bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microwave preionization and electron cyclotron resonance plasma current startup in the EXL-50 spherical tokamak
Authors: CHEN Bin , ZHU Yubao , ZHOU Qing , DING Jiangbo , SONG Xianming , SONG Shaodong , YANG Yuanming , ZHAO Xin , YANG Enwu , LIU Minsheng 
Published: November 2021

Abstract
Preionization has been widely employed to create initial plasma and help the toroidal plasma current formation. This research focuses on implementing a simple, economical and practical electron cyclotron resonance (ECR) preionization technique on the newly constructed EXL-50 spherical tokamak, and evaluating the effectiveness on improving the plasma current startup. Two types ECR microwave preionization experiments for the plasma initialization without the central solenoid are reported: (1) 2.45 GHz microwave preionization and current startup with 2.45 GHz ECR source; (2) 2.45 GHz microwave preionization and current startup with 28 GHz ECR source. Application of the 2.45 GHz ECR microwave preionization to the experiments has contributed to (1) getting rid of the plasma breakdown delay; (2) the significant improvement of the discharge quality: the discharge is much longer and more stable while the driven plasma current is larger, compared to the discharge without preionization.
Strichartz Estimates for Wave Equations with Charge Transfer Hamiltonians
Authors: Chen Gong 
Published: November 2021

We prove Strichartz estimates (both regular and reversed) for a scattering state to the wave equation with a charge transfer Hamiltonian in

R

3

\mathbb {R}^{3}

:
\[

∂

t
t

u
−
Δ
u
+

∑

j
=
1

m

V

j

(
x
−

v
→

j

t
)

u
=
0.

\partial _{tt}u-\Delta u+\sum _{j=1}^{m}V_{j}\left (x-\vec {v}_{j}t\right )u=0.

\]
The energy estimate and the local energy decay of a scattering state are also established. In order to study nonlinear multisoltion systems, we will present the inhomogeneous generalizations of Strichartz estimates and local decay estimates. As an application of our results, we show that scattering states indeed scatter to solutions to the free wave equation. These estimates for this linear models are also of crucial importance for problems related to interactions of potentials and solitons, for example, in [Comm. Math. Phys. 364 (2018), no. 1, pp. 45–82].
Literary Theory on Acid
Authors: Fawaz Ramzi 
Published: November 2021

Abstract
This essay argues for the value of psychedelic experience as a framework for amplifying the social and political impacts of literature on the affective lives of readers and viewers. Psychedelics are chemical compounds that induce a hypersaturated experience of life that represents facets of the world to us in unfamiliar, intensified form. Neurochemical studies of the psychedelically “tripping” brain suggest that the experience can have wide-reaching, long-term positive outcomes including the expansion of one’s sensory apprehension of the world, a stronger ability to grapple with life’s contingency and human mortality, and the mitigation of depression, anxiety, and addiction. The author identifies several crucial ways in which literary criticism and pedagogy’s enhancement of cultural meaning making dovetails with the best aspects of psychedelic states, including the activation of readers’ and students’ aesthetic sensibilities. A psychedelically inflected criticism aims to achieve the psychedelic experience’s “blossoming of mental states” by revitalizing the literary text as a site for exploring, refining, and retuning the sensorium, thereby enriching one’s perceptual and imaginative capacities. The author unpacks how the insights of psychedelic experiences can shape distinct pedagogical and interpretative practices that respond to our current global political crises. This can potentially revivify the therapeutic value of the humanities as an institution invested in honing the creative and ethical faculties of generations of youth while attending to their long-term affective well-being.
3DFI: a pipeline to infer protein function using structural homology
Authors: Julian Alexander Thomas , Mascarenhas dos Santos Anne Caroline , Pombert Jean-François 
Published: November 2021

Abstract

Summary
Inferring protein function is an integral part of genome annotation and analysis. This process is usually performed in silico, and most in silico inferences are based on sequence homology approaches, which can fail when in presence of divergent sequences. However, because protein structures and their biological roles are intertwined, protein function can also be inferred by searching for structural homology. Many excellent tools have been released in recent years with regards to protein structure prediction, structural homology searches and protein visualization. Unfortunately, these tools are disconnected from each other and often use a web server-based approach that is ill-suited to high-throughput genome-wide analyses. To help assist genome annotation, we built a structural homology-based pipeline called 3DFI (for tridimensional functional inference) leveraging some of the best structural homology tools. This pipeline was built with simplicity of use in mind and enables genome-wide structural homology inferences.

Availability and implementation
3DFI is available on GitHub https://github.com/PombertLab/3DFI under the permissive MIT license. The pipeline is written in Perl and Python.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures
Authors: Velloso João Paulo L , Ascher David B , Pires Douglas E V 
Published: November 2021

Abstract

Motivation
G protein-coupled receptors (GPCRs) can selectively bind to many types of ligands, ranging from light-sensitive compounds, ions, hormones, pheromones and neurotransmitters, modulating cell physiology. Considering their role in many essential cellular processes, they are one of the most targeted protein families, with over a third of all approved drugs modulating GPCR signalling. Despite this, the large diversity of receptors and their multipass transmembrane architectures make the identification and development of novel specific, and safe GPCR ligands a challenge. While computational approaches have the potential to assist GPCR drug development, they have presented limited performance and generalization capabilities. Here, we explored the use of graph-based signatures to develop pdCSM-GPCR, a method capable of rapidly and accurately screening potential GPCR ligands.

Results
Bioactivity data (IC50, EC50, Ki and Kd) for individual GPCRs were curated. After curation, we used the data for developing predictive models for 36 major GPCR targets, across 4 classes (A, B, C and F). Our models compose the most comprehensive computational resource for GPCR bioactivity prediction to date. Across stratified 10-fold cross-validation and blind tests, our approach achieved Pearson’s correlations of up to 0.89, significantly outperforming previous methods. Interpreting our results, we identified common important features of potent GPCRs ligands, which tend to have bicyclic rings, leading to higher levels of aromaticity. We believe pdCSM-GPCR will be an invaluable tool to assist screening efforts, enriching compound libraries and ranking candidates for further experimental validation.

Availability and implementation
pdCSM-GPCR predictive models and datasets used have been made available via a freely accessible and easy-to-use web server at http://biosig.unimelb.edu.au/pdcsm_gpcr/.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Current State of Laboratory Automation in Clinical Microbiology Laboratory
Authors: Antonios Kritikos , Croxatto Antony , Culbreath Karissa 
Published: November 2021

Abstract

Background
Although it has been 30 years since the first automation systems were introduced in the microbiology laboratory, total laboratory automation (TLA) has only recently been recognized as a valuable component of the laboratory. A growing number of publications illustrate the potential impact of automation. TLA can improve standardization, increase laboratory efficiency, increase workplace safety, and reduce long-term costs.

Content
This review provides a preview of the current state of automation in clinical microbiology and covers the main developments during the last years. We describe the available hardware systems (that range from single function devices to multifunction workstations) and the challenging alterations on workflow and organization of the laboratory that have to be implemented to optimize automation.

Summary
Despite the many advantages in efficiency, productivity, and timeliness that automation offers, it is not without new and unique challenges. For every advantage that laboratory automation provides, there are similar challenges that a laboratory must face. Change management strategies should be used to lead to a successful implementation. TLA represents, moreover, a substantial initial investment. Nevertheless, if properly approached, there are a number of important benefits that can be achieved through implementation of automation in the clinical microbiology laboratory. Future developments in the field of automation will likely focus on image analysis and artificial intelligence improvements. Patient care, however, should remain the epicenter of all future directions and there will always be a need for clinical microbiology expertise to interpret the complex clinical and laboratory information.
Courtesy Stigma Management: Social Identity Work among China’s “Leftover Women”
Authors: Liu Chihling , Kozinets Robert V 
Published: November 2021

AbstractPrior consumer research has tended to focus on identity-related stigma management of individuals toward their own stigma. However, little is known about the consumption-related identity work that stigmatized individuals undertake to discharge the courtesy stigma attached to close associates such as family members. Courtesy stigma refers to the discredit directed toward people who are closely associated with a stigmatized individual or group. Drawing on interview, ethnographic, and netnographic data on China’s ‘Leftover Women,’ our research analyzes the personal and, more centrally, the social identity work related consumption counternarratives that these women construct—through combinations of specific kinds of consumption and gift-giving practices—to counteract family and courtesy stigma. Counternarratives are the resistance stories that people tell and live to either implicitly or explicitly challenge the dominant cultural narrative. The findings of our investigation help to build an enhanced understanding of how stigmatized individuals act as consumers in the market and via digital channels to tackle the family identity challenges of courtesy stigma that have not been explored in extant studies of consumer stigma identity work.
Fatty acid secretion by the white-rot fungus,Trametes versicolor
Authors: Hao Guyu , Barker Guy C 
Published: November 2021

AbstractFungi can acquire and store nutrients through decomposing and converting organic matter into fatty acids. This research demonstrates for the first time that the white-rot fungus Trametes versicolor has the ability to secrete extracellular droplets which can contain a high concentration of long-chain fatty acids and unsaturated fatty acids as well as monosaccharides and polysaccharides. The concentration and composition of the fatty acids varied according to the age of the droplet and the feedstock used for growth of the fungi. The results raise the possibility that these droplets could be harvested offering a new approach for the microbial generation of oil from waste.
The HrpX Protein Activates Synthesis of the RaxX Sulfopeptide, Required for Activation of XA21-Mediated Immunity to Xanthomonas oryzae pv. oryzae
Authors: Joe Anna , Stewart Valley , Ronald Pamela C. 
Published: November 2021

Upon encountering a susceptible plant host, a bacterial pathogen expresses specific virulence factors. For example, in planta, the Xanthomonas HrpX protein activates transcription of roughly 150 genes encoding components of the type III secretion system or its translocated effectors, as well as other secreted proteins implicated in pathogenesis. Here, we show that X. oryzae pv. oryzae growth in planta or in HrpX-inducing XOM2 media resulted in HrpX-dependent transcription of the raxX and raxST genes that control production of the RaxX sulfopeptide, exported through a type I secretion system. The RaxX protein is required for activation of XA21-mediated immunity in Xa21+ rice lines. We identified potential plant-inducible promoter elements upstream of the likely 5′ ends of the raxX and raxST transcripts. Deletions and nucleotide substitutions confirmed that these elements are required for HrpX-dependent expression of raxX and raxST. We conclude that raxX-raxST gene expression is induced by HrpX during growth in planta and, therefore, is coordinately expressed with other genes required for pathogenesis. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Postoperative Pain and Age: A Retrospective Cohort Association Study
Authors: van Dijk Jacqueline F. M. , Zaslansky Ruth , van Boekel Regina L. M. , Cheuk-Alam Juanita M. , Baart Sara J. , Huygen Frank J. P. M. , Rijsdijk Mienke 
Published: November 2021

Background
As the population ages, the number of elderly people undergoing surgery increases. Literature on the incidence and intensity of postoperative pain in the elderly is conflicting. This study examines associations between age and pain-related patient reported outcomes and perioperative pain management in a dataset of surgical patients undergoing four common surgeries: spinal surgery, hip or knee replacement, or laparoscopic cholecystectomy. Based on the authors’ clinical experience, they hypothesize that pain scores are lower in older patients.

Methods
In this retrospective cohort, study data were collected between 2010 and 2018 as part of the international PAIN OUT program. Patients filled out the International Pain Outcomes Questionnaire on postoperative day 1.

Results
A total of 11,510 patients from 26 countries, 59% female, with a mean age of 62 yr, underwent one of the aforementioned types of surgery. Large variation was detected within each age group for worst pain, yet for each surgical procedure, mean scores decreased significantly with age (mean Numeric Rating Scale range, 6.3 to 7.3; β = –0.2 per decade; P ≤ 0.001), representing a decrease of 1.3 Numeric Rating Scale points across a lifespan. The interference of pain with activities in bed, sleep, breathing deeply or coughing, nausea, drowsiness, anxiety, helplessness, opioid administration on the ward, and wish for more pain treatment also decreases with age for two or more of the procedures. Across the procedures, patients reported being in severe pain on postoperative day one 26 to 38% of the time, and pain interfered moderately to severely with movement.

Conclusions
The authors’ findings indicate that postoperative pain decreases with increasing age. The change is, however, small and of questionable clinical significance. Additionally, there are still too many patients, at any age, undergoing common surgeries who suffer from moderate to severe pain, which interferes with function, supporting the need for tailoring care to the individual patient.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
Effect of Global Ventilation to Perfusion Ratio, for Normal Lungs, on Desflurane and Sevoflurane Elimination Kinetics
Authors: Baumgardner James E. , Kretzschmar Moritz , Kozian Alf , Hachenberg Thomas , Schilling Thomas , Larsson Anders , Hedenstierna Göran 
Published: November 2021

Background
Kinetics of the uptake of inhaled anesthetics have been well studied, but the kinetics of elimination might be of more practical importance. The objective of the authors’ study was to assess the effect of the overall ventilation/perfusion ratio (VA/Q), for normal lungs, on elimination kinetics of desflurane and sevoflurane.

Methods
The authors developed a mathematical model of inhaled anesthetic elimination that explicitly relates the terminal washout time constant to the global lung VA/Q ratio. Assumptions and results of the model were tested with experimental data from a recent study, where desflurane and sevoflurane elimination were observed for three different VA/Q conditions: normal, low, and high.

Results
The mathematical model predicts that the global VA/Q ratio, for normal lungs, modifies the time constant for tissue anesthetic washout throughout the entire elimination. For all three VA/Q conditions, the ratio of arterial to mixed venous anesthetic partial pressure Part/Pmv reached a constant value after 5 min of elimination, as predicted by the retention equation. The time constant corrected for incomplete lung clearance was a better predictor of late-stage kinetics than the intrinsic tissue time constant.

Conclusions
In addition to the well-known role of the lungs in the early phases of inhaled anesthetic washout, the lungs play a long-overlooked role in modulating the kinetics of tissue washout during the later stages of inhaled anesthetic elimination. The VA/Q ratio influences the kinetics of desflurane and sevoflurane elimination throughout the entire elimination, with more pronounced slowing of tissue washout at lower VA/Q ratios.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
Systemic Immunosuppression for Prevention of Recurrent Tendon Adhesions
Authors: Mailey Brian , O’Shea Grace , Romanelli Michael , West Bradley 
Published: November 2021

Background:
The recovery for patients after tendon repair is frequently limited by development of tendon adhesions. This scar tissue formation is dependent on immune system activation. Tacrolimus has unique properties that may contribute to the prevention of overactive scarring by inhibition of inflammatory cytokines.

Methods:
Herein, we present a case using systemic immunosuppression to prevent recurrent adhesion accumulation in a patient with a prior spaghetti wrist injury. Tacrolimus began 1 week before repeat-secondary tenolysis surgery, and it continued for 3 months postoperative. Dosing was tapered to a serum level between 5 and 8 µg/L.

Results:
The 27-year-old male patient suffered a volar wrist laceration transecting all flexor tendons and volar wrist nerves. He underwent immediate repair but had a poor outcome despite early range of motion therapy. A primary tenolysis only improved his average arc of finger motion from 72 to 95 degrees. Secondary tenolysis augmented with systemic tacrolimus improved his arc of finger motion from 95 to 202 degrees. Mechanistically, tacrolimus prevents proper function of activated T and B cells. This results in decreased proliferation, angiogenesis, and cytoskeletal organization of fibroblasts on inflammation and integrin adhesions, and it potentially explains the reduced tendon molecule adhesions seen in this patient.

Conclusions:
Tacrolimus may be effective in reducing motion, limiting tendon adhesions. The novel use of this medication resulted in the return of near-normal hand function in a patient placed on low-dose tacrolimus after primary tenolysis had failed.
Subtotal Nasal Reconstruction in a 91-year-old Patient: Expanded Double Forehead Flaps and Costal Cartilage
Authors: Nakajima Yuta , Iwasawa Motonao , Mishima Yoshito 
Published: November 2021

Summary:
Nasal reconstruction in very elderly patients is challenging. We attempted subtotal nasal reconstruction with an expanded double forehead flap and autologous costal cartilage support in a 91-year-old woman presenting with subtotal nasal defects after sebaceous carcinoma resection. Only small parts of the bilateral alae and the columella base remained after resection, and the frontal area of the septum was also resected. We planned to use an expanded double forehead flap to reconstruct the whole external skin cover and lining of the nose. We chose a 200-mL tissue expander and injected 152 mL of saline over 15 weeks. The expansion course in this patient was slower than that in younger patients because of the limited expansibility of her forehead skin. However, the skin tolerated the repeated expansions well, and the double forehead flap was expanded to the planned size preoperatively. The nasal support grafts were composed of the L-strut and alar battens from the eighth and ninth costal cartilages, and were fixed using nonabsorbable sutures. Histological examination revealed cartilage matrix degeneration and a reduced number of living chondrocytes, yet no calcification or fragility. After 18 months of follow-up, the framework maintained its shape, and the dorsum was straight without warping. The autologous costal cartilage provided a natural nasal shape and nostrils. Thus, an expanded double forehead flap with careful tissue expansion and a rib cartilage graft can allow natural nose reconstruction without a microvascular technique in very elderly patients.
Minimally Invasive Micro Sclerostomy (MIMS) Procedure: A Novel Glaucoma Filtration Procedure
Authors: Geffen Noa , Kumar Dhivya A. , Barayev Edward , Gershoni Assaf , Rotenberg Michael , Zahavi Alon , Glovinsky Yoseph , Agarwal Amar 
Published: November 2021

Précis:
Intermediate-term results suggest that ab interno Minimally Invasive Micro Sclerostomy (MIMS) stent-less subconjunctival filtration procedure is a promising treatment option for patients with open-angle glaucoma (OAG).

Purpose:
MIMS is a novel ab interno, stent-less, subconjunctival filtration procedure. This study set to investigate the safety, performance, and efficacy of MIMS in OAG patients.

Methods:
Prospective, open-label, single arm clinical trial with intrasubject comparisons. Study participants were adults with OAG who were candidates for a filtration procedure. Patients were operated by a single surgeon (A.A.) in Chennai, India. Following mitomycin-C pretreatment, ab interno MIMS procedure was performed alone or combined with phacoemulsification surgery. Procedure-related complications and adverse events were assessed. Primary outcomes: patients (%) achieving an intraocular pressure (IOP) ≥5 mm Hg and ≤18 mm Hg, and an IOP reduction of >20% as compared with baseline, with or without hypotensive medications, with no need for recurrent surgery.

Results:
Twenty-one phacoemulsification-MIMS and 10 standalone MIMS procedures were performed. Mean age was 63.94±6.33 years. Mean duration of MIMS was 1:58±0:25 (min:s). Scleral tunnels were achieved in all cases. No device malfunctions, intraoperative complications, or serious adverse events were reported. Five (16.12%) patients presented with iris clogging 1 to 24 weeks following procedure. Two were treated with laser and 3 required trabeculectomy. Mean IOP change from baseline at 24 weeks was 47.4% (31.2 to 16.4 mm Hg, P<0.0001, n=23). The mean difference was −14.8 mm Hg (95% confidence interval: −17.6, −11.9) with no statistically significant differences between groups. Qualified success was achieved in 21 (84%), 17 (74%), and 13 (93%) after 12, 24, and 52 weeks, respectively. Complete success was achieved in 17 (68%), 13 (57%), and 8 (57%) after 12, 24, and 52 weeks, respectively.

Conclusions:
The interim results suggest that MIMS procedure may be a simple and effective surgical option for early OAG patients requiring target IOP in high teens although iris clogging of incision site is the major concern with this procedure.