bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Efficiency and Effectiveness Between a Slap Hammer and Rigid C-Frame Device for Extraction of an Intramedullary Nail
Authors: Gosik-Wolfe Adam , Singh Suvleen K. , Welsh Megan E. , Eichinger Josef K.
Published: March 2023

Background:

Removal of orthopaedic intramedullary implants can be difficult and time-consuming. Instrumentation for implant removal is frequently deficient for effective removal. The purpose of this study was to compare the efficiency of a C-type jig with a standard slap hammer attachment. We hypothesize that a C-type jig will be a more energy-efficient method for implant removal.

Methods:

An intramedullary (IM) nail removal was simulated in a series of 10 tests using 40 PCF Sawbones bone blocks with drilled holes and custom-made IM nails. Each attachment was secured to a Shukla Medical threaded connector from their IM nail revision product. A camera recorded each hammer swing, and a caliper recorded the distance the nail traveled out of the bone block. The data were then analyzed to determine extraction rate and efficiency.

Results:

The c-frame hammer exerted a greater force, had a greater extraction efficiency, and required 37.4% less energy expenditure than the slap hammer to extract the nail the same distance. The c-frame hammer also removed the nail 38.1% faster with the same energy expenditure and possessed greater usable kinetic energy, whereas the slap hammer had more “lost” energy.

Conclusions:

The c-frame hammer attachment was found to have a considerably higher extraction rate and efficiency than the slap hammer. It will be a more useful method of implant extraction, especially for cases involving larger bones or larger implants. However, the slap hammer may be more suitable for smaller tools or bones for which larger impact loading would be detrimental.
Can the Shriners Hospital Upper Extremity Evaluation (SHUEE) Detect Change in Dynamic Position and Spontaneous Function of the Upper Limb in People With Hemiplegic Cerebral Palsy?
Authors: Lennon Nancy , Church Chris , Shields Thomas , Kee John , Henley John D. , Salazar-Torres Jose J. , Niiler Tim , Shrader M. Wade , Ty Jennifer M.
Published: March 2023

Background:

The Shriners Hospital Upper Extremity Evaluation (SHUEE) is a video-based measure designed to assess upper extremity function in people with cerebral palsy (CP). The SHUEE completes both dynamic positional analysis (DPA; position during functional activities) and spontaneous functional analysis (spontaneous use of the involved limb). Although the SHUEE has been suggested as a measure for planning upper limb interventions and evaluating outcomes, limited evidence of its ability to detect change exists. Thus, this study aimed to describe responsiveness of the SHUEE to detect change after orthopaedic surgery.

Methods:

In this Institutional Review Board-approved retrospective cohort study, we identified children with CP who were administered SHUEE on≥2 encounters. We formed pairs of initial and follow-up visits between temporally adjacent visits. Pairs were assigned to a surgery or non-surgery group based on intervening upper limb orthopaedic surgery. We compared differences in baseline SHUEE scores between groups and differences in temporally adjacent SHUEE scores within groups using Welch unequal variancesttests and pairedttests, respectively.

Results:

Nineteen people (7 female) with hemiplegic CP had≥2 SHUEE assessments; Manual Ability Classification System levels I (3), II (8), III (7), IV (1); Gross Motor Function Classification System levels I (10), II (7), IV (2); mean age at baseline 11.9 (5.1 to 19.1) years; and follow-up at 13.4 (5.5 to 19.7) years. Six people had≥2 visits leading to 14 surgical pairs and 10 non-surgical pairs. At baseline, DPA of the wrist and forearm were significantly lower in the surgical group (P<0.05). At follow-up, no significant difference between the groups existed in DPA measures (P>0.05). After surgical intervention, there was a significant change in overall and wrist DPA (P<0.05).

Conclusions:

The DPA measures demonstrated responsiveness to expected positional changes in the arm after orthopaedic surgery in people with CP. The SHUEE was useful in identifying abnormal segmental alignment pre-surgically and documenting changes in alignment postoperatively. As orthopaedic surgery does not address limb neglect or bimanual ability, spontaneous functional analysis scores were as expected-unchanged.

Level of Evidence:

Level III, retrospective cohort study.
Effects of Self-Administered Acupressure on Fatigue Following Traumatic Brain Injury: A Randomized Controlled Trial
Authors: Chen Shu-Mei , Chen Wan-Ling , Tai Chen-Jei , Hsieh Shu-Hua , Lin Che-Kuang , Chen Pin-Yuan , Huang Hui-Chuan , Fan Yen-Chun , Chiu Hsiao-Yean
Published: March 2023

Background:

Fatigue is a common symptom after a traumatic brain injury (TBI) and may persist for weeks or years. However, nonpharmacological management strategies for fatigue alleviations are almost nonexistent; thus, effective fatigue management programs are needed urgently.

Purposes:

We aimed to evaluate the effects of self-administered acupressure programs on post-TBI fatigue and heart rate variability and identify the possible correlation between the improvements in fatigue symptoms and the changes in heart rate variability.

Design:

This randomized controlled trial included 2-point acupressure (TPA; n = 27), 5-point acupressure (FPA; n = 27), and usual care (UC, control; n = 27) groups who underwent several assessments before and after the study intervention. Heart rate variability was evaluated at baseline, weeks 2 and 3, and treatment completion.

Methods:

The TPA and FPA groups self-administered acupressure (3 minutes per acupoint; bilateral), thrice daily for 4 weeks, whereas the UC group received routine treatment without acupressure.

Results:

Both the TPA and FPA groups exhibited substantial improvements in fatigue symptoms compared with the baseline findings in the UC group. In addition, the TPA and FPA groups exhibited increased high-frequency power and mean number of times per hour in which the changes in successive normal sinus intervals (RR) gradually exceeded 50 ms (pNN50). Changes in high-frequency power and pNN50 were correlated with improvements in post-TBI fatigue symptoms.

Conclusion:

Acupressure may alleviate chronic fatigue and enhance parasympathetic activity in TBI survivors. The enhancement of parasympathetic activity may be correlated with improvements in post-TBI fatigue symptoms.

Relevance to Clinical Practice:

Healthcare providers should incorporate self-administered acupressure into the care plans for TBI survivors to improve their fatigue symptoms.
Mesenchymal Stem Cells in the Treatment of Acute Kidney Injury (AKI), Chronic Kidney Disease (CKD) and the AKI-to-CKD Transition
Authors: Allinson Charles Stuart , Pollock Carol A. , Chen Xinming
Published: March 2023

Acute kidney injury (AKI) and chronic kidney disease (CKD) are global health burdens that result in high economic costs to healthcare systems. AKI is a known risk factor for progression to CKD. The global absolute CKD prevalence increased by 28.2% from 2007–2017 among females and 25.4% among males. Current best clinical practice only slows the progress of renal fibrosis, the final pathological consequence of renal injury, in CKD. Kidney transplantation and dialysis are the only options for the management of kidney failure, which results in a significant burden on the health system. Hence innovative strategies are urgently needed to both prevent and treat CKD. Many studies have demonstrated that mesenchymal stem cells (MSCs) exert a therapeutic role through regenerating/repairing damaged tissues primarily through cargo secreted in extracellular vesicles. In recent years, the therapeutic effect of stem cells in the treatment of acute and chronic kidney disease have been primarily assessed in preclinical studies. This review outlines the safety and efficacy of MSCs in AKI, CKD and the AKI-to-CKD transition based on recent animal studies and clinical trials. It elucidates the antifibrotic mechanisms of MSCs and provides novel insights into MSC therapy in AKI, CKD and the transition from AKI to CKD.
Therapeutic Effects of Jin Shui Bao Capsules on Kidney Diseases
Authors: Chen Hongyu , Cheng Qingli
Published: March 2023

Several clinical studies have demonstrated that Jin Shui Bao capsules can attenuate the occurrence and progression of multiple types of kidney diseases. However, there is a lack of consensus regarding its therapeutic effects. Mounting evidence indicates that Jin Shui Bao capsules can effectively ameliorate kidney microcirculation and proteinuria, thereby improving kidney function and delaying disease progression. This review presents a discussion of the effects of Jin Shui Bao capsules on chronic glomerulonephritis, chronic kidney disease, diabetic kidney disease, and hemodialysis treatments. This paper may serve as a valuable reference for kidney disease treatments involving Chinese herbal medicines.
Early Experience With an Occupational JYNNEOS (Orthopoxvirus) Vaccination Program
Authors: Swift Melanie D. , McDermott Mary C. , Hainy Caitlin M. , Arendt Christopher J. , Anderson Jennifer A. , Mahoo Jacqueline J. , Breeher Laura E.
Published: March 2023

Objective

The aim of the study is to identify lessons learned implementing JYNNEOS vaccination for laboratory workers exposed to orthopoxviruses such as mpox.

Methods

Workers at risk of laboratory exposure were offered vaccine in a carefully planned occupational health program. Vaccine was procured from the Centers for Disease Control and Prevention (CDC) Drug Service, which has special requirements. Reasons for accepting or declining vaccine and adverse effects were obtained by survey.

Results

Most workers accepted JYNNEOS, and occupational risk was the most commonly cited reason for acceptance. Most experienced mild local adverse effects. The administrative requirements of the Centers for Disease Control and Prevention Drug Service are documented.

Conclusions

Occupational health programs caring for laboratory workers handling unusual biological agents require careful planning and coordination to facilitate access to vaccines that are not commercially available, anticipate and mitigate barriers to vaccination, and comply with special Centers for Disease Control and Prevention requirements.
Molecular alterations and therapeutic targets in pancreatic neuroendocrine tumors
Authors: Ma Yarui , Wang Xiaoyue , Zhao Hong , Jiao Yuchen
Published: March 2023

Human pancreatic neuroendocrine tumors (PanNETs) are a rare, deadly tumor type that is sporadic or arises in the background of a hereditary syndrome. A critical genetic event in sporadic tumors is inactivation of the gene menin 1 (MEN1) on chromosome 11, and indeed, PanNETs occur in patients with the hereditary syndrome multiple endocrine neoplasia type 1 (MEN1) due to germline mutations in the gene. Here, we review the recent progress in the field of molecular genetics and therapeutic targets of PanNETs. The key genomic alterations, including MEN1, ATRX/DAXX, mammalian target of rapamycin (mTOR), DNA damage and repair associated genes, vascular endothelial growth factor receptor (VEGFR) and SSTRs, and epigenetic aberrations in PanNETs are discussed. In addition, the commonly used preclinical models for PanNETs are enumerated.
Predictors of left ventricular thrombus after acute myocardial infarction: a systematic review and meta-analysis
Authors: Kwok Chun Shing , Bennett Sadie , Borovac Josip A. , Schwarz Konstatin , Lip Gregory Y.H.
Published: March 2023

Left ventricular thrombus (LVT) is a recognized complication of acute myocardial infarction (AMI) which can cause significant morbidity and mortality from systemic embolism. We conducted a systematic review and meta-analysis of factors that have been shown in studies to be independently predictive of LVT post-AMI. A total of 23 studies met the inclusion criteria with 1 047 785 patients. The proportion of patients with LVT ranged from 0.2% in the nationwide study in the USA to 36.1% in the cohort of patients with LV aneurysm. Pooled results from nine studies suggest that greater values for left ventricular ejection fraction is associated with reduced odds of LVT formation [odds ratio (OR) 0.90; 95% confidence interval (CI), 0.86–0.93; I
2 = 76%]. Left ventricular aneurysm was a significant predictor of LVT formation (OR 6.07; 95% CI, 2.27–16.19; I
2 = 91%; seven studies) and anterior location of MI was also a significant predictor (OR 7.72; 95% CI, 2.41–24.74; I
2 = 69%; four studies). Three studies suggest that there was an increase in odds of LVT formation with greater values of C-reactive protein (OR 2.06; 95% CI, 1.07–3.97; I
2 = 89%; three studies). The use of glycoprotein IIb/IIIa inhibitors (OR 2.52; 95% CI, 1.55–4.10; I
2 = 0%; two studies) and greater SYNTAX score (OR 1.21; 95% CI, 1.08–1.36; I
2 = 46%; two studies) were associated with LVT. In conclusion, patients with reduced ejection fraction, AMI and with left ventricular aneurysm are at risk of LVT formation and careful imaging evaluation should be performed to identify LVT in these patients to prevent stroke or peripheral embolism.
An evidence-based evaluation of left ventricular thrombus treatment, outcomes, and resolution: a systematic review, pooled analysis and meta-analysis
Authors: Kwok Chun Shing , Bennett Sadie , Borovac Josip A. , Will Maximilliam , Schwarz Konstantin , Lip Gregory Y. H.
Published: March 2023

Left ventricular thrombus (LVT) is a recognized complication of acute myocardial infarction which is associated with stroke. There has yet to be a published systematic review that focuses on outcomes for patients with LVT. We conducted a systematic review on treatments, adverse events and thrombus resolution in patients with LVT. Meta-analysis and numerical pooling were used to evaluate the difference in outcomes based on treatment and the presence or absence of LVT. A total of 39 studies were included (5475 patients with LVT and 356 589 patients with no LVT). The use of direct oral anticoagulants (DOACs) was associated with reduced mortality [RR, 0.66; 95% confidence interval (CI), 0.45–0.97; I
2 = 9%] and bleeding (RR, 0.64; 95% CI, 0.48–0.85; I
2 = 0%) compared to warfarin but there was a nonsignificant reduction in stroke/embolic events (RR, 0.95; 95% CI, 0.76–1.19; I
2 = 3%). For patients with any treatment, the rate of stroke/embolic events, bleeding and mortality at follow-up of up to 12 months was 6.4, 3.7 and 7.9%, respectively. Pooled results from six studies that evaluated resolution at 6 months suggest that 80% of LVT were resolved. Apixaban was associated with the highest rate of (93.3%) whereas warfarin exhibited the lowest rate of resolution 73.1%. LVT is best managed with DOAC compared to warfarin therapy. An individualized approach to antithrombotic therapy is warranted as there appears to be no duration of therapy that clearly results in the resolution of all cases of LVT so follow-up imaging after discontinuation of anticoagulant is needed.
The Microbiome and Its Impact on Allogeneic Hematopoietic Cell Transplantation
Authors: Malard Florent , Jenq Robert R.
Published: March 2023

Allogeneic hematopoietic cell transplantation (alloHCT) is a standard curative therapy for a variety of benign and malignant hematological diseases. Previously, patients who underwent alloHCT were at high risk for complications with potentially life-threatening toxicities, including a variety of opportunistic infections as well as acute and chronic manifestations of graft-versus-host disease (GVHD), where the transplanted immune system can produce inflammatory damage to the patient. With recent advances, including newer conditioning regimens, advances in viral and fungal infection prophylaxis, and novel GVHD prophylactic and treatment strategies, improvements in clinical outcomes have steadily improved. One modality with great potential that has yet to be fully realized is targeting the microbiome to further improve clinical outcomes.

In recent years, the intestinal microbiota, which includes bacteria, fungi, viruses, and other microbes that reside within the intestinal tract, has become established as a potent modulator of alloHCT outcomes. The composition of intestinal bacteria, in particular, has been found in large multicenter prospective studies to be strongly associated with GVHD, treatment-related mortality, and overall survival. Murine studies have demonstrated a causal relationship between intestinal microbiota injury and aggravated GVHD, and more recently, clinical interventional studies of repleting the intestinal microbiota with fecal microbiota transplantation have emerged as effective therapies for GVHD. How the composition of the intestinal bacterial microbiota, which is often highly variable in alloHCT patients, can modulate GVHD and other outcomes is not fully understood. Recent studies, however, have begun to make substantial headway, including identifying particular bacterial subsets and/or bacterial-derived metabolites that can mediate harm or benefit. Here, the authors review recent studies that have improved our mechanistic understanding of the relationship between the microbiota and alloHCT outcomes, as well as studies that are beginning to establish strategies to modulate the microbiota with the hope of optimizing clinical outcomes.
The Gut Microbiome and Pancreatic Cancer Development and Treatment
Authors: Attebury Holly , Daley Donnele
Published: March 2023

Changes in the gut microbiome have been increasingly shown to accompany oncogenesis across various tumors. Similarly, microbial dysbiosis was found to be associated with pancreatic cancer progression and survival outcomes, expanding the field of tumor microenvironment research in pancreatic cancer. Mechanistic studies in pancreatic cancer models implicate components of the gut and pancreatic cancer microbiome in regulating tumorigenesis by altering cancer cell signaling, modulating immune function, and influencing the efficacy of current therapies in pancreatic cancer. This review discusses the outcomes of microbial modulation across various preclinical and clinical studies and highlights ongoing trials targeting the microbiome for pancreatic cancer therapy.
Subjective and Objective Evaluation of Speech in Adult Patients With Repaired Cleft Palate
Authors: Lou Qun , Wang Xudong , Chen Yang , Wang Guomin , Jiang Liping , Liu Qiong
Published: March 2023

Objective:

To explore the speech outcomes of adult patients with repaired cleft palate through subjective perception evaluation and objective acoustic analysis, and to compare the differences in pronunciation characteristics between speakers with complete velopharyngeal closure (VPC) and velopharyngeal insufficiency (VPI) patients.

Participants and Intervention:

Subjective evaluation indicators included speech intelligibility, nasality and consonant missing rate, for objective acoustic analysis, we used speech sample normalization and objective acoustic parameters included normalized vowel formants, voice onset time and the analysis of 3-dimensional spectrogram and spectrum, were carried out on speech samples produced by 3 groups of speakers: (a) speakers with velopharyngeal competence after palatorrhaphy (n=38); (b) speakers with velopharyngeal incompetence after palatorrhaphy (n=70), (c) adult patients with cleft palate (n=65) and (d) typical speakers (n=30)

Results:

There was a highly negative correlation between VPC grade and speech intelligibility (ρ=-0.933), and a highly positive correlation between VPC and nasality (ρ=0.813). In subjective evaluation, the speech level of VPI patients was significantly lower than that of VPC patients and normal adults. Although the nasality and consonant loss rate of VPC patients were significantly higher than that of normal adults, the speech intelligibility of VPC patients was not significantly different from that of normal adults. In acoustic analysis, patients with VPI still performed poorly compared with patients with VPC.

Conclusions:

The speech function of adult cleft palate patients is affected by abnormal palatal structure and bad pronunciation habits. In subjective evaluation, there was no significant difference in speech level between VPC patients and normal adults, whereas there was significant difference between VPI patients and normal adults. The acoustic parameters were different between the 2 groups after cleft palate repair. The condition of palatopharyngeal closure after cleft palate can affect the patient’s speech.
Crassaminicella indica sp. nov., a novel thermophilic anaerobic bacterium isolated from a deep-sea hydrothermal vent
Authors: Jiao Ze-Xi , Li Xue-Gong , Zhang Huan-Huan , Xu Jun , Bai Shi-Jie , Dai Jie , Lin Jin , Zhang Wei-Jia , Qi Xiao-Qing , Wu Long-Fei
Published: March 2023

A novel moderately thermophilic heterotrophic bacterium, designated strain 143-21T, was isolated from a deep-sea hydrothermal chimney sample collected from the Central Indian Ridge at a depth of 2 440 m. Phylogenetic analysis indicated that strain 143-21T belongs to the genus

Crassaminicella

. It was most closely related to

Crassaminicella thermophila

SY095T (96.79 % 16S rRNA gene sequence similarity) and

Crassaminicella profunda

Ra1766HT (96.52 %). Genomic analysis showed that strain 143-21T shares 79.79–84.45 % average nucleotide identity and 23.50–29.20 % digital DNA–DNA hybridization with the species of the genus

Crassaminicella

, respectively. Cells were rod-shaped, non-motile, Gram-positive-staining. Terminal endospores were observed in stationary-phase cells when strain 143-21T was grown on Thermococcales rich medium. Strain 143-21T was able to grow at 30–60 °C (optimum, 50 °C), pH 6.5–8.5 (optimum, pH 7.0) and in 1.0–7.0 % NaCl (w/v; optimum 2.0 %, w/v). Strain 143-21T utilized fructose, glucose, maltose, mannose, ribose, N-acetyl-d-(+)-glucosamine and casamino acids, as well as amino acids including glutamate, lysine, histidine and cysteine. The main fermentation products from glucose were acetate (2.07 mM), H2 and CO2. It did not reduce elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and Fe (III). The predominant cellular fatty acids were C14 : 0 (48.8 %), C16 : 0 (12.9 %), and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 10.2 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, as well as two unidentified phospholipids and four unidentified aminolipids. No respiratory quinones were detected. Based on its phylogenetic analysis and physiological characteristics, strain 143-21T is considered to represent a novel species of the genus

Crassaminicella

, for which the name Crassaminicella indica sp. nov. is proposed. The type strain is strain 143-21T (=DSM 114408T= MCCC 1K06400T).
Novosphingobium kaempferiae sp. nov., a phosphate-solubilizing bacterium isolated from stem of Kaempferia marginata Carey
Authors: Sitlaothaworn Kanchana , Yukphan Pattaraporn , Budsabun Tanakwan , Charoenyingcharoen Piyanat , Phongsopitanun Wongsakorn , Savarajara Ancharida , Tanasupawat Somboon
Published: March 2023

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming and yellow-pigment-producing bacterium, designated as Sx8-5T, was isolated from stem tissue of Kaempferia marginata Carey in Kanchanaburi Province, Thailand. The strain exhibited tricalcium phosphate solubilizing activity. Its taxonomic position was investigated using a polyphasic approach. Sx8-5T grew at 25–37 °C (optimum 30 °C), pH 6–9 (optimum 7) and with 0 and 1% NaCl (optimum 0 %). According to the 16S rRNA gene phylogeny, Sx8-5T represents a member of genus

Novosphingobium

and shared the highest sequence similarities to

Novosphingobium barchaimii

LL02T of 99.4 % and shared sequence similarities with other species of the genus

Novosphingobium

of less than 99.4 %. The whole-genome size was 5.7 Mb, comprised of one contig, with a DNA G+C content of 66 %. The average nucleotide identity using BLASTn (ANIb) or MUMMER (ANIm) values for whole genome comparisons between Sx8-5T and

Novosphingobium barchaimii

LL02T and six closely related type strains were 72.33–82.14 % and 83.82–87.38 %, respectively, and the digital DNA–DNA hybridization (dDDH) values ranged from 21.0 to 28.6% when compared with the type strains of the members of the genus

Novosphingobium

. Major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1 
ω6c), C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c), respectively. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, unidentified phospholipids and unidentified polar lipids. The major isoprenoid quinone was Q-10. According to results obtained using a polyphasic approach, Sx8-5T represents a novel species of the genus

Novosphingobium

, the name Novosphingobium kaempferiae sp. nov. is proposed. The type strain is Sx8-5T (=JCM 35076T =TBRC 15600T).
Global population structure, genomic diversity and carbohydrate fermentation characteristics of clonal complex 119 (CC119), an understudied Shiga toxin-producing E. coli (STEC) lineage including O165:H25 and O172:H25
Authors: Nakamura Keiji , Seto Kazuko , Lee Kenichi , Ooka Tadasuke , Gotoh Yasuhiro , Taniguchi Itsuki , Ogura Yoshitoshi , Mainil Jacques Georges , Piérard Denis , Harada Tetsuya , Etoh Yoshiki , Ueda Saori , Hamasaki Mitsuhiro , Isobe Junko , Kimata Keiko , Narimatsu Hiroshi , Yatsuyanagi Jun , Ohnishi Makoto , Iyoda Sunao , Hayashi Tetsuya
Published: March 2023

Among Shiga toxin (Stx)-producing

Escherichia coli

(STEC) strains of various serotypes, O157:H7 and five major non-O157 STEC (O26:H11, O111:H8, O103:H2, O121:H19 and O145:H28) can be selectively isolated by using tellurite-containing media. While human infections by O165:H25 STEC strains have been reported worldwide, their detection and isolation are not easy, as they are not resistant to tellurite. Systematic whole-genome sequencing (WGS) analyses have not yet been conducted. Here, we defined O165:H25 strains and their close relatives, including O172:H25 strains, as clonal complex 119 (CC119) and performed a global WGS analysis of the major lineage of CC119, called CC119 sensu stricto (CC119ss), by using 202 CC119ss strains, including 90 strains sequenced in this study. Detailed comparisons of 13 closed genomes, including 7 obtained in this study, and systematic analyses of Stx phage genomes in 50 strains covering the entire CC119ss lineage, were also conducted. These analyses revealed that the Stx2a phage, the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS), many prophages encoding T3SS effectors, and the virulence plasmid were acquired by the common ancestor of CC119ss and have been stably maintained in this lineage, while unusual exchanges of Stx1a and Stx2c phages were found at a single integration site. Although the genome sequences of Stx2a phages were highly conserved, CC119ss strains exhibited notable variation in Stx2 production levels. Further analyses revealed the lack of SpLE1-like elements carrying the tellurite resistance genes in CC119ss and defects in rhamnose, sucrose, salicin and dulcitol fermentation. The genetic backgrounds underlying these defects were also clarified.
ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies
Authors: Yassine Iman , Hansen Elisabeth E. , Lefèvre Sophie , Ruckly Corinne , Carle Isabelle , Lejay-Collin Monique , Fabre Laetitia , Rafei Rayane , Pardos de la Gandara Maria , Daboussi Fouad , Shahin Ahmad , Weill François-Xavier
Published: March 2023

Shigella

is one of the commonest causes of diarrhoea worldwide and a major public health problem.

Shigella

serotyping is based on a standardized scheme that splits

Shigella

strains into four serogroups and 60 serotypes on the basis of biochemical tests and O-antigen structures. This conventional serotyping method is laborious, time-consuming, impossible to automate, and requires a high level of expertise. Whole-genome sequencing (WGS) is becoming more affordable and is now used for routine surveillance, opening up possibilities for the development of much-needed accurate rapid typing methods. Here, we describe ShigaPass, a new in silico tool for predicting

Shigella

serotypes from WGS assemblies on the basis of rfb gene cluster DNA sequences, phage and plasmid-encoded O-antigen modification genes, seven housekeeping genes (EnteroBase’s MLST scheme), fliC alleles and clustered regularly interspaced short palindromic repeats (CRISPR) spacers. Using 4879 genomes, including 4716 reference strains and clinical isolates of

Shigella

characterized with a panel of biochemical tests and serotyped by slide agglutination, we show here that ShigaPass outperforms all existing in silico tools, particularly for the identification of

Shigella boydii

and

Shigella dysenteriae

serotypes, with a correct serotype assignment rate of 98.5 % and a sensitivity rate (i.e. ability to make any prediction) of 100 %.
Using clustering of genetic variants in Mendelian randomization to interrogate the causal pathways underlying multimorbidity
Authors: Liang Xiaoran , Mounier Ninon , Apfel Nicolas , Khalid Sara , Frayling Timothy M , Bowden Jack
Published: March 2023

Mendelian randomization (MR) is an epidemiological approach that utilizes genetic variants as instrumental variables to estimate the causal effect of a modifiable but likely confounded exposure on a health outcome. This paper investigates an MR scenario in which different subsets of genetic variants identify different causal effects. These variants may aggregate into clusters, and such variant clusters are likely to emerge if they affect the exposure and outcome via distinct biological pathways. In the framework of multi-outcome MR, where a common risk factor causally impacts several disease outcomes simultaneously, these variant clusters can reflect the heterogeneous effects this shared risk factor concurrently exerts on all the diseases under examination. This, in turn, can provide insights into the disease-causing mechanisms underpinning the co-occurrence of multiple long-term conditions, a phenomenon known as multimorbidity. To identify such variant clusters, we adapt the general method of Agglomerative Hierarchical Clustering (AHC) to the summary data MR setting, enabling cluster detection based on the variant-specific causal estimates, using only genome-wide summary statistics. In particular, we tailor the method for multi-outcome MR to aid the elucidation of the potentially multifaceted causal pathways underlying multimorbidity stemming from a shared risk factor. We show in various Monte Carlo simulations that our ‘MR-AHC’ method detects variant clusters with high accuracy, outperforming the existing multi-dimensional clustering methods. In an application example, we use the method to analyze the causal effects of high body fat percentage on a pair of well-known multimorbid conditions, type 2 diabetes (T2D) and osteoarthritis (OA), discovering distinct variant clusters reflecting heterogeneous causal effects. Pathway analyses of these variant clusters indicate interconnected cellular processes underlying the co-occurrence of T2D and OA; while the protective effect of higher adiposity on T2D could possibly be linked to the enhanced activity of ion channels related to insulin secretion.
Sustained In Vivo Perfusion of a Re-Endothelialized Tissue Engineered Kidney Graft in a Human-Scale Animal Model
Authors: Uzarski Joseph S. , Beck Emily C. , Russell Emily E. , Vanderslice Ethan J. , Holzner Matthew L. , Wadhera Vikram , Adamson Dylan , Shapiro Ron , Davidow Dominique S. , Ross Jeff J. , Florman Sander S.
Published: March 2023

Introduction

Despite progress in whole-organ decellularization and recellularization, maintaining long-term perfusionin vivoremains a hurdle to realizing clinical translation of bioengineered kidney grafts. The objectives for the present study were to define a threshold glucose consumption rate (GCR) that could be used to predictin vivograft hemocompatibility and utilize this threshold to assess thein vivoperformance of clinically relevant decellularized porcine kidney grafts recellularized with human umbilical vein endothelial cells (HUVECs).

Materials and Methods

Twenty-two porcine kidneys were decellularized and 19 were re-endothelialized using HUVECs. Functional revascularization of control decellularized (n=3) and re-endothelialized porcine kidneys (n=16) was tested using anex vivoporcine blood flow model to define an appropriate metabolic glucose consumption rate (GCR) threshold above which would sustain patent blood flow. Re-endothelialized grafts (n=9) were then transplanted into immunosuppressed pigs with perfusion measured using angiography post-implant and on days 3 and 7 with 3 native kidneys used as controls. Patent recellularized kidney grafts underwent histological analysis following explant.

Results

The glucose consumption rate of recellularized kidney grafts reached a peak of 41.3±10.2 mg/hour at 21±5 days, at which point the grafts were determined to have sufficient histological vascular coverage with endothelial cells. Based on these results, a minimum glucose consumption rate threshold of 20 mg/hour was set. The revascularized kidneys had a mean perfusion percentage of 87.7±10.3%, 80.9±33.1%, and 68.5±38.6% post-reperfusion on Days 0, 3 and 7, respectively. The 3 native kidneys had a mean post-perfusion percentage of 98.4±1.6%. These results were not statistically significant.

Conclusion

This study is the first to demonstrate that human-scale bioengineered porcine kidney grafts developed via perfusion decellularization and subsequent re-endothelialization using HUVEC can maintained patency with consistent blood flow for up to 7 daysin vivo. These results lay the foundation for future research to produce human-scale recellularized kidney grafts for transplantation.
Printing double network tough hydrogels using Temperature-Controlled Projection Stereolithography (TOPS)
Authors: Kunwar Puskal , Andrada Bianca Louise , Poudel Arun , Xiong Zheng , Aryal Ujjwal , Geffert Zachary J , Poudel Sajag , Fougnier Daniel , Gitsov Ivan , Soman Pranav
Published: March 2023

We report a new method to shape double-network (DN) hydrogels into customized microscale 3D structures that exhibit superior mechanical properties in both tension and compression. A one-pot prepolymer formulation containing photo-cross-linkable acrylamide and thermo-reversible sol-gel κ-carrageenan with a suitable crosslinker, and photo-initiator/absorbers are optimized. A new TOPS system is utilized to photo-polymerize the primary acrylamide network into a 3D structure above the sol-gel transition of κ-carrageenan (80°C), while cooling down generates the secondary physical κ-carrageenan network to realize tough DN hydrogel structures. 3D structures, printed with high lateral (37μm) and vertical (180μm) resolutions and superior 3D design freedoms (internal voids), exhibit ultimate stress and strain of 200 kPa and 2400% respectively under tension, and simultaneously exhibit high compression stress of 15 MPa with a strain of 95%, both with high recovery rates. The roles of swelling, necking, self-healing, cyclic loading, dehydration, and rehydration on the mechanical properties of printed structures are also investigated. To demonstrate the potential of this technology to make mechanically reconfigurable flexible devices, we print an axicon lens and show that a Bessel beam can be dynamically tuned via user-defined tensile stretching of the device. This technique can be broadly applied to other hydrogels to make novel smart multifunctional devices for a range of applications.
A meta-analysis of immune cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes
Authors: Luo Qi , Dwaraka Varun B. , Chen Qingwen , Tong Huige , Zhu Tianyu , Seale Kirsten , Raffaele Joseph M , Zheng Shijie C. , Mendez Tavis L. , Chen Yulu , Begum Sofina , Mendez Kevin , Voisin Sarah , Eynon Nir , Lasky-Su Jessica A. , Smith Ryan , Teschendorff Andrew E.
Published: March 2023

Abstract

Background:

Changes in cell-type composition of complex tissues are associated with a wide range of diseases, environmental risk factors and may be causally implicated in disease development and progression. However, these shifts in cell-type fractions are often of a low magnitude, or involve similar cell-subtypes, making their reliable identification challenging. DNA methylation profiling in a tissue like blood is a promising approach to discover shifts in cell-type abundance, yet studies have only been performed at a relatively low cellular resolution and in isolation, limiting their power to detect these shifts in tissue composition.

Methods:

Here we derive a DNA methylation reference matrix for 12 immune cell-types in human blood and extensively validate it with flow-cytometric count data and in whole-genome bisulfite sequencing data of sorted cells. Using this reference matrix and Stouffer’s method, we perform a meta-analysis encompassing 25,629 blood samples from 22 different cohorts, to comprehensively map associations between the 12 immune-cell fractions and common phenotypes, including health outcomes.

Results:

Our meta-analysis reveals many associations with age, sex, smoking and obesity, many of which we validate with single-cell RNA-sequencing. We discover that T-regulatory and naïve T-cell subsets are higher in women compared to men, whilst the reverse is true for monocyte, natural killer, basophil and eosinophil fractions. In a large subset encompassing 5000 individuals we find associations with stress, exercise, sleep and health outcomes, revealing that naïve T-cell and B-cell fractions are associated with a reduced risk of all-cause mortality independently of age, sex, race, smoking, obesity and alcohol consumption. We find that decreased natural killer cell counts are associated with smoking, obesity and stress levels, whilst an increased count correlates with exercise, sleep and a reduced risk of all-cause mortality.

Conclusions:

This work derives and extensively validates a high resolution DNAm reference matrix for blood, and uses it to generate a comprehensive map of associations between immune cell fractions and common phenotypes, including health outcomes.

Availability:

The 12 immune cell-type DNAm reference matrices for Illumina 850k and 450k beadarrays alongside tools for cell-type fraction estimation are freely available from our EpiDISH Bioconductor R-packagehttp://www.bioconductor.org/packages/devel/bioc/html/EpiDISH.html
Learning Perturbation-specific Cell Representations for Prediction of Transcriptional Response across Cellular Contexts
Authors: Keinan Gal , Sayal Karen , Gonen Alon , Zhu Jiang , Granovsky Lena , England Jeremy
Published: March 2023

High-throughput screens (HTS) are widely utilized to profile transcriptional states across multiple cell types and perturbations, and are often the first step on the bridge to the patient. However, their representative capacity to encompass all the cellular contexts encountered in a patient is limited. Thus, we present PerturbX, a novel deep learning model that leverages the rich information obtained from HTS to predict transcriptional responses to chemical or genetic perturbations in unobserved cellular contexts, and demonstrate its effectiveness in an experimental setting. Further-more, we show that the model is able to uncover interpretable genetic signatures associated with the predicted response, which can ultimately be translated into the clinical setting.
Bis[5-methyl-2,3-bis(thiophen-2-yl)quinoxaline-κN
1](nitrato-κ2
O,O′)silver(I)
Authors: Crundwell Guy , Ellis Kristin M.
Published: March 2023

The crystal structure of the title silver(I) complex, [Ag(NO3)(C17H12N2S2)2], has monoclinic (C2/c) symmetry, with the silver(I) atom and the nitrate group sitting on a twofold rotation axis. The complex also exhibits a thienyl-ring flip disorder, which is common for unsubstituted thiophene rings.
Does organizational resilience matter? Fix it through improvisation!
Authors: Shela V. , Ramayah T. , Ahmad Noor Hazlina
Published: March 2023

Purpose

This study explores the potential role of improvisation capability in enhancing organizational resilience. Additionally, this paper unravels novel strategies to support the development of organizational improvisation capability.

Design/methodology/approach

An in-depth review of the latest development of organizational resilience and improvisation provided insight into the linkages between the concepts. The current literature gap provides reasons to discuss the latest strategies to foster improvisation capability to amplify organizational resilience.

Findings

This study identifies the pertinent role of improvisation capability in amplifying organizational resilience and discusses various feasible strategies to cultivate organizational improvisation capability.

Originality/value

This research provides valuable insights to help organizations remain resilient in a disruptive environment. The study also offers cutting-edge strategies to nurture improvisation capability as a way forward to drive organizational resilience.
Judge and fury: instrumentality, feedback formats and turnover intention in schools
Authors: Dahle Dag Yngve , Urstad Sivert Skålvoll
Published: March 2023

Purpose

In the deregulated public sector upper secondary school field in Oslo, Norway, turnover among teachers is found to be high. The purpose is to examine whether instrumental practices like control-oriented HRM, performance appraisal and heteronomy directly or indirectly lead to turnover intention, as a crucial pre-stage to turnover. Another purpose is to examine whether this varies with feedback format.

Design/methodology/approach

The present study is based on a survey (N = 1,055) carried out among upper secondary school teachers in Norway. Data were analyzed with path analysis, and mediation and moderation analyses were performed.

Findings

The study shows that control-oriented HRM, PA dissatisfaction and heteronomy are antecedents to turnover intention for teachers receiving feedback in three different feedback formats. The effect of control-oriented HRM and PA dissatisfaction on turnover intention was generally not stronger among numerically rated than among those rated otherwise. For most feedback format groups, leader–member exchange mediated between turnover intention and PA dissatisfaction and heteronomy, respectively, but not between turnover intention and control-oriented HRM. For teachers rated with text, figures or colors, LMX moderated between control-oriented HRM and turnover intention.

Research limitations/implications

The paper advances that introduction of instrumental practices will be seen as breaches of the psychological contract, but this does not apply to all feedback format groups, for example those receiving numerically rating. Limitations involve self-reported measures, direction of causality issues and a relatively low sample size for some groups.

Practical implications

Practitioners should note that both control-oriented HRM, performance appraisal and little autonomy may cause teachers to consider leaving their jobs. Practitioners should also be aware of the importance of the relationship between employee and leader, as negative responses to instrumentality may work through the leader–employee relationship, leading to turnover intention and, possibly, turnover.

Originality/value

The present study is among the first to examine whether and how antecedents to turnover intention vary with feedback format. A rare interaction between HRM and LMX is uncovered. Few other studies have analyzed the relationship between instrumental practices and turnover intention in light of psychological contract theory.
Strategic foresight of entrepreneurial firms in energy transition
Authors: Datta Deepmalya , Joshi Manoj , Gandhi Meenakshi
Published: March 2023

Purpose

The purpose of this study is to explore the principal research query and whether strategic foresight deployed by entrepreneurial firms in energy transition aims at crafting future readiness.

Design/methodology/approach

With a focus on entrepreneurial firms working in the alternative energy segment in the Indian context, the intent is to examine the deployment of strategic foresight by incumbent firms and their entrepreneurial journey. The authors have adopted the approach of Eisenhardt for this research. The area of interest for the authors entailing strategic foresight by entrepreneurial firms in energy transition aligns with defining features reflecting the aim of Eisenhardt method for this exploratory research coupled with constructivism.

Findings

While the future scenarios in the energy sector have to be necessarily multiple, their alignment with different geographic, economic, demographic and political outlooks shall be defined by the pathways niched through the deployment of strategic foresight for arriving at those scenarios.

Research limitations/implications

Strategic foresight deployed by entrepreneurial firms has the potential to create future readiness through self-reliant sustainable economic value chains for local populace, thus propagating holistic development in remote regions.

Originality/value

This paper attempts to knit together the domains of strategic foresight, entrepreneurial firms and energy transition through case research and present the future thinking deployed for navigation in uncharted pathways by capturing the foresight component of these incumbent firms chosen through careful case selection. The narrative has been strengthened by the varied interviews across participants and the observations made by the authors during the research work.
Social media branding in the food industry: comparing B2B and B2C companies’ use of sustainability messaging on Twitter
Authors: Garner Benjamin , Mady Ashraf
Published: March 2023

Purpose

Supply chains are under increased scrutiny as consumers have become aware of the dark side of downstream production practices. Many articles and exposés have led consumers to be more conscious of purchasing products from companies who source materials in a socially responsible and ethical manner. As a result, business-to-business (B2B) and business-to-consumers (B2C) companies are under increased pressure to source raw materials in a transparent and ethical way. Because of the associated costs, companies then look to benefit from increased brand equity by promoting to consumers how ethical their products are. The purpose of this study is to look at the case of the food industry to analyze sustainability messaging on Twitter in both B2B and B2C companies to determine which of the dimensions of sustainability (people, profit, planet) are being emphasized.

Design/methodology/approach

In this study, two published dictionaries were combined to capture the three dimensions of “sustainability,” and these scales were then used to analyze Twitter posts. This study created a unique software package to classify, mine, collect and analyze Twitter data. This study used these tools to analyze 246,386 Twitter posts within a sample of 39 leading B2C and B2B food companies over a 10-year period (2012–2021) to explore brand messaging and engagement rate.

Findings

This research revealed several interesting results. These include how B2B companies have emphasized the employee (people) dimensions of sustainability, while B2C companies have had a more balanced approach that overall has prioritized the economic dimension (profit) of sustainability. The data on audience engagement revealed a mismatch between the types of sustainability messaging B2B companies and B2C companies in the food industry are posting and what engages audiences.

Originality/value

This study fills several gaps, including analyzing how B2B and B2C companies use sustainability language in their social media brand management, as well as looking at which dimensions of sustainability they emphasize and which ones engage audiences the most. This research is also novel in combining multiple existing scales under one project to analyze the triple bottom line in the analysis of qualitative texts.