bluuebunny/crossref_metadata_2025 huggingface dataset:
Light, rather than circadian rhythm, regulates gas exchange in ferns and lycophytes
Authors: Aros-Mualin Daniela , Guadagno Carmela Rosaria , Silvestro Daniele , Kessler Michael
Published: January 2023

Circadian regulation plays a vital role in optimizing plant responses to the environment. However, while circadian regulation has been extensively studied in angiosperms, very little is known for lycophytes and ferns, leaving a gap in our understanding of the evolution of circadian rhythms across the plant kingdom. Here, we investigated circadian regulation in gas exchange through stomatal conductance and photosynthetic efficiency in a phylogenetically broad panel of 21 species of lycophytes and ferns over a 46 h period under constant light and a selected few under more natural conditions with day–night cycles. No rhythm was detected under constant light for either lycophytes or ferns, except for two semi-aquatic species of the family Marsileaceae (Marsilea azorica and Regnellidium diphyllum), which showed rhythms in stomatal conductance. Furthermore, these results indicated the presence of a light-driven stomatal control for ferns and lycophytes, with a possible passive fine-tuning through leaf water status adjustments. These findings support previous evidence for the fundamentally different regulation of gas exchange in lycophytes and ferns compared to angiosperms, and they suggest the presence of alternative stomatal regulations in Marsileaceae, an aquatic family already well known for numerous other distinctive physiological traits. Overall, our study provides evidence for heterogeneous circadian regulation across plant lineages, highlighting the importance of broad taxonomic scope in comparative plant physiology studies.
SU(4)C × SU(2)L × U(1)R models with modular A4 symmetry
Authors: Nomura Takaaki , Okada Hiroshi , Shoji Yutaro
Published: January 2023

We study SU(4)C × SU(2)L × U(1)R models with modular A4 symmetry that provide a unified description of the quark and lepton sectors including the flavor structures. The models are distinguished by the assignments of the modular weight to matter superfields. We carry out numerical χ2 analysis and search for parameter sets that accommodate the experimental results. We provide a benchmark point for each model to illustrate the implications of our models.
Claims against directors of trustee companies—the next frontier?
Authors: Walker Nathaniel , Wilson Nic
Published: January 2023

Corporate trustees work to (among other things) shield directors from liability as trustees. This article explores whether and how beneficiaries can bring proceedings against errant trustee company directors. It does so in four parts. First, the possibility of direct fiduciary or trustee-like duties is considered. Secondly, the authors address accessory liability for dishonest assistance or knowing receipt. Thirdly, the particular difficulties posed by a director’s diversion of opportunities are explored. Finally, the authors consider developing claims, being the dog-leg claim and a direct duty of care in tort owed by the trustee company director to the beneficiary.
Physiological responses ofQuercus acutissimaandQuercus rubraseedlings to drought and defoliation treatments
Authors: Wang Ning , Song Meixia , Zhang Yang , Liu Xiao , Wu Pan , Qi Luyu , Song Huijia , Du Ning , Wang Hui , Zheng Peiming , Wang Renqing
Published: January 2023

Ongoing global climate change is increasing the risk of drought stress in some areas, which may compromise forest health. Such drought events also increase outbreaks of insect herbivores, resulting in plant defoliation. Interactions between drought and defoliation are poorly understood. In a greenhouse experiment, we selected a native species, Quercus acutissima Carr. and an alien species, Quercus rubra L. to explore their physiological responses to drought and defoliation treatments. After the treatments, we determined the seedlings’ physiological responses on Days 10 and 60. Our results showed that the defoliation treatment accelerated the carbon reserve consumption of plants under drought stress and inhibited the growth of both seedling types. Under the drought condition, Q. rubra maintained normal stem-specific hydraulic conductivity and normal growth parameters during the early stage of stress, whereas Q. acutissima used less water and grew more slowly during the experiment. Sixty days after defoliation treatment, the stem starch concentration of Q. acutissima was higher than that of the control group, but the stem biomass was lower. This indicates that Q. acutissima adopted a ‘slow strategy’ after stress, and more resources were used for storage rather than growth, which was conducive to the ability of these seedlings to resist recurrent biotic attack. Thus, Q. acutissima may be more tolerant to drought and defoliation than Q. rubra. The resource acquisition strategies of Quercus in this study suggest that the native Quercus species may be more successful at a long-term resource-poor site than the alien Quercus species.
Complete Genome Sequence of Pantoea agglomerans CHTF15, a Walnut Pathogen
Authors: Xiao Jiawen , Liu Zhaosha , Sun Shangyi , Fan Chenxi , Wang Dongmei , Zhang Dongdong
Published: January 2023

The phytopathogen Pantoea agglomerans belongs to the Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacterales, Erwiniaceae in species classification. It causes disease symptoms in many plants such as corn, banana, and walnut. This study aimed to report the complete genome of P. agglomerans CHTF15, which represents the first whole-genome sequence of an isolate from diseased walnut leaves. The total length of the assembled genome was 4,820,607 bp, with an average GC content of 55.3%, including a circular chromosome and three circular plasmids, two of which were previously unreported sequences and one was announced previously. The CHTF15 genome helps understand the pathogenic mechanism of this important plant pathogen and provides an important theoretical basis for disease epidemic and field control.

[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
ADP‐ribose transferase PARP16 mediated‐unfolded protein response contributes to neuronal cell damage in cerebral ischemia/reperfusion
Authors: Wang Jinghuan , Xu Jie , Dong Yejun , Su Zhenghua , Su Haibi , Cheng Qianwen , Liu Xinhua
Published: January 2023

Ischemic stroke is known to cause the accumulation of misfolded proteins and loss of calcium homeostasis, leading to impairment of endoplasmic reticulum (ER) function and activating the unfolded protein response (UPR). PARP16 is an active (ADP‐ribosyl)transferase known tail‐anchored ER transmembrane protein with a cytosolic catalytic domain. Here, we find PARP16 is highly expressed in ischemic cerebral hemisphere and oxygen–glucose deprivation/reoxygenation (OGD/R)‐treated immortalized hippocampal neuronal cell HT22. Using an adeno‐associated virus‐mediated PARP16 knockdown approach in mice, we find PARP16 knockdown decreases infarct demarcations and has a better neurological outcome after ischemic stroke. Our data indicate PARP16 knockdown decreases ER stress and neuronal death caused by OGD/R, whereas PARP16 overexpression promotes ER stress‐mediated cell damage in primary cortical neurons. Furthermore, PARP16 functions mechanistically as ADP‐ribosyltransferase to modulate the level of ADP‐ribosylation of the corresponding PERK and IRE1α arm of the UPR, and such modifications mediate activation of PERK and IRE1α. Indeed, pharmacological stimulation of the UPR using Brefeldin A partly counteracts PARP16 knockdown‐mediated neuronal protection upon OGD/R treatment. In conclusion, PARP16 plays a crucial role in post‐ischemic UPR and PARP16 knockdown alleviates brain injury after ischemic stroke. This study demonstrates the potential of the PARP16‐PERK/IRE1α axis as a target for neuronal survival in ischemic stroke.
Getting to the core of the matter: the importance of biopsy in an unusual case of acute liver failure
Authors: Lee Joshua , Arbogast Mitchell , Kappus Matthew R. , Brady Carla W.
Published: January 2023

Watch the interview with the author.
Thioredoxin reductase 1 regulates hepatic inflammation and macrophage activation during acute cholestatic liver injury
Authors: Shearn Colin T. , Anderson Aimee L. , Miller Colin G. , Noyd Reed C. , Devereaux Michael W. , Balasubramaniyan Nata , Orlicky David J. , Schmidt Edward E. , Sokol Ronald J.
Published: January 2023

Background and Aims:

Cholestatic liver diseases, including primary sclerosing cholangitis, are characterized by periportal inflammation with progression to hepatic fibrosis and ultimately cirrhosis. We recently reported that the thioredoxin antioxidant response is dysregulated during primary sclerosing cholangitis. The objective of this study was to examine the impact of genetic and pharmacological targeting of thioredoxin reductase 1 (TrxR1) on hepatic inflammation and liver injury during acute cholestatic injury.

Approach and Results:

Primary mouse hepatocytes and intrahepatic macrophages were isolated from 3-day bile duct ligated (BDL) mice and controls. Using wildtype and mice with a liver-specific deletion of TrxR1 (TrxR1LKO), we analyzed the effect of inhibition or ablation of TrxR1 signaling on liver injury and inflammation. Immunohistochemical analysis of livers from BDL mice and human cholestatic patients revealed increased TrxR1 staining in periportal macrophages and hepatocytes surrounding fibrosis. qPCR analysis of primary hepatocytes and intrahepatic macrophages revealed increased TrxR1 mRNA expression following BDL. Compared with sham controls, BDL mice exhibited increased inflammation, necrosis, and increased mRNA expression of pro-inflammatory cytokines, fibrogenesis, the NLRP3 inflammatory complex, and increased activation of NFkB, all of which were ameliorated in TrxR1LKO mice. Importantly, following BDL, TrxR1LKO induced periportal hepatocyte expression of Nrf2-dependent antioxidant proteins and increased mRNA expression of basolateral bile acid transporters with reduced expression of bile acid synthesis genes. In the acute BDL model, the TrxR1 inhibitor auranofin (10 mg/kg/1 d preincubation, 3 d BDL) ameliorated BDL-dependent increases in Nlrp3, GsdmD, Il1β, and TNFα mRNA expression despite increasing serum alanine aminotransferase, aspartate aminotransferase, bile acids, and bilirubin.

Conclusions:

These data implicate TrxR1-signaling as an important regulator of inflammation and bile acid homeostasis in cholestatic liver injury.
Human VH-based chimeric antigen receptor T cells targeting glypican 3 eliminate tumors in preclinical models of HCC
Authors: Kolluri Aarti , Li Dan , Li Nan , Duan Zhijian , Roberts Lewis R. , Ho Mitchell
Published: January 2023

Background and Aims:

Efficacy of chimeric antigen receptor (CAR) T cells for treating solid tumors, including HCC, remains a challenge. Nanobodies are emerging building blocks of CAR T cells due to their small size and high expression. Membrane proximal sites have been shown as attractive epitopes of CAR T cells. However, current CAR formats are not tailored toward nanobodies or targeting membrane distal epitopes.

Approach and Results:

Using hYP7 Fv (membrane proximal) and HN3 VH nanobody (membrane distal) as GPC3 targeting elements, we sought to determine how hinges and transmembrane portions of varying structures and sizes affect CAR T-cell function. We generated multiple permutations of CAR T cells containing CD8, CD28, IgG4, and Fc domains. We show that engineered HN3 CAR T cells can be improved by 2 independent, synergistic changes in the hinge and transmembrane domains. The T cells expressing the HN3 CAR which contains the hinge region of IgG4 and the CD28 transmembrane domain (HN3-IgG4H-CD28TM) exhibited high cytotoxic activity and caused complete HCC tumor eradication in immunodeficient mice. HN3-IgG4H-CD28TM CAR T cells were enriched for cytotoxic-memory CD8+ T cells and NFAT signals, and reduced β catenin levels in HCC cells.

Conclusion:

Our findings indicate that altering the hinge and transmembrane domains of a nanobody-based CAR targeting a distal GPC3 epitope, in contrast to a membrane proximal epitope, lead to robust T-cell signaling and induce swift and durable eradication of HCC tumors.
Staffing transformation following Patient-Centered Medical Home recognition among Health Resources & Services Administration-funded health centers
Authors: Pourat Nadereh , Lu Connie , Chen Xiao , Zhou Weihao , Hair Brionna , Bolton Joshua , Hoang Hank , Sripipatana Alek
Published: January 2023

Introduction

Patient-Centered Medical Home (PCMH) recognition is designed to promote whole-person team-based and integrated care.

Purpose

Our goal was to assess changes in staffing infrastructure that promoted team-based and integrated care delivery before and after PCMH recognition in Health Resources & Services Administration (HRSA)-funded health centers (HCs).

Methodology/Approach

We identified changes in staffing 2 years before and 3 years after PCMH recognition using 2010–2019 Uniform Data System data among three cohorts of HCs that received PCMH recognition in 2013 (n = 346), 2014 (n = 207), and 2015 (n = 115). Our outcomes were team-based ratio (full-time equivalent medical and nonmedical providers and staff to one primary care physician) and a multidisciplinary staff ratio (allied medical and nonmedical staff to 1,000 patients). We used mixed-effects Poisson regression models.

Results

The earlier cohorts served fewer complex patients and were larger before PCMH recognition. Three years following recognition, the 2013 and 2014 cohorts had significantly larger team-based ratios, and all three cohorts had significantly larger multidisciplinary staff ratios. Cohorts varied, however, in the type of staff that drove this change. Both ratios increased in the longer term.

Conclusion

Our study suggests that growth in team-based and multidisciplinary staff ratios in each cohort may have been due to a combination of HCs’ perceptions of need for specific services, HRSA funding, and technical assistance opportunities.

Policy Implications

Further research is needed to understand barriers such as costs of employing a multidisciplinary staff, particularly those that cannot directly bill for services as well as whether such changes lead to practice transformation and improved quality of care.
What Do We Know About the Health Status of Asylum Seekers in the United States?
Authors: Beer Jessica , Dorris C. Scott , Fateen Dahlia , Mishori Ranit
Published: January 2023

Data about US asylum seekers' health are lacking. We assessed the medical literature by performing a bibliometric scoping review of the literature from 1946 to 2020. Of 114 articles identified, 48 (42.1%) were empirical studies and 66 (57.9%) were editorials or commentaries. Empirical studies focused on mental health (60.42%), African asylees (45.83%). Editorials and commentaries focused on detention and medicolegal processes (31.82% and 30.3%). Empirical data on the health of US asylum seekers are limited. Research expansion requires increased commitment, funding, and participatory engagement of asylees. This limited representation in the scientific literature can impact their care and health system preparedness.
Gender Disparities in Physician Assistant Educator Promotion and Compensation: A Mixed Methods Approach
Authors: Loder Rayne , Coombs Jennifer , Najmabadi Shahpar , Henry Trenton , Ryujin Darin , Valentin Virginia
Published: January 2023

Introduction

The gender wage gap is well documented in many industries. A disparity in salary between female and male physician assistant (PA) educators has been demonstrated, but disparities in academic rank have not been shown. The purpose of this study was to re-examine gender disparities in compensation to PA educators and to explore whether gender-based disparities exist in promotion to higher academic rank in this field.

Methods

An explanatory sequential mixed-methods design was used to determine differences in salary and rank by gender. PA Education Association Faculty and Directors Survey data from 2014, 2017, and 2019 were analyzed. A focus group was conducted to explain the findings and understand the barriers to promotion for female faculty.

Results

Female PA faculty members earn $7573 less than their male colleagues when controlling for all other variables. Female faculty members have an increased likelihood (RR 1.150) for being in early career stage versus late career stage. Obtaining a doctoral degree decreased the risk for being in an early career stage (RR 0.567) with men twice as likely to have a doctoral degree as women.

Discussion

Rank and salary disparities exist in PA faculty by gender. Female faculty are less likely to hold doctoral degrees or to be promoted to higher academic ranks, and they earn less than men. Degree level and career track are themes unique to the PA education profession, and further research is needed to understand their impact. With more women entering PA education, pay equity and promotion need to be addressed.
Patient Experience Coordinator
Authors: Oehlert Julie Kennedy , Montana-Rhodes Lou , Hill Kevin N. , Maldonado Julio , Bishop Brandon , Wei Holly
Published: January 2023

OBJECTIVE

The aim of this study was to test the impact of an innovative nonclinical support role to improve patient experiences while supporting nurse work on inpatient units.

BACKGROUND

On the basis of the Hospital Consumer Assessment of Health Care Providers and Systems (HCAHPS) survey, patients' experience declined nationally during the COVID-19 pandemic. A nonclinical support role, titled an Experience Coordinator, was created as a test of change to collaborate with care teams and respond to patients' and families' nonclinical needs.

METHODS

This is a quality improvement (QI) project for a supportive role development and implementation. The health system's HCAHPS data were compared before and after the role was tested on 3 inpatient units.

RESULTS

The HCAHPS data indicated that 5 of the 10 domains' top box ratings increased during the QI project month compared with the previous month.

CONCLUSION

The study findings may support the implementation of new innovative nonclinical positions to alleviate nurses' workload and promote patients' hospital experience.
A post-transplant infection by Nocardia cyriacigeorgica
Authors: GANDHAM NAGESWARI , Kannuri Sriram , Gupta Aryan , Mukhida Sahjid , DAS NIKUNJA , Mirza Shahzad
Published: January 2023

Nocardia are gram-positive bacilli that cause opportunistic infections in susceptible populations. We describe a case of post-transplant infection of pulmonary Nocardiosis caused by the rare strain Nocardia cyriacigeorgica and the challenges faced in reaching a definitive diagnosis. This case report emphasizes on keeping Nocardiosis as a differential diagnosis in transplant recipients as this disease is largely underdiagnosed and underreported.
CHALLENGES IN THE DIAGNOSIS AND MANAGEMENT OF ATYPICAL FUNGAL KERATITIS DURING COVID-19 PANDEMIC: A CASE SERIES
Authors: Ali Dideeya , Vijayan Ajith , Shenoy Kashinatha , Antony Ann Tresa , Ramachandran Reshmi
Published: January 2023

Fungal keratitis is a time-sensitive ocular infection that often requires a high index of suspicion followed by intensive medical/surgical interventions to achieve a successful clinical outcome. The COVID-19 pandemic-related restrictions necessitated modification of conventional protocols and guidelines related to the plan of care of keratomycosis. We report four cases of atypical fungal keratitis presenting with poorly differentiated clinical   characteristics. The challenges faced during their management were: 1) dilemma to clinically differentiate fungal (Scedosporium and Purpureocillium lilacinum) from bacterial keratitis; 2) treatment of Scedosporium and Trichosporon  keratitis with natamycin monotherapy; 3) mixed infection of  Candida albicans and Aureobasidium pullulans and continuing medications before rescraping the corneal ulcer against the recommended treatment guidelines; 4) phenotypic identification and differentiation among morphologically resembling fungi; and 5) decision making related to disparities between KOH and fungal culture results. Three patients responded well to conservative treatments. However, the fourth patient needed therapeutic keratoplasty, and was lost to follow-up due to travel related pandemic restrictions.  This case series seeks to broaden the clinician's knowledge of rare but emerging moulds as presumptive aetiologies of keratomycosis.  It also intends to reinforce the significance of early microbiological investigations, (direct microscopy and culture) in resource limited settings, for initiating empirical treatment towards a better visual prognosis.
Methanocaldococcus lauensis sp. nov., a novel deep-sea hydrothermal vent hyperthermophilic methanogen
Authors: L'Haridon Stéphane , Goulaouic Steven , St John Emily , Fouteau Stephanie , Reysenbach Anna-Louise
Published: January 2023

Three hyperthermophilic methanogens, designated strain SG7T, strain SG1 and strain SLH, were isolated from the ABE and Tu’i Malila deep-sea hydrothermal vent fields along the Eastern Lau Spreading Center. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strains SG7T, SG1 and SLH were affiliated with the genusMethanocaldococcuswithin the familyMethanocaldococcaceae, orderMethanococcales. They shared 95.5–99.48 % 16S rRNA gene sequence similarity to otherMethanocaldococcusspecies and were most closely related toMethanocaldococcus bathoardescens. Cells of strains SG7T, SG1 and SLH were cocci, with a diameter of 1.0–2.2 µm. The three strains grew between 45 and 93 °C (optimum, 80–85 °C), at pH 5.0–7.1 (optimum pH 6.2) and with 10–50 g l−1NaCl (optimum 20–25 g l−1). Genome analysis revealed the presence of a 5.1 kbp plasmid in strain SG7T. Based on the results of average nucleotide identity and digital DNA–DNA hybridization analyses, we propose that strains SG1 and SG7Tare representatives of a novel species, for which the nameMethanocaldococcus lauensissp. nov. is proposed; the type strain is SG7T(=DSM 109608T=JCM 39049T).
High quality genome and transcriptome data for two new species ofMantamonas, a deep-branching eukaryote clade
Authors: Blaz Jazmin , Galindo Luis Javier , Heiss Aaron A. , Kaur Harpreet , Torruella Guifré , Yang Ashley , Thompson L. Alexa , Filbert Alexander , Warring Sally , Narechania Apurva , Shiratori Takashi , Ishida Ken-ichiro , Dacks Joel B. , López-García Purificación , Moreira David , Kim Eunsoo , Eme Laura
Published: January 2023

Mantamonads were long considered to represent an “orphan” lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the “CRuMs” supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads,Mantamonas vickermanisp. nov. andMantamonas sphyraenaesp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of theM. sphyraenaegenome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup.
COVision: Convolutional Neural Network for the Differentiation of COVID-19 from Common Pulmonary Conditions Using CT Scans
Authors: Parikh Kush V. , Mathew Timothy J.
Published: January 2023

With the growing amount of COVID-19 cases, especially in developing countries with limited medical resources, it is essential to accurately and efficiently diagnose COVID-19. Due to characteristic ground-glass opacities (GGOs) and other types of lesions being present in both COVID-19 and other acute lung diseases, misdiagnosis occurs often — 26.6% of the time in manual interpretations of CT scans. Current deep-learning models can identify COVID-19 but cannot distinguish it from other common lung diseases like bacterial pneumonia. Concretely, COVision is a deep-learning model that can differentiate COVID-19 from other common lung diseases, with high specificity using CT scans and other clinical factors. COVision was designed to minimize overfitting and complexity by decreasing the number of hidden layers and trainable parameters while still achieving superior performance. Our model consists of two parts: the CNN which analyzes CT scans and the CFNN (clinical factors neural network) which analyzes clinical factors such as age, gender, etc. Using federated averaging, we ensembled our CNN with the CFNN to create a comprehensive diagnostic tool. After training, our CNN achieved an accuracy of 95.8% and our CFNN achieved an accuracy of 88.75% on a validation set. We found a statistical significance that COVision performs better than three independent radiologists with at least 10 years of experience, especially in differentiating COVID-19 from pneumonia. We analyzed our CNN’s activation maps through Grad-CAMs and found that lesions in COVID-19 presented peripherally, closer to the pleura, whereas pneumonia lesions presented centrally.
Genome expansion by a CRISPR trimmer-integrase
Authors: Wang Joy Y. , Tuck Owen T. , Skopintsev Petr , Soczek Katarzyna M. , Li Gary , Al-Shayeb Basem , Zhou Julia , Doudna Jennifer A.
Published: January 2023

CRISPR-Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR-Cas1:Cas2 integrase is necessary but not sufficient. In some microbes, the Cas4 endonuclease assists CRISPR adaptation, but many CRISPR-Cas systems lack Cas4. We show here that an elegant alternative pathway employs an internal exonuclease to select and process DNA for integration using the protospacer adjacent motif (PAM). A natural Cas1:Cas2-exonuclease fusion (trimmer-integrase) catalyzes coordinated DNA capture, trimming and integration. Five cryo-EM structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited exonucleases for faithful acquisition of new CRISPR immune sequences.
The pGinger family of expression plasmids
Authors: Pearson Allison N. , Thompson Mitchell G. , Kirkpatrick Liam D. , Ho Cindy , Vuu Khanh M. , Waldburger Lucas M. , Keasling Jay D. , Shih Patrick M.
Published: January 2023

The pGinger suite of expression plasmids comprises 43 plasmids that will enable precise constitutive and inducible gene expression in a wide range of gram-negative bacterial species. Constitutive vectors are composed of 16 synthetic constitutive promoters upstream of RFP, with a broad host range BBR1 origin and a kanamycin resistance marker. The family also has seven inducible systems (Jungle Express, Psal/NahR, Pm/XylS, Prha/RhaS, LacO1/LacI, LacUV5/LacI, and Ptet/TetR) controlling RFP expression on BBR1/kanamycin plasmid backbones. For four of these inducible systems (Jungle Express, Psal/NahR, LacO1/LacI, and Ptet/TetR), we created variants that utilize the RK2 origin and spectinomycin or gentamicin selection. Relevant RFP expression and growth data have been collected in the model bacteriumEscherichia colias well asPseudomonas putida. All pGinger vectors are available via the Joint BioEnergy Institute (JBEI) Public Registry.
Rhythmically bursting songbird vocomotor neurons are organized into multiple sequences, suggesting a network/intrinsic properties model encoding song and error, not time
Authors: Fetterman Graham C. , Margoliash Daniel
Published: January 2023

In zebra finch, basal ganglia projecting “HVCX” neurons emit one or more spike bursts during each song motif (canonical sequence of syllables), which are thought to be driven in part by a process of spike rebound excitation. Zebra finch songs are highly stereotyped and recent results indicate that the intrinsic properties of HVCXneurons are similar within each bird, vary among birds depending on similarity of the songs, and vary with song errors. We tested the hypothesis that the timing of spike bursts during singing also evince individual-specific distributions. Examining previously published data, we demonstrated that the intervals between bursts of multibursting HVCXare similar for neurons within each bird, in many cases highly clustered at distinct peaks, with the patterns varying among birds. The fixed delay between bursts and different times when neurons are first recruited in the song yields precisely timed multiple sequences of bursts throughout the song, not the previously envisioned single sequence of bursts treated as events having statistically independent timing. A given moment in time engages multiple sequences and both single bursting and multibursting HVCXsimultaneously. This suggests a model where a population of HVCXsharing common intrinsic properties driving spike rebound excitation influence the timing of a given HVCXburst through lateral inhibitory interactions. Perturbations in burst timing, representing error, could propagate in time. Our results extend the concept of central pattern generators to complex vertebrate vocal learning and suggest that network activity (timing of inhibition) and HVCXintrinsic properties become coordinated during developmental birdsong learning.
Molecular Interactions and Forces that Make Proteins Stable: A Quantitative Inventory from Atomistic Molecular Dynamics Simulations
Authors: Galano-Frutos Juan José , Sancho Javier
Published: January 2023

Protein design requires a deep control of protein folding energetics, which can be determined experimentally on a case-by-case basis but is not understood in sufficient detail. Calorimetry, protein engineering and biophysical modeling have outlined the fundamentals of protein stability, but these approaches face difficulties in elucidating the specific contributions of the intervening molecules and elementary interactions to the folding energy balance. Recently, we showed that, using Molecular Dynamics (MD) simulations of native proteins and their unfolded ensembles, one can calculate, within experimental error, the enthalpy and heat capacity changes of the folding reaction. Analyzing MD simulations of four model proteins (CI2, barnase, SNase and apoflavodoxin) whose folding enthalpy and heat capacity changes have been successfully calculated, we dissect here the energetic contributions to protein stability made by the different molecular players (polypeptide and solvent molecules) and elementary interactions (electrostatic, van der Waals and bonded) involved. Although the proteins analyzed differ in length (65-168 amino acid residues), isoelectric point (4.0-8.99) and overall fold, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformation is enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and it is nearly equally destabilized by interactions between protein and solvent molecules. From the perspective of elementary physical interactions, the native conformation is stabilized by van de Waals and coulombic interactions and is destabilized by bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by protein-solvent interactions or, from the alternative perspective, by coulombic interactions.
Autofluorescence lifetime imaging classifies human lymphocyte activation and subtype
Authors: Schmitz Rebecca L. , Tweed Kelsey E. , Rehani Peter , Samimi Kayvan , Riendeau Jeremiah , Jones Isabel , Maly Elizabeth M. , Guzman Emmanuel Contreras , Forsberg Matthew H. , Shahi Ankita , Capitini Christian M. , Walsh Alex J. , Skala Melissa C.
Published: January 2023

New non-destructive tools are needed to reliably assess lymphocyte function for immune profiling and adoptive cell therapy. Optical metabolic imaging (OMI) is a label-free method that measures the autofluorescence intensity and lifetime of metabolic cofactors NAD(P)H and FAD to quantify metabolism at a single-cell level. Here, we investigate whether OMI can resolve metabolic changes between human quiescent versus IL4/CD40 activated B cells and IL12/IL15/IL18 activated memory-like NK cells. We found that quiescent B and NK cells were more oxidized compared to activated cells. Additionally, the NAD(P)H mean fluorescence lifetime decreased and the fraction of unbound NAD(P)H increased in the activated B and NK cells compared to quiescent cells. Machine learning classified B cells and NK cells according to activation state (CD69+) based on OMI parameters with up to 93.4% and 92.6% accuracy, respectively. Leveraging our previously published OMI data from activated and quiescent T cells, we found that the NAD(P)H mean fluorescence lifetime increased in NK cells compared to T cells, and further increased in B cells compared to NK cells. Random forest models based on OMI classified lymphocytes according to subtype (B, NK, T cell) with 97.8% accuracy, and according to activation state (quiescent or activated) and subtype (B, NK, T cell) with 90.0% accuracy. Our results show that autofluorescence lifetime imaging can accurately assess lymphocyte activation and subtype in a label-free, non-destructive manner.

Teaser

Label-free optical imaging can assess the metabolic state of lymphocytes on a single-cell level in a touch-free system.
Machine learning for scattering data: strategies, perspectives and applications to surface scattering
Authors: Hinderhofer Alexander , Greco Alessandro , Starostin Vladimir , Munteanu Valentin , Pithan Linus , Gerlach Alexander , Schreiber Frank
Published: January 2023

Machine learning (ML) has received enormous attention in science and beyond. Discussed here are the status, opportunities, challenges and limitations of ML as applied to X-ray and neutron scattering techniques, with an emphasis on surface scattering. Typical strategies are outlined, as well as possible pitfalls. Applications to reflectometry and grazing-incidence scattering are critically discussed. Comment is also given on the availability of training and test data for ML applications, such as neural networks, and a large reflectivity data set is provided as reference data for the community.
Syntheses and crystal structures of two dinaphtho[2,1-d:1′,2′-f][1,3]dithiepine atropisomers
Authors: Beare Neil , Painter Gavin F. , McAdam C. John
Published: January 2023

The closely related title compounds, 1-(dinaphtho[2,1-d:1′,2′-f][1,3]dithiepin-4-yl)-2,2-dimethylpropan-1-ol, C26H24OS2, 1 and 2-(dinaphtho[2,1-d:1′,2′-f][1,3]dithiepin-4-yl)-3,3-dimethylbutan-2-ol, C27H26OS2, 2, both comprise an atropisomeric binaphthyl dithioacetal unit substituted at the methylene carbon atom with a chiral neopentyl alcohol grouping. The overall stereochemistry of the racemate in each case is defined as aS,R and aR,S. In 1, the hydroxyl group generates inversion dimers via pairwise intermolecular O—H...S hydrogen bonds whereas in 2, the O—H...S link is intramolecular. Weak C—H...π interactions link the molecules into extended arrays in both structures.
Lagrange multiplier optimization method for high current–low frequency inductor design
Authors: Marques Hugo dos Santos , Borges Maria Beatriz
Published: January 2023

Purpose

This paper aims to overcome the lack of methodologies for optimizing the volume of bulky low-frequency inductors that the authors came across with when working on the design of hybrid active power filters. Sound work was published concerning this well-known technology, but it became evident that the mentioned optimization topic was left unaddressed.

Design/methodology/approach

Using the Lagrange multipliers optimization method combined with the electromagnetic laws of inductor design, it was possible to establish a new design method to determine the optimal solutions that fulfil any given scenario of specifications. In other words, it is now possible to obtain the inductor’s geometric and electric parameters that not only satisfy the system’s electromagnetic requirements but also lead to smaller, lighter or economical solutions.

Findings

A generalized set of equations was obtained to facilitate the calculations of all the inductor-building parameters. As expected, these equations take as inputs the inductor’s required inductance, its maximum current and the desired resistance, but also a customizable cost function. The later cost function will optimize the inductor’s volumes of copper and iron and can be settled, among other purposes, for minimizing the total weight, volume or cost.

Originality/value

All the mathematical expressions to obtain the general optimal solutions are given as well as practical graphics for the three above-mentioned optimization criteria. Using these charts, the reader will be able to obtain by simple inspection the optimal solutions for a large, generalized universe of intended specifications.
Assessing the effect of domestic and foreign R&D on export: empirical evidence from China
Authors: Rauf Abdul , Bao Yongwen
Published: January 2023

Purpose

Although the theoretical arguments provide several channels through which innovation affects export, empirical validation of this relationship is scarce. Further, the impact of the diverse channels of domestic and foreign research and development (R&D) on export is assessed in isolation by previous studies. This paper empirically investigates the impact of technological innovation on export capacity and intensity of industrial enterprises in emerging countries by considering three channels of domestic innovation and foreign R&D spillovers, namely internal R&D, embodied knowledge and disembodied knowledge in a unified framework.

Design/methodology/approach

Data on China's industrial enterprises in the manufacturing sector are extracted from the China National Bureau of Statistics (NBSC), the Ministry of Science and Technology of China (MST) and the UN Comtrade database for the period from 1998 to 2020. The instrumental variables two-stage least squares (IV-2SLS) and three-stage least squares (IV-3SLS) methods are used to control for the possible endogeneity bias and the problem of cross-equation correlation between residuals.

Findings

The results show that internal R&D is a critical factor to enhance the export performance of enterprises in emerging countries, while the effect of embodied spillovers and public–private collaboration on export capacity and intensity of industrial enterprises is substantial. Further, disembodied knowledge that is acquired through licensing of technology from advanced countries does not directly contribute to the export performance of enterprises but requires a threshold level of internal R&D capability. This study’s results also report a greater effect of embodied knowledge spillovers on export capacity and export intensity than internal R&D in emerging countries. The results are consistent to changes in the sample period and the estimation methods. The findings of the paper suggest that developing countries can speed up the process of export upgrading by relying on both domestic and foreign R&D efforts.

Practical implications

The findings would help policymakers to keep in mind the relative importance of internal R&D and embodied and disembodied knowledge spillovers for export performance before formulating a catch-up strategy and the outcome would encourage them to consider prior related knowledge in terms of internal R&D capability while acquiring external technology.

Originality/value

This study fills the gap in the existing literature by providing empirical validation of the innovation–export interplay and simultaneously assessing the effect of three diverse channels of technological innovation on the export performance of industrial enterprises. This paper enunciates important policy lessons for emerging countries' smooth transition to a knowledge-based economy.
Proposing a new loan recommendation framework for loan allocation strategies in online P2P lending
Authors: Rong Yuting , Liu Shan , Yan Shuo , Huang Wei Wayne , Chen Yanxia
Published: January 2023

Purpose

Lenders in online peer-to-peer (P2P) lending platforms are always non-experts and face severe information asymmetry. This paper aims to achieve the goals of gaining high returns with risk limitations or lowering risks with expected returns for P2P lenders.

Design/methodology/approach

This paper used data from a leading online P2P lending platform in America. First, the authors constructed a logistic regression-based credit scoring model and a linear regression-based profit scoring model to predict the default probabilities and profitability of loans. Second, based on the predictions of loan risk and loan return, the authors constructed linear programming model to form the optimal loan portfolio for lenders.

Findings

The research results show that compared to a logistic regression-based credit scoring method, the proposed new framework could make more returns for lenders with risks unchanged. Furthermore, compared to a linear regression-based profit scoring method, the proposed new framework could lower risks for lenders without lowering returns. In addition, comparisons with advanced machine learning techniques further validate its superiority.

Originality/value

Unlike previous studies that focus solely on predicting the default probability or profitability of loans, this study considers loan allocation in online P2P lending as an optimization research problem using a new framework based upon modern portfolio theory (MPT). This study may contribute theoretically to the extension of MPT in the specific context of online P2P lending and benefit lenders and platforms to develop more efficient investment tools.
Laughter, mental health and cancer: a case study of Ros Ben-Moshe
Authors: Ben-Moshe Ros , Gonot-Schoupinsky Freda
Published: January 2023

Purpose

The purpose of this paper is to meet Ros Ben-Moshe, a cancer survivor – or rather thriver – and lecturer in positive psychology at La Trobe University, describes how she uses laughter to boost levity and mental health.

Design/methodology/approach

This case study is divided into two parts: an autoethnographic life story of Ros Ben-Moshe, followed by 10 questions and answers.

Findings

Regular laughter is an enjoyable way to stimulate the feel-good chemicals dopamine, oxytocin, serotonin and endorphins. A laughter mindset is an important tool for overall wellbeing. It can help build connections and re-frame negative situations.

Research limitations/implications

This is a personal narrative and gives the perspective of one person who harnessed the benefits of laughter following a cancer diagnosis.

Practical implications

Laughter can be used strategically to reset our internal mindset and prime ourselves towards optimal mental health and wellbeing, even while struggling with serious health issues. Research into how and when to prescribe laughter for mental health and overall wellbeing is therefore of interest.

Social implications

Social laughter is important and rewarding. For those anxious about social laughter, finding people to laugh with who do not judge you is recommended, as are affirmations to lessen anxiety.

Originality/value

To the best of the authors’ knowledge, this is the first case study and interview with a cancer survivor on the topic of laughter, cancer and mental health.
Positive addiction recovery for an online audience: implementation design and user evaluation
Authors: Ogilvie Lisa , Prescott Julie
Published: January 2023

Purpose

The positive addiction recovery website (https://positiveaddictionrecovery.com) has been created following a successful pilot study of a programme of work known as positive addiction recovery therapy (PART). The aim of the website is to disseminate PART to an online audience, extending its reach to a larger population. The purpose of this study is to explain the process of creating this online resource and to conduct a user evaluation to understand how well received the website is likely to be to its target audience.

Design/methodology/approach

An implementation framework cognisant of positive computing, positive technology, contemporary understanding of human–computer interaction and knowledge acquired from the delivery of eHealth interventions from the past decade was used to create the website. To understand user opinion of the resultant website, data were collected using the mobile application ratings scale user version.

Findings

By adopting a tailored implementation framework, with appropriate determinant factors of wellbeing and evidenced theoretical input, a website resource was created that users considered engaging and informative. The findings also suggest that participants appreciated the importance of intended behavioural change, having interacted with the interventions on the website.

Originality/value

To the best of the authors’ knowledge, the website is the first online version of PART, a new programme of work aimed at people in addiction recovery.
Health behaviours and COVID‐19 prevention among immigrants in the United States
Authors: Thomas Kevin J. A.
Published: January 2023

Recent studies indicate that the COVID‐19 pandemic has had negative implications for the welfare of immigrant communities. However, few studies have examined the behavioural responses used by immigrants to respond to the spread of the virus. This study uses data from the U.S.‐based COVID‐19 in American Communities study to examine whether there are disparities in the use of COVID‐19 prevention behaviours between first‐generation immigrants (i.e., foreign‐born persons), second‐generation immigrants (i.e., U.S.‐born persons with at least one immigrant parent), and third‐generation individuals (i.e., U.S.‐born persons with only U.S.‐born parents). The results indicate that recent first‐generation immigrants and second‐generation immigrants use the behaviours recommended to prevent the spread of COVID‐19 less intensively compared to third‐generation individuals. Furthermore, increased exposure to U.S. society is found to have a non‐linear relationship with the intense use of these behaviours. Results from the analysis of each preventive behaviour show that there are larger gaps between immigrants and U.S. natives in the use of frequent hand washing and comparatively smaller gaps in the practice of avoiding large crowds. However, the most consistent pattern of low use of COVID‐19 prevention behaviours was found among recently arrived first‐generation immigrants.