bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precursor of pair-density wave in doping Kitaev spin liquid on the honeycomb lattice
Authors: Peng Cheng , Jiang Yi-Fan , Devereaux Thomas P. , Jiang Hong-Chen 
Published: July 2021

AbstractWe study the effects of doping the Kitaev model on the honeycomb lattice where the spins interact via the bond-directional interaction JK, which is known to have a quantum spin liquid as its exact ground state. The effect of hole doping is studied within the t-JK model on a three-leg cylinder using density-matrix renormalization group. Upon light doping, we find that the ground state of the system has a dominant quasi-long-range charge-density-wave correlations but short-range single-particle correlations. In the pairing channel, the even-parity superconducting correlation is dominant with d-wave-like symmetry, which oscillates in sign as a function of separation with a period equal to that of the spin-density wave and two times the charge-density wave. Although these correlations fall rapidly (possibly exponentially) at long distances, this is never-the-less the example where a pair-density wave is the leading instability in the pairing channel on the honeycomb lattice.
Consolidated bioprocessing for bioethanol production by metabolically engineered Bacillus subtilis strains
Authors: Maleki Fatemeh , Changizian Mohammad , Zolfaghari Narges , Rajaei Sarah , Noghabi Kambiz Akbari , Zahiri Hossein Shahbani 
Published: July 2021

AbstractBioethanol produced by fermentative microorganisms is regarded as an alternative to fossil fuel. Bioethanol to be used as a viable energy source must be produced cost-effectively by removing expense-intensive steps such as the enzymatic hydrolysis of substrate. Consolidated bioprocessing (CBP) is believed to be a practical solution combining saccharification and fermentation in a single step catalyzed by a microorganism. Bacillus subtills with innate ability to grow on a diversity of carbohydrates seems promising for affordable CBP bioethanol production using renewable plant biomass and wastes. In this study, the genes encoding alcohol dehydrogenase from Z. mobilis (adhZ) and S. cerevisiae (adhS) were each used with Z. mobilis pyruvate decarboxylase gene (pdcZ) to create ethanologenic operons in a lactate-deficient (Δldh) B. subtilis resulting in NZ and NZS strains, respectively. The S. cerevisiae adhS caused significantly more ethanol production by NZS and therefore was used to make two other operons including one with double copies of both pdcZ and adhS and the other with a single pdcZ but double adhS genes expressed in N(ZS)2 and NZS2 strains, respectively. In addition, two fusion genes were constructed with pdcZ and adhS in alternate orientations and used for ethanol production by the harboring strains namely NZ:S and NS:Z, respectively. While the increase of gene dosage was not associated with elevated carbon flow for ethanol production, the fusion gene adhS:pdcZ resulted in a more than two times increase of productivity by strain NS:Z as compared with NZS during 48 h fermentation. The CBP ethanol production by NZS and NS:Z using potatoes resulted in 16.3 g/L and 21.5 g/L ethanol during 96 h fermentation, respectively. For the first time in this study, B. subtilis was successfully used for CBP ethanol production with S. cerevisiae alcohol dehydrogenase. The results of the study provide insights on the potentials of B. subtilis for affordable bioethanol production from inexpensive plant biomass and wastes. However, the potentials need to be improved by metabolic and process engineering for higher yields of ethanol production and plant biomass utilization.
Normal colour perception in developmental prosopagnosia
Authors: Smith Chelsea , Susilo Tirta 
Published: July 2021

AbstractDevelopmental prosopagnosia (DP) is a selective neurodevelopmental condition defined by lifelong impairments in face recognition. Despite much research, the extent to which DP is associated with broader visual deficits beyond face processing is unclear. Here we investigate whether DP is accompanied by deficits in colour perception. We tested a large sample of 92 DP individuals and 92 sex/age-matched controls using the well-validated Ishihara and Farnsworth–Munsell 100-Hue tests to assess red–green colour deficiencies and hue discrimination abilities. Group-level analyses show comparable performance between DP and control individuals across both tests, and single-case analyses indicate that the prevalence of colour deficits is low and comparable to that in the general population. Our study clarifies that DP is not linked to colour perception deficits and constrains theories of DP that seek to account for a larger range of visual deficits beyond face recognition.
Isolation and structure elucidation of pyridine alkaloids from the aerial parts of the Mongolian medicinal plant Caryopteris mongolica Bunge
Authors: Mishig Dumaa , Gruner Margit , Lübken Tilo , Ganbaatar Chunsriimyatav , Regdel Duger , Knölker Hans-Joachim 
Published: July 2021

AbstractThe seven pyridine alkaloids 1–7, the flavonoid acacetin (8), and L-proline anhydride (9) have been isolated from the aerial parts of the Mongolian medicinal plant Caryopteris mongolica Bunge. The structures of the natural products 1–9 have been assigned by MS, as well as IR, 1D NMR (1H, 13C, DEPT), and 2D NMR (COSY, HSQC, HMBC, NOESY) spectroscopic methods. The compounds 2 and 4–7 represent new chemical structures. Acacetin (8) and L-proline anhydride (9) have been obtained from C. mongolica for the first time.
Exploring the sequence features determining amyloidosis in human antibody light chains
Authors: Rawat Puneet , Prabakaran R. , Kumar Sandeep , Gromiha M. Michael 
Published: July 2021

AbstractThe light chain (AL) amyloidosis is caused by the aggregation of light chain of antibodies into amyloid fibrils. There are plenty of computational resources available for the prediction of short aggregation-prone regions within proteins. However, it is still a challenging task to predict the amyloidogenic nature of the whole protein using sequence/structure information. In the case of antibody light chains, common architecture and known binding sites can provide vital information for the prediction of amyloidogenicity at physiological conditions. Here, in this work, we have compared classical sequence-based, aggregation-related features (such as hydrophobicity, presence of gatekeeper residues, disorderness, β-propensity, etc.) calculated for the CDR, FR or VLregions of amyloidogenic and non-amyloidogenic antibody light chains and implemented the insights gained in a machine learning-based webserver called “VLAmY-Pred” (https://web.iitm.ac.in/bioinfo2/vlamy-pred/). The model shows prediction accuracy of 79.7% (sensitivity: 78.7% and specificity: 79.9%) with a ROC value of 0.88 on a dataset of 1828 variable region sequences of the antibody light chains. This model will be helpful towards improved prognosis for patients that may likely suffer from diseases caused by light chain amyloidosis, understanding origins of aggregation in antibody-based biotherapeutics, large-scale in-silico analysis of antibody sequences generated by next generation sequencing, and finally towards rational engineering of aggregation resistant antibodies.
Radiomics models based on enhanced computed tomography to distinguish clear cell from non-clear cell renal cell carcinomas
Authors: Wang Ping , Pei Xu , Yin Xiao-Ping , Ren Jia-Liang , Wang Yun , Ma Lu-Yao , Du Xiao-Guang , Gao Bu-Lang 
Published: July 2021

AbstractThis study was to assess the effect of the predictive model for distinguishing clear cell RCC (ccRCC) from non-clear cell RCC (non-ccRCC) by establishing predictive radiomic models based on enhanced-computed tomography (CT) images of renal cell carcinoma (RCC). A total of 190 cases with RCC confirmed by pathology were retrospectively analyzed, with the patients being randomly divided into two groups, including the training set and testing set according to the ratio of 7:3. A total of 396 radiomic features were computationally obtained and analyzed with the Correlation between features, Univariate Logistics and Multivariate Logistics. Finally, 4 features were selected, and three machine models (Random Forest (RF), Support Vector Machine (SVM) and Logistic Regression (LR)) were established to discriminate RCC subtypes. The radiomics performance was compared with that of radiologist diagnosis. In the testing set, the RF model had an area under the curve (AUC) value of 0.909, a sensitivity of 0.956, and a specificity of 0.538. The SVM model had an AUC value of 0.841, a sensitivity of 1.0, and a specificity of 0.231, in the testing set. The LR model had an AUC value of 0.906, a sensitivity of 0.956, and a specificity of 0.692, in the testing set. The sensitivity and specificity of radiologist diagnosis to differentiate ccRCC from non-ccRCC were 0.850 and 0.581, respectively, with the AUC value of the radiologist diagnosis as 0.69. In conclusion, radiomics models based on CT imaging data show promise for augmenting radiological diagnosis in renal cancer, especially for differentiating ccRCC from non-ccRCC.
Novel use of social media to assess and improve coastal flood forecasts and hazard alerts
Authors: Brown J. M. , Yelland M. J. , Pullen T. , Silva E. , Martin A. , Gold I. , Whittle L. , Wisse P. 
Published: July 2021

AbstractCoastal communities and infrastructure need protection from flooding and wave overtopping events. Assessment of hazard prediction methods, used in sea defence design, defence performance inspections and forecasting services, requires observations at the land-sea interface but these are rarely collected. Here we show how a database of hindcast overtopping events, and the conditions that cause them, can be built using qualitative overtopping information obtained from social media. We develop a database for a case study site at Crosby in the Northwest of England, use it to test the standard methods applied in operational flood forecasting services and new defence design, and suggest improvements to these methods. This novel approach will become increasingly important to deliver long-term, cost-effective coastal management solutions as sea-levels rise and coastal populations grow. At sites with limited, or no, monitoring or forecasting services, this approach, especially if combined with citizen science initiatives, could underpin the development of simplified early warning systems.
Interlaboratory study for the evaluation of three microtiter plate-based biofilm quantification methods
Authors: Allkja Jontana , van Charante Frits , Aizawa Juliana , Reigada Inés , Guarch-Pérez Clara , Vazquez-Rodriguez Jesus Augusto , Cos Paul , Coenye Tom , Fallarero Adyary , Zaat Sebastian A. J. , Felici Antonio , Ferrari Livia , Azevedo Nuno F. , Parker Albert E. , Goeres Darla M. 
Published: July 2021

AbstractMicrotiter plate methods are commonly used for biofilm assessment. However, results obtained with these methods have often been difficult to reproduce. Hence, it is important to obtain a better understanding of the repeatability and reproducibility of these methods. An interlaboratory study was performed in five different laboratories to evaluate the reproducibility and responsiveness of three methods to quantify Staphylococcus aureus biofilm formation in 96-well microtiter plates: crystal violet, resazurin, and plate counts. An inter-lab protocol was developed for the study. The protocol was separated into three steps: biofilm growth, biofilm challenge, biofilm assessment. For control experiments participants performed the growth and assessment steps only. For treatment experiments, all three steps were performed and the efficacy of sodium hypochlorite (NaOCl) in killing S. aureus biofilms was evaluated. In control experiments, on the log10-scale, the reproducibility SD (SR) was 0.44 for crystal violet, 0.53 for resazurin, and 0.92 for the plate counts. In the treatment experiments, plate counts had the best responsiveness to different levels of efficacy and also the best reproducibility with respect to responsiveness (Slope/SR = 1.02), making it the more reliable method to use in an antimicrobial efficacy test. This study showed that the microtiter plate is a versatile and easy-to-use biofilm reactor, which exhibits good repeatability and reproducibility for different types of assessment methods, as long as a suitable experimental design and statistical analysis is applied.
Acute effects of high-potency cannabis flower and cannabis concentrates on everyday life memory and decision making
Authors: Cuttler Carrie , LaFrance Emily M. , Stueber Amanda 
Published: July 2021

AbstractStatewide legislation has increased public access to high-potency cannabis flower and concentrates, yet federal restrictions limit researchers’ access to relatively low-potency whole-plant cannabis. The goal of this study was to examine the acute effects of high-potency cannabis on cognition using a novel methodology. We further sought to compare cognitive effects of high-potency cannabis flower with and without cannabidiol (CBD), as well as cannabis concentrates to cannabis flower. 80 cannabis users were randomly assigned to stay sober or use their funds to purchase one of three high-potency cannabis products: (1) high-potency flower (≥ 20% THC) without CBD, (2) high-potency flower with CBD, (3) high-potency concentrates (≥ 60% THC) with CBD. Participants were observed over Zoom videoconferencing while inhaling their product or remaining sober and then were administered tests of everyday life memory (prospective, source, temporal order, and false memory) and decision making (risky choice framing, consistency in risk perception, resistance to sunk cost, and over/under confidence) over Zoom. High-potency cannabis flower with CBD impaired free recall, high-potency flower without CBD and concentrates had detrimental effects on source memory, and all three products increased susceptibility to false memories. CBD did not offset impairments and concentrates were self-titrated producing comparable intoxication and impairment as flower.
Three-dimensional virtual histology in unprocessed resected tissues with photoacoustic remote sensing (PARS) microscopy and optical coherence tomography (OCT)
Authors: Ecclestone Benjamin R. , Hosseinaee Zohreh , Abbasi Nima , Bell Kevan , Dinakaran Deepak , Mackey John R. , Haji Reza Parsin 
Published: July 2021

AbstractHistological images are critical in the diagnosis and treatment of cancers. Unfortunately, current methods for capturing these microscopy images require resource intensive tissue preparation that may delay diagnosis for days or weeks. To streamline this process, clinicians are limited to assessing small macroscopically representative subsets of tissues. Here, a combined photoacoustic remote sensing (PARS) microscope and swept source optical coherence tomography system designed to circumvent these diagnostic limitations is presented. The proposed multimodal microscope provides label-free three-dimensional depth resolved virtual histology visualizations, capturing nuclear and extranuclear tissue morphology directly on thick unprocessed specimens. The capabilities of the proposed method are demonstrated directly in unprocessed formalin fixed resected tissues. The first images of nuclear contrast in resected human tissues, and the first three-dimensional visualization of subsurface nuclear morphology in resected Rattus tissues, captured with a non-contact photoacoustic system are presented here. Moreover, the proposed system captures the first co-registered OCT and PARS images enabling direct histological assessment of unprocessed tissues. This work represents a vital step towards the development of a rapid histological imaging modality to circumvent the limitations of current histopathology techniques.
The effect of topical ocular moxifloxacin on conjunctival and nasal mucosal flora
Authors: Celebi Ali Riza Cenk , Onerci Celebi Ozlem 
Published: July 2021

AbstractTo determine the short-term effect of topically administered ocular moxifloxacin on conjunctival and nasal bacterial mucosal flora. The study included 20 patients with newly diagnosed age-related macular degeneration. Each patient’s diseased eye was selected as the treatment eye and the fellow eye was selected as the control eye. All treatment eyes constituted the treatment group and all controls eyes constituted the control group. All patients received intravitreal injection of ranibizumab. Cultures were obtained from the inferior conjunctival fornix and the nostrils in all patients. Patients were instructed to administer moxifloxacin eye drops to the treatment eye 4 times daily for 1 week. The patients were instructed to come for a follow-up exam 1 week post intravitreal injection. The bacterial culture positivity rate and the bacteria isolated from the conjunctiva and nostrils were recorded in the 2 groups before and after use of topical ocular moxifloxacin. Mean age of the patients (12 female and 8 male) was 64.9 years. Before use of topical ocular moxifloxacin the conjunctival and nasal culture positivity rates in the treatment group were both 100%, versus 90% and 95%, respectively, in the control group. At the follow-up exam the conjunctival and nasal mucosa culture positivity rates in the treatment group decreased to 20% (4/20) and 30% (6/20), respectively (P < 0.001), versus 85% (17/20) and 80% (16/20), respectively, in the control group (P = 0.68 and P = 0.72 for conjunctival and nasal). This is the first study to show that moxifloxacin applied to the ocular surface topically has a significant effect on nasal flora. Daily administration of topical ocular moxifloxacin for 1 week significantly reduces the nasal bacterial flora in addition to conjunctival flora.
A 1-year follow-up study on immunological changes following deep brain stimulation in patients with epilepsy
Authors: Basnyat Pabitra , Järvenpää Soila , Raitanen Jani , Pesu Marko , Lehtimäki Kai , Peltola Jukka 
Published: July 2021

AbstractThe aim of this study was to evaluate the effects of deep brain stimulation of the anterior nucleus of the thalamus (ANT-DBS) on systemic inflammatory responses in patients with drug-resistant epilepsy (DRE). Twenty-two Finnish patients with ANT-DBS implantation were enrolled in this pilot study. Changes in plasma interleukin-6 (IL-6) and interleukin-10 (IL-10) levels were examined using generalized estimating equation models at seven time points (before DBS surgery and 1, 2, 3, 6, 9 and 12 months after implantation). In the whole group, the IL-6/IL-10 ratio decreased significantly over time following ANT-DBS, while the decrease in IL-6 levels and increase in IL-10 levels were not significant. In the responder and nonresponder groups, IL-6 levels remained unchanged during the follow-up. Responders had significantly lower pre-DBS IL-10 levels before the ANT-DBS treatment than nonresponders, but the levels significantly increased over time after the treatment. In addition, responders had a higher pre-DBS IL-6/IL-10 ratio than nonresponders, and the ratio decreased for both groups after treatment, but the decrease did not reach the level of statistical significance. The rate of decrease in the ratio per month tended to be higher in responders than in nonresponders. These results may highlight the anti-inflammatory properties of ANT-DBS treatment associated with its therapeutic effectiveness in patients with DRE. Additional studies are essential to evaluate the potential of the proinflammatory cytokine IL-6, the anti-inflammatory cytokine IL-10, and their ratio as biomarkers to evaluate the therapeutic response to DBS treatment, which could facilitate treatment optimization.
Prognostic factors of restrictive myopathy in thyroid eye disease
Authors: Choi Jae Hwan , Noh Hoon , Kim Yoon-Duck , Woo Kyung In 
Published: July 2021

AbstractTo investigate the prognostic factors of extraocular muscle restriction in patients with thyroid eye disease (TED), 65 patients with TED and restrictive myopathy were evaluated. Demographics, clinical activity score (CAS), smoking status, thyroid disease status, thyroid hormone status, thyroid autoantibody status, orbital computed tomography (CT) scan at initial presentation, and treatment regimens were assessed. The movements of the most severely affected extraocular muscles were categorized into five grades. The patients were divided into the improved and the not-improved group based on the improvement in the limitation of the extraocular muscle excursion (LOM) throughout the follow-up, and the groups were compared using clinical factors. The mean LOM significantly improved from 2.3 ± 1.1 to 1.7 ± 1.2 after 1 year of follow-up. The excursion of the most restricted muscle improved in 32 patients but not in 33 patients during the follow-up. The initial concentration of the thyroid-stimulating antibody (TSAb) was significantly lower in the improved (229.3 ± 114.1) than in the not-improved group (345.0 ± 178.6) (P = 0.02) Age, sex, smoking status, CAS, thyroid status, and muscle thickness on the CT scan did not significantly differ in the groups. This study showed that the initial concentration of TSAb is a factor affecting the recovery of restrictive myopathy.
Therapeutic efficacy of biofeedback pelvic floor muscle exercise in women with dysfunctional voiding
Authors: Chiang Ching-Hsiang , Jiang Yuan-Hong , Kuo Hann-Chorng 
Published: July 2021

AbstractDysfunctional voiding (DV), a voiding dysfunction due to hyperactivity of the external urethral sphincter or pelvic floor muscles leading involuntary intermittent contractions during voiding, is not uncommon in neurologically normal women with lower urinary tract symptoms (LUTS). We aimed to investigate the therapeutic efficacy of biofeedback pelvic floor muscle training (PFMT) in female patients with DV and to identify the therapeutic efficacy. Thirty-one patients diagnosed with DV. All participates completed the 3-month biofeedback PFMT program, which was conducted by one experienced physiotherapist. At 3 months after treatment, the assessment of treatment outcomes included global response assessment (GRA), and the changes of clinical symptoms, quality of life index, and uroflowmetry parameters. 25 (80.6%) patients had successful outcomes (GRA ≥ 2), and clinical symptoms and quality of life index significantly improved after PFMT. Additionally, uroflowmetry parameters including maximum flow rate, voided volume, voiding efficiency, total bladder capacity, voiding time, and time to maximum flow rate significantly improved after PFMT treatment. Patients with the history of recurrent urinary tract infection in recent 1 year were found to have unsatisfied therapeutic outcomes. In conclusion, biofeedback PFMT is effective in female patients with DV with significant improvements in clinical symptoms, quality of life, and uroflowmetry parameters. The history of urinary tract infection in recent 1 year is a negative predictor of successful outcome.