relations as Interlocking Regional Worlds
Authors: Fisher-Onar Nora , Kavalski Emilian
Published: January 2023

The apparent transition underway from a trans-Atlantic, liberal world order to one of multiple, overlapping orders has caused much policy, scholarly, and public anxiety. In tandem with this structural development, in the field of international relations (IR), heated contests are underway between alternative visions of how to read this transformation. In this introduction to the special forum, we outline an approach for grappling with these dynamics. Our overarching question is: How to make sense of emergent regional imaginaries, the ways that they interlock, and the implications for IR theory and practice? To begin answering, we first challenge the increasingly widespread view that the return of great power politics—or what we call the “great game” vision of multipolarity—is the only or best register with which to read emerging patterns. Instead, we propose the idea of “interlocking regional worlds,” a notion inspired by “Afro-Eur-Asia” as a site that evokes multiple meanings. A historically sensitive and sociologically nuanced analytical modality, we argue for theory as “itinerant translation” across regional worlds. This relational framework, we contend, can help to better understand and explain, observe and encounter one another, the problems that collectively embroil us, and the transformative processes to which we are bearing witness. The exercises in itinerant translation across the interlocking regional worlds of Afro-Eur-Asia on offer in this special forum likewise reveal the globe as a pluriversal space where multiple realities can and do coexist (and always have).
Skin for Skin: Biblical Language in Jamaica’s Morant Bay Rebellion
Authors: Russell Stephen C
Published: January 2023

In October, 1865, Paul Bogle and a few hundred Black residents of rural Jamaica rebelled against the vagaries of an overly zealous magistrate. They set the courthouse at Morant Bay on fire and killed over a dozen people, mostly white. In the savage government reprisals that followed, over 430 Black Jamaicans were executed. Here, I observe how biblical language played a central role in public discourse about the rebellion. I focus on the rebellion’s slogan: skin for skin. I trace the interpretive history of this phrase drawn from the book of Job, showing how it became associated with advocacy for Black rights. And I examine the social context of Bogle’s use of the phrase to call for a Black alliance that crossed ethnic, religious, and class lines. I thus further a critical trajectory that has recognized the importance of biblical language to race talk in the age of emancipation.
Identification of outcomes reported for hospital antimicrobial stewardship interventions using a systematic review of reviews
Authors: Yousuf Shazia , Rzewuska Magdalena , Duncan Eilidh , Ramsay Craig
Published: January 2023

Background

Randomized trials of hospital antimicrobial stewardship (AMS) interventions aimed to optimize antimicrobial use contribute less to the evidence base due to heterogeneity in outcome selection and reporting. Developing a core outcome set (COS) for these interventions can be a way to address this problem. The first step in developing a COS is to identify and map all outcomes.

Objectives

To identify outcomes reported in systematic reviews of hospital AMS interventions.

Methods

Cochrane Database of Systematic Reviews, MEDLINE and Embase were searched for systematic reviews published up until August 2019 of interventions relevant to reducing unnecessary antimicrobial use for inpatient populations in secondary care hospitals. The methodological quality of included reviews was assessed using AMSTAR-2, A (revised) MeaSurement Tool to Assess systematic Reviews. Extracted outcomes were analysed using deductive and inductive thematic analysis. A list of overarching (unique) outcomes reflects the outcomes identified within the systematic reviews.

Results

Forty-one systematic reviews were included. Thirty-three (81%) systematic reviews were of critically low or low quality. A long list of 1739 verbatim outcomes was identified and categorized under five core areas of COMET (Core Outcome Measures in Effectiveness Trials) taxonomy: ‘resources use’ (45%), ‘physiological/clinical’ (27%), ‘life impact’ (16%), ‘death’ (8%) and ‘adverse events’ (4%). A total of 421 conceptually different outcomes were identified and grouped into 196 overarching outcomes.

Conclusions

There is significant heterogeneity in outcomes reported for hospital AMS interventions. Reported outcomes do not cover all domains of the COMET framework and may miss outcomes relevant to patients (e.g. emotional, social functioning, etc.). The included systematic reviews lacked methodological rigour, which warrants further improvements.
Vitamin C Status of US Adults Assessed as Part of the National Health and Nutrition Examination Survey Remained Unchanged between 2003–2006 and 2017–2018
Authors: Powers Carissa D , Sternberg Maya R , Patel Sweta B , Pfeiffer Christine M , Storandt Renee J , Schleicher Rosemary L
Published: January 2023

Background

We compared serum vitamin C (VIC) status of the adult (≥20 y) US population in the National Health and Nutrition Examination Survey (NHANES) 2017–2018 with combined data from 2003–2004 and 2005–2006.

Methods

VIC was measured using HPLC with electrochemical detection. Mean data were stratified by age, sex, race/Hispanic origin, income, body mass index, dietary intake, supplement use, and smoking status. Prevalence of VIC deficiency (<11.4 μmol/L) was calculated.

Results

In NHANES 2017–2018, the mean VIC was 8 μmol/L higher in people ≥60 y compared with those 20–59 y of age, 10 μmol/L lower in men vs women, 8 μmol/L lower in low vs high income, 11 μmol/L lower in obese vs healthy weight, and 15 μmol/L lower in smokers vs nonsmokers. Differences in mean VIC across race/Hispanic origin groups ranged from 2 to 7 μmol/L. Mean VIC was 27 μmol/L higher with vitamin C-containing supplement use and positively associated (Spearman ρ = 0.33; P < 0.0001) with increasing dietary intake. The associations between mean VIC and the investigated covariates were generally consistent and the prevalence of deficiency was not significantly different between survey periods (6.8% vs 7.0%; P = 0.83). However, a few subgroups had double the risk. We found no significant survey differences in mean VIC (51.2 vs 54.0 μmol/L; P = 0.09).

Conclusions

Overall VIC status of the US adult population has remained stable since last assessed in the NHANES 2005–2006 survey. Vitamin C deficiency remained high for those with low dietary intake and who smoke.