bluuebunny/crossref_metadata_2025 huggingface dataset:
The optimum oxygen level in hypoxic culture conditions of ligament derived stem cells: experimental research
Authors: Rhatomy Sholahuddin , Utomo Dwikora N. , Prakoeswa Cita R. S. , Suroto Heri , Tinduh Damayanti , Notobroto Hari B. , Arfian Nur , Rantam Fedik A. , Mahyudin Ferdiansyah
Published: August 2023

Background:

The hypoxic condition is a physiological norm for various stem cells. The natural microenvironment contains lower oxygen pressures. Recent studies reported significant increases in the cultured cells’ proliferation in the presence of a low oxygen pressure.

Objective:

This study aimed to investigate the optimum oxygen level for rabbit cruciate ligament fibroblast cells culture and Ligament Derived Conditioned Medium/LD-CM (Secretome) preparation in vitro.

Materials and methods:

Fibroblasts were isolated from the cruciate ligament of the rabbit’s knee. Cultured of rabbit cruciate ligament Fibroblast Cells (fifth passage) were assigned to the slight (5% O2), middle (3% O2), and severe hypoxia (1% O2) groups and the normoxia (21% O2) group. Measurement of growth factors: TGF-β1, PDGF, FGF, and VEGF in LD-CM (Secretome) used an enzyme-linked immunosorbent assay.

Results:

The highest number of cultured cells were in the 5% O2 group compared to the normoxia, 1 and 3% groups. The hypoxia 5% group also had increased productions of PDGF, FGF, and VEGF proteins in LD-CM (secretome) compared to the 1, 3%, and normoxia groups. TGF-β1 production was slightly higher in the 3 group than the 5% group.

Conclusion:

The hypoxic precondition of 5% oxygen was the optimum condition for ligament culture and ligament derived conditioned medium (secretome) preparation in vitro.
Quantification of Hepatic Steatosis on Dual-Energy CT in Comparison With MRI mDIXON-Quant Sequence in Breast Cancer
Authors: Wang Xiaoxia , Pan Xianjun , Zhou Wenqi , Jing Zhouhong , Yu Feng , Wang Yali , Zeng Junjie , Wu Jiaxing , Zeng Xiaohua , Zhang Jiuquan
Published: August 2023

Objective

The study aimed to evaluate the correlation and diagnostic value of liver fat quantification in unenhanced dual-energy CT (DECT) using quantitative magnetic resonance imaging (MRI) mDIXON-Quant sequence as reference standard in patients with breast cancer.

Methods

Patients with breast cancer were prospectively recruited between June 2018 and April 2020. Each patient underwent liver DECT and MRI mDIXON-Quant examination. The DECT–fat volume fraction (FVF) and liver-spleen attenuation differences were compared with the MRI–proton density fat fraction using scatterplots, Bland-Altman plots, and concordance correlation coefficient. Receiver operating characteristic curves were established to determine the diagnostic accuracy of hepatic steatosis by DECT.

Results

A total of 216 patients with breast cancer (mean age, 50.08 ± 9.33 years) were evaluated. The DECT-FVF correlated well with MRI–proton density fat fraction (r
2 = 0.902; P < 0.001), which was higher than the difference in liver-spleen attenuation (r
2 = 0.728; P < 0.001). Bland-Altman analysis revealed slight positive bias; the mean difference was 3.986. The DECT-FVF yielded an average concordance correlation coefficient of 0.677, which was higher than the difference of liver-spleen attenuation (−0.544). The DECT-FVF and the difference in liver-spleen attenuation both lead to mild overestimation of hepatic steatosis. The areas under the curve of DECT-FVF (0.956) were higher than the difference in liver-spleen attenuation (0.807) in identifying hepatic steatosis (P < 0.001).

Conclusions

Dual-energy CT–FVF may serve as a reliable screening and quantitative tool for hepatic steatosis in patients with breast cancer.
Study of Anatomical Changes of the Inferior Nasal Passage After Le Fort I Osteotomy With Superior Repositioning
Authors: Tomomatsu Nobuyoshi , Nakamura Taishi , Takahara Namiaki , Kurasawa Yasuhiro , Kachi Hirokazu , Yoda Tetsuya
Published: August 2023

The relationship between postoperative morphological changes in the inferior nasal cavity and inferior turbinate after Le Fort I osteotomy remains unclear. This study aimed to investigate how the bone volume of the inferior turbinate affects contact with the inferior nasal cavity of patients who underwent superior repositioning. We evaluated the 3-dimensional relationship between the anatomical changes in the inferior nasal passage before and after surgery in 51 patients who underwent Le Fort I osteotomy with an elevation of >4.0 mm in the first molar. The soft tissue and bone volumes of the inferior turbinate and airway volume of the inferior nasal passage were calculated using Proplan CMF 3.0 and compared according to the size of the bone volume of the inferior turbinate. In addition, we reclassified the maxillary movements in the pitch direction and compared the results. The contact rates of the postoperative inferior nasal airway and the inferior turbinate in the large-bone group was 72.3% and that in the small-bone group was 40.0% in the χ2 test. The reduction in the inferior nasal passage volume was significantly greater in the large-bone group (pitch+) than in the small-bone group (pitch+). For patients with well-developed bony tissue of the inferior turbinate, caution is advised if the maxillary elevation is ≥4.0 mm, because the possibility of postoperative obstruction of the inferior nasal passages exist, which may lead to deterioration of nasal ventilation.
Current Postoperative Feeding Practices Following Surgical Repairs for Infants With Cleft Palate
Authors: Williams Jessica L. , Kotlarek Katelyn J.
Published: August 2023

Background:

Nearly all surgeons have restrictive postoperative feeding protocols in place after primary cleft lip and cleft palate repairs. There are no standardized recommendations, potentially resulting in widely variable practices among cleft surgeons and teams. The purpose of this study was to examine current postoperative feeding practices for infants with cleft palate after lip and palate repairs.

Methods:

A survey of 50 questions was sent to members of the American Cleft Palate-Craniofacial Association (ACPA). Inclusion criteria included providers from North America that have either currently or previously served on a cleft palate team and reached the surgical question set within the survey.

Results:

Sixty-four respondents met inclusion criteria. The majority were in speech-language pathology (47%) or nursing (41%) disciplines, involved in feeding consultations frequently (84%), and working in an outpatient setting (69%). After lip surgery, respondents recommended cleft-adapted bottle feeding (88%), spoon feeding (9%), cup feeding (13%), and syringe/squeeze bottle feeding (23%). The majority of respondents (69%) indicated infants could return to their preoperative feeding modality immediately after lip surgery. After palate surgery, respondents recommended cleft-adapted bottle feeding (55%), typical bottle feeding (3%), spoon feeding (36%), cup feeding (64%), and syringe/squeeze bottle feeding (30%). Infants could use a feeding system that required suction at an average of 20 days postoperatively and return to an age-appropriate diet at an average of 15 days postoperatively.

Conclusions:

The present study describes the wide variation of postoperative feeding guidelines used by cleft teams after lip and palate repairs.
Decreased Lymphocytic Bronchitis Severity in the Era of Azithromycin Prophylaxis
Authors: Santos Jesse , Hays Steven R. , Golden Jeffrey A. , Calabrese Daniel R. , Kolaitis Nicholas , Kleinhenz Mary Ellen , Shah Rupal , Estrada Aida Venado , Leard Lorriana E. , Kukreja Jasleen , Singer Jonathan P. , Greenland John R.
Published: August 2023

Background.

Large-airway lymphocytic inflammation (LB), assessed on endobronchial biopsies, has been associated with acute cellular rejection and chronic lung allograft dysfunction (CLAD). Azithromycin (AZI) prophylaxis has been used to prevent airway inflammation and subsequent CLAD, with inconsistent results. We hypothesized that AZI prophylaxis would be associated with reduced LB, changes in bronchoalveolar lavage (BAL) immune cell populations, and improved CLAD-free survival.

Methods.

We compared frequencies of LB from endobronchial biopsies before (N = 1856) and after (N = 975) protocolized initiation of AZI prophylaxis at our center. LB was classified as none, minimal, mild, or moderate by histopathologic analysis. LB grades were compared using ordinal mixed-model regression. Corresponding automated BAL leukocyte frequencies were compared using mixed-effects modeling. The effect of AZI prophylaxis on CLAD-free survival was assessed by a Cox proportional hazards model adjusted for age, sex, ethnicity, transplant indication, and cytomegalovirus serostatus.

Results.

Biopsies in the pre-AZI era had 2-fold increased odds (95% confidence interval, 1.5-2.7; P < 0.001) of higher LB grades. LB was associated with BAL neutrophilia in both eras. However, there was no difference in risk for CLAD or death between AZI eras (hazard ratio 1.3; 95% confidence interval, 0.7-2.0; P = 0.45).

Conclusions.

Decreased airway inflammation in the era of AZI prophylaxis may represent a direct effect of AZI therapy or reflect other practices or environmental changes. In this cohort, AZI prophylaxis was not associated with improved CLAD-free survival.
Effect of β-Nicotinamide Adenine Dinucleotide on Acute Allograft Rejection After Rat Lung Transplantation
Authors: Ehrsam Jonas P. , Chen Jin , Haberecker Martina , Arni Stephan , Inci Ilhan
Published: August 2023

Background.

Acute rejection is still a major limitation for a successful outcome in lung transplantation. Since β-nicotinamide adenine dinucleotide (NAD+) has been shown to have various immunomodulatory properties on the innate and adaptive immune system, we evaluate here a potential protective effect of NAD+ against acute lung rejection.

Methods.

Rat single-lung transplantation was performed in 2 groups (n = 8 per group), using Brown-Norway donors and major histocompatibility complex–mismatched Lewis recipients. Recipients of the NAD+ group received 1000 mg/kg NAD+ intraperitoneally before transplantation and daily thereafter until euthanasia, whereas the control group received saline solution. At autopsy on day 5, blood samples were analyzed and the lung allograft was assessed by bronchioalveolar lavage, histology, and immunochemistry.

Results.

The NAD+ group maintained an intact compliant lung tissue, a strong trend of lower acute cellular rejection (A3 versus A3-A4) and significantly less lymphocytic bronchiolitis (B0-B2R versus B1R-Bx). In addition, a trend of fewer alveolar CD68+ macrophages and significantly fewer interstitial CD163+ macrophages was observed. Bronchoalveolar lavage in the NAD+ group showed significantly fewer proinflammatory cytokines interleukin (IL)-6, IL-13, TNFα, and a protective IL-6/IL-10-ratio. In blood samples, we observed significantly fewer neutrophils, and proinflammatory GRO/KC in the NAD+ group.

Conclusions.

NAD+ might be a promising substance in prevention of acute allograft rejection in lung transplantation.
Klotho and Fibroblast Growth Factor 23 Are Independent of Vitamin D, and Unlike Vitamin D, Are Not Associated With Graft- and Patient Survival After Kidney Transplantation
Authors: Thorsen Inga Strand , Bleskestad Inger Hjørdis , Åsberg Anders , Jonsson Grete , Skadberg Øyvind , Heldal Kristian , Gøransson Lasse Gunnar
Published: August 2023

Background.

Short-term survival after kidney transplantation is excellent but long-term survival remains suboptimal. The aim of the study was to explore the relationship between soluble α-Klotho (sKlotho) and intact fibroblast growth factor 23 (iFGF23) measured 8 wk and 1 y posttransplant with long-term graft- and patient survival in a cohort of kidney transplant recipients with deficient and nondeficient vitamin D (25[OH]D) levels.

Methods.

Vitamin D, sKlotho, and iFGF23 were measured 8 wk and 1 y posttransplant in 132 recipients transplanted between November 2012 and October 2013.

Results.

Of the 132 kidney transplant recipients, 49 had deficient vitamin D levels (<30 nmol/L) and 83 had nondeficient vitamin D levels (≥30 nmol/L) at 8 wk posttransplant. The mean age was 51 y and the median follow-up was 7.4 y. At 1 y posttransplant, vitamin D increased significantly. There were no significant differences in sKlotho or iFGF23 levels between the 2 vitamin D groups neither at 8 wk nor 1 y. sKlotho increased significantly and iFGF23 decreased significantly in the whole cohort. During the follow-up, there were 36 graft losses (27%) and 27 deaths (20%). Ninety-four percent of the transplant recipients with nondeficient vitamin D levels were alive with a well-functioning graft after 5 y using Kaplan-Meier survival estimates, compared with 84% of the patients with deficient vitamin D levels (P = 0.014). Klotho and FGF23 levels did not influence graft- and patient survival.

Conclusions.

In this nationwide cohort of kidney transplant recipients, long-term graft- and patient survival were significantly better in patients with vitamin D ≥30 nmol/L 8 wk posttransplant compared with those with vitamin D <30 nmol/L. sKlotho levels increased and iFGF23 levels decreased from 8 wk to 1 y posttransplant. Klotho and FGF23 levels were not associated with graft- and patient survival.
Alzheimer’s Behavioral and Psychiatric Burden in Saudi Arabia
Authors: Tayeb Haythum O. , Butt Nadeem S. , Khallaf Roaa , Yaghmoor Bassam , Basheikh Mohammed A. , Alamri Sultan H. , Baduwailan Abrar O. , Alzaben Faten , Abdulghaffar Haifa K. , Koenig Harold G.
Published: August 2023

Background:

The burden of behavioral and psychiatric symptoms in dementia (BPSD) has not been characterized in Saudi patients with Alzheimer disease (AD). Moreover, the Saudi version of the Neuropsychiatric Inventory (SNPI) has not been validated.

Objectives:

The purpose of this study was to validate the SNPI and describe frequency and determinants of BPSD in Saudi AD patients.

Methods:

The SNPI and BEHAVE-AD instruments were administered to community-dwelling Saudi AD patients and their caregivers.

Results:

The sample size was 192. The first 59 constituted the validation cohort. Cronbach alpha of the SNPI and BEHAVE-AD were 0.91 and 0.79, respectively. There were significant correlations between: (1) the total SNPI and BEHAVE-AD scores (r=0.84, P<0.001); (2) analogous SNPI and BEHAVE-AD symptom subscores (P<0.05); (3) SNPI and BEHAVE-AD caregiver distress (F=22.6, P<0.001). Inter-rater reliability of the SNPI was excellent (kappa=0.74). Ninety percent of patients experienced 4 SNPI symptoms or more. Patients with stroke and prior psychiatric history were most likely to experience BPSDs. The most common symptom was apathy (82%). Caregiver distress was determined by the total NPI score and impulsiveness subscale score.

Conclusions:

The SNPI is valid and reliable for assessing BPSD in Saudi AD patients. Longitudinal studies of BPSDs in Saudi specialized dementia clinics are needed.
Electroconvulsive Therapy in Heart Transplant Patients
Authors: Ketcham Evan , Glass Oliver M. , Hermida Adriana P.
Published: August 2023

Patients with heart disease are at an increased risk of depression. Electroconvulsive therapy (ECT) is a highly effective treatment for severe depressive episodes. However, ECT may increase the risk for adverse outcomes in certain patients because of changes in blood pressure and heart rate secondary to an initial parasympathetic surge followed by a sympathetic surge and peripheral catecholamine release. In post–cardiac transplant patients, these acute hemodynamic changes on a denervated heart may bring clinical challenges. The available data on ECT in heart transplant patients are limited. The authors of this article present a summary of the available literature relating to ECT in heart transplant patients.

The authors performed a literature search of 6 online databases yielding 6 English-language case reports of ECT in cardiac transplant patients. All patients experienced changes in hemodynamic variables during and immediately after ECT, ranging from moderate decrease in blood pressure to extreme hypertension. The cases did not report any serious cardiac complications during the course of ECT. In the 5 patients whose psychiatric responses to treatment were detailed, all had improvement in their depressive symptoms. Electroconvulsive therapy may be considered for severe cases of depression in patients with a history of cardiac transplant, but the potential benefit of ECT needs to be weighed against risks. In the limited number of cases reported in the literature, ECT seems to have been relatively safe and effective.
Electroconvulsive Therapy Credentialing for Psychiatrists—Review of Required Standards Across States and Territories in Australia
Authors: Purushothaman Subramanian , Simpson Brett , Hussain Salam , Loo Colleen K. , Gill Shane , Chamoli Suneel , Weiss Alan , Sarma Shanthi , Fitzgerald Paul B. , Fasnacht Matthew , Gandhi Ashu
Published: August 2023

Electroconvulsive therapy (ECT) is a complex medical procedure, the delivery of which requires specialist knowledge and skills. We reviewed the standards required for ECT credentialing in different jurisdictions in Australia. We reviewed the Chief Psychiatrist guidelines and statewide policy standards on ECT and focused on standards required for initial credentialing and ongoing privileging in ECT. We compared the credentialing requirements within these documents with the standards specified in the Royal Australian and New Zealand College of Psychiatrists professional practice guideline for ECT. Most of the jurisdictions had specific standards for initial credentialing and maintenance of this credentialing; however, there was significant variance in the credentialing process and standards required. It would be useful to have a minimum standard for credentialing for ECT psychiatrists and prescribers. This standard would be relevant for practice of ECT internationally. States and territories would have the responsibility for implementation of these standards. Appropriate training and establishing good clinical governance processes are essential to the provision of high quality ECT.
Identification of NpdA as the protein forming the surface layer in Paracidovorax citrulii and evidence of its occurrence as a surface layer protein in diverse genera of the Betaproteobacteria and Gammaproteobacteria
Authors: Gajbhiye Shabda , Gonzales Erin D. , Toso Daniel B. , Kirk Natalie A. , Hickey William James
Published: August 2023

The phytopathogen Paracidovorax citrulli possesses an ortholog of a newly identified surface layer protein (SLP) termed NpdA but has not been reported to produce a surface layer (S-layer). This study had two objectives. First, to determine if P. citrulli formed a NpdA-based S-layer and, if so, assess the effects of S-layer formation on virulence, production of nanostructures termed nanopods, and other phenotypes. Second, to establish the distribution of npdA orthologs throughout the Pseudomonadota and examine selected candidate cultures for physical evidence of S-layer formation. Formation of a NpdA-based S-layer by P. citrulli AAC-001 was confirmed by gene deletion mutagenesis (ΔnpdA), proteomics, and cryo-electron microscopy. There were no significant differences between the wild type and mutant in virulence assays with detached watermelon fruit. Nanopods contiguous with S-layers of multiple biofilm cells were visualized by transmission electron microscopy. Orthologs of npdA were identified in 62 Betaproteobacteria species and 49 Gammaproteobacteria species.  In phylogenetic analyses, NpdA orthologs largely segregated into distinct groups. Cryo-electron microscopy imaging revealed a NpdA-like S-layer in all but one of the 16 additional cultures examined. We conclude that NpdA represents a new family of SLP, forming an S-layer in P. citrulli and other Pseudomonadota. While the S-layer didn’t contribute to virulence in watermelon fruit, a potential role of the P. citrulli S-layer in another dimension of pathogenesis cannot be ruled out. Lastly, formation of cell-bridging nanopods in biofilms is a new property of S-layers; it remains to be determined if nanopods can mediate intercellular movement of materials.
Roseovarius pelagicus sp. nov., a facultatively anaerobic bacterium with potential for degrading polypropylene, isolated from Arctic seawater
Authors: Hong Yeon Woo , Jang Gwang Il , Kim Soo Yoon , Choi Jy Young , Kim Bok Jin , Shin Dong Young , Kang Jin Kyeong , Kim Seung-Kyu , Cho Byung Cheol , Hwang Chung Yeon
Published: August 2023

A Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped bacterial strain, designated HL-MP18T, was isolated from Arctic seawater after a prolonged incubation employing polypropylene as the sole carbon source. Phylogenetic analyses of the 16S rRNA gene sequence revealed that strain HL-MP18Twas affiliated to the genusRoseovariuswith close relativesRoseovarius carneusLXJ103T(96.8 %) andRoseovarius litorisediminisKCTC 32327T(96.5 %). The complete genome sequence of strain HL-MP18Tcomprised a circular chromosome of 3.86 Mbp and two circular plasmids of 0.17 and 0.24 Mbp. Genomic comparisons based on average nucleotide identity and digital DNA–DNA hybridization showed that strain HL-MP18Twas consistently discriminated from its closely related taxa in the genusRoseovarius. Strain HL-MP18Tshowed optimal growth at 25 °C, pH 7.0 and 2.5 % (w/v) sea salts. The major cellular fatty acids were C18 : 1 ω6cand/or C18 : 1 ω7c(49.6 %), C19 : 0cycloω8c(13.5 %), and C16 : 0(12.8 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and three unidentified lipids. The genomic DNA G+C content of the strain was 59.2 mol%. The phylogenetic, genomic, phenotypic and chemotaxonomic results indicate that strain HL-MP18Tis distinguishable from the recognized species of the genusRoseovarius. Therefore, we propose that strain HL-MP18Trepresents a novel species belonging to the genusRoseovarius, for which the nameRoseovarius pelagicussp. nov. is proposed. The type strain is HL-MP18T(=KCCM 90405T=JCM 35639T).
Tract-based disconnection induced by WMH in patients with minor stroke is related to long-term post-stroke cognition
Authors: Lopes Renaud , Kuchcinski Grégory , Dondaine Thibaut , Duron Loïc , Mendyk Anne-Marie , Hénon Hilde , Cordonnier Charlotte , Pruvo Jean-Pierre , Bordet Régis , Leclerc Xavier
Published: August 2023

Background

Over a third of minor stroke patients will suffer from post-stroke cognitive impairment (PSCI) but there are no validated tools to clearly identify at-risk patients in the early phase. We aimed to investigate the short and long-term cognitive decline using disconnection features from infarct and white matter hyperintensities (WMH) in first-ever minor ischemic stroke patients.

Methods

First-ever minor ischemic stroke patients (NIHSS≤7) were prospectively followed-up at 72-hour, 6- and 36-month post-stroke with cognitive tests and conventional brain MRI. Infarct and WMH volumes were semi-automatically evaluated on DWI and FLAIR sequences respectively. Bayesian models using tract-based structural disconnection were used to estimate the remote pathological effects of cerebral infarct and/or WMH. The disconnection approach was compared to features extracted from cerebral infarct and WMH volumes and locations. All lesion-based features were compared between patients with and without cognitive impairment at 6- and 36-month post-stroke. The potential association between the features and cognitive domains alterations was assessed by canonical correlation analyses. All statistical analyses were corrected for age, education and multiple comparisons.

Results

105 patients (female, 31%) with a mean (± SD) age of 63 ± 12 years were enrolled. Infarct volume was 10.28 ± 17.10 cm3 and involved the middle cerebral artery territory in 83% of patients. The burden of WMH was higher within frontal periventricular white matter. Infarct-based features showed no significant relationship with 6 and 36-month PSCI. However, a WMH disconnection factor involving the commissural and frontal tracts was associated with 6- and 36-month PSCI, particularly in executive/attention, language and visuospatial domains. Memory domain alterations were associated with higher WMH burden in right temporal regions.

Conclusions

WMH-induced disconnectivity may predict short and long-term PSCI in minor ischemic stroke. These neuroimaging features extracted from routine MR sequences could help identifying at-risk patients to test future rehabilitation interventions.
EasyFlow: An open source, user friendly cytometry analyzer with graphic user interface (GUI)
Authors: Ma Yitong , Antebi Yaron
Published: August 2023

Flow cytometry enables quantitative measurements of fluorescence in single cells. The technique was widely used for immunology to identify populations with different surface protein markers. More recently, the usage of flow cytometry has been extended to additional readouts, including intracellular proteins and fluorescent protein transgenes, and is widely utilized to study development, systems biology, microbiology, and many other fields. A common file format (FCS format, defined by International Society for Advancement of Cytometry (ISAC)) has been universally adopted, facilitating data exchange between different machines. A diverse spectrum of software packages have been developed for analysis of flow cytometry data. However, those are either 1) costly proprietary softwares, 2) open source packages with prerequisite installation of R or Python and sometimes require users to have experience in coding or 3) online tools that are limiting for analysis of large data sets. Here we present EasyFlow, an open source flow cytometry analysis GUI based on Matlab or Python, that can be installed and run locally cross-platform-ly (Windows and MacOS), without prerequisite user having previous knowledge on coding. The python version (EasyFlowQ) is also developed on a popular plotting framework (Matplotlib) and modern user interface (UI) toolkit (Qt), allowing more advanced users to customize and keep contributing to the software, as well as its tutorials. Overall, EasyFlow serves as a simple-to-use tool for inexperienced users with little coding experience to use locally, as well as a platform for advanced users to further customize for their own needs.
Synthetic rescue of XPC phenotype via PIK3C3 downregulation
Authors: Kobaisi Farah , Sulpice Eric , Nasrallah Ali , Fayyad-Kazan Hussein , Rachidi Walid , Gidrol Xavier
Published: August 2023

Xeroderma Pigmentosum C is a dermal hereditary disease. It is caused by a mutation in the DNA damage recognition protein XPC that belongs to the Nucleotide excision repair pathway. XPC patients exhibit a photosensitive phenotype and fail to repair UV induced DNA lesions leading to their accumulation and ultimate conversion to mutations and carcinomas. In an attempt to normalize this phenotype, we screened a library of siRNAs targeting the human kinases, given their role in different DNA repair pathways. WT and XPC immortalized patient fibroblasts were transfected with the library then irradiated with UVB to induce DNA damage. XPC phenotypic reversal was monitored by the quantification of decreased photosensitivity and increased DNA damage repair. Out of the 1292 kinase siRNAs tested, twenty-eight were selected cellular survival compared to cells transfected with non-targeting siRNA in XP-C irradiated cells. Out of the selected hits, two kinases, PIK3C3 and LATS1, induce more than 20% repair of 6-4PP DNA lesions. The down regulation of autophagy-related protein PIK3C3 alone had an exclusive photo protective effect on XP-C irradiated cells validated these effects also on primary XP-C patient fibroblasts and CRISPR-Cas9 generated XPC-KO keratinocytes. PIK3C3 knock down in XP-C cells ameliorated in UVB dose response analysis, decreased apoptosis and lowered phosphorylation of P53 with no effect on proliferation. More importantly, PIK3C3 knock down induced an increase in UVRAG expression, a previously reported cDNA conveying lower photosensitivity in XP-C cells. Attempts to improve the XPC photosensitive and deficient repair phenotype using PIK3C3 inhibitors could thus pave a way for new therapeutic approaches delaying or preventing tumor initiation.
In silico thermodynamic evaluation of the effectiveness of RT-LAMP primers to SARS-CoV-2 variants detection
Authors: Miranda Pâmella , Alves Pedro A. , do Monte-Neto Rubens L. , Weber Gerald
Published: August 2023

Viral mutations are the primary cause of mismatches in primer-target hybridisation, affecting the sensibility of molecular techniques, potentially leading to detection dropouts. Despite its importance, little is known about the quantitative effect of mismatches in primer-target hybridisation. We use up-to-date and highly detailed thermodynamic model parameters of DNA mismatches to evaluate the sensibility to variants of SARS-CoV-2 RT-LAMP primers. We aligned 18 RT-LAMP primer sets, which were underwent clinical validation, to the genomes of Wuhan strain (ws), 7 variants and 4 subvariants, and calculated hybridisation temperatures allowing up to three consecutive mismatches. We calculate the coverage when the mismatched melting temperature falls by more than 5°C in comparison to the matched alignments. If no mismatches are considered, the average coverage found would be 94% for ws, falling the lowest value for Omicron: 84%. However, considering mismatches the coverage is much higher: 97% (ws) to 88% (Omicron). Stabilizing mismatches (higher melting temperatures), account for roughly 1/3 of this increase. The number of primer dropouts increases for new each variant, however the effect is much less severe if mismatches are considered. We suggest using melting temperature calculations to continuously assess the trend of primer dropouts.
Cryo-EM structure of DDM1-HELLS chimera bound to nucleosome reveals a mechanism of chromatin remodeling and disease regulation
Authors: Nartey Wilson , Goodarzi Aaron A. , Williams Gareth J.
Published: August 2023

Human HELicase, Lymphoid Specific (HELLS), and plant homolog Deficient in DNA Methylation 1 (DDM1), belong to a distinct class of chromatin remodelers that play important roles in DNA repair, transcription, and maintenance of DNA methylation in heterochromatin. HELLS also promotes the growth of hard-to-treat cancers including glioblastoma and hepatocellular carcinoma. Here, we identify an auto-inhibitory HELLS N-terminal coiled-coil, unravelling a long-standing question of HELLS inactivityin vitro. Using cryo-EM, we determine the 3.5 Å structure of an active DDM1-HELLS chimera in complex with a nucleosome. The structure reveals that a HELLS-specific insertion in the ATPase lobe 2 interacts with the nucleosome acidic patch to enhance chromatin remodeling. At the C-terminus, we resolve a unique motif, and disease hot spot, that binds and stabilizes the ATPase motor of the HELLS family of remodelers. Finally, we provide mechanistic insights for how post-translational modifications in the motor domain and midloop could modulate HELLS activity to regulate cancer stem cell state.
Genomic and epidemiological evidence for the emergence of a putativeL. donovani/L. infantumhybrid with unusual epidemiology in Northern Italy
Authors: Bruno F. , Castelli G. , Li B. , Reale S. , Carra E. , Vitale F. , Scibetta S. , Calzolari M. , Varani S. , Ortalli M. , Franceschini E. , Gennari W. , Rugna G. , Späth G.F.
Published: August 2023

Leishmania (L.) infantumis the main causative agent of animal and human leishmaniasis in the Mediterranean basin. Despite its clinical significance, little is known on the genetic diversity ofL. infantumparasites circulating in Italy. Here, we apply a comparative genomics approach on sevenL. infantumisolates from different hosts (human, dog, cat, marten) and geographic regions (Emilia-Romagna, Sicily, Sardinia) as a first attempt to explore the breadth of parasite genetic heterogeneity in Italy. We revealed important genome instability at karyotype levels, with each isolate presenting a unique aneuploidy profile. Read depth analysis further identified strain-specific changes in gene dosage, which affected important virulence factors most of which are encoded by multi-copy gene arrays, such as amastins or surface antigen-like proteins. SNP-based clustering analysis of these genomes together with over 80 publicly availableL. infantumandL. donovanigenomes placed the Italian isolates into three geographically distinct clusters, with two isolates grouping with Spanish strains, two isolates grouping with Tunisian strains, and three isolates clustering with putativeL. infantum/L. donovanihybrids isolated in Cyprus. As judged by microsatellite profiling of 73 isolates from dogs, sand flies and VL cases, these hybrid isolates are representative of a sub-population of parasites circulating in northeastern Italy that preferentially infects humans, but not dogs. In conclusion, our data uncover a remarkable heterogeneity ofL. infantumisolates that indicates different geographic origin, including a novel hybrid-like genotype associated with an unusual infection pattern, placing Italy at the crossroad ofLeishmaniainfection in the Mediterranean region.
Casein kinase II promotes piRNA production through direct phosphorylation of USTC component TOFU-4
Authors: Zhang Gangming , Zheng Chunwei , Ding Yue-he , Mello Craig
Published: August 2023

Piwi-interacting RNAs (piRNAs) are genomically encoded small RNAs that engage Piwi Argonaute proteins to direct mRNA surveillance and transposon silencing. Despite advances in understanding piRNA pathways and functions, how the production of piRNA is regulated remains elusive. Here, using a genetic screen, we identify casein kinase II (CK2) as a factor required for piRNA pathway function. We show that CK2 is required for the localization of PRG-1 and for the proper localization of several factors that comprise the ‘upstream sequence transcription complex’ (USTC), which is required for piRNA transcription. Loss of CK2 impairs piRNA levels suggesting that CK2 promotes USTC function. We identify the USTC component twenty-one-U fouled-up 4 (TOFU-4) as a direct substrate for CK2. Our findings suggest that phosphorylation of TOFU-4 by CK2 promotes the assembly of USTC and piRNA transcription. Notably, during the aging process, CK2 activity declines, resulting in the disassembly of USTC, decreased piRNA production, and defects in piRNA-mediated gene silencing, including transposons silencing. These findings highlight the significance of posttranslational modification in regulating piRNA biogenesis and its implications for the aging process. Overall, our study provides compelling evidence for the involvement of a posttranslational modification mechanism in the regulation of piRNA biogenesis.
ISWI1 complex proteins facilitate developmental genome editing inParamecium
Authors: Singh Aditi , Häußermann Lilia , Emmerich Christiane , Nischwitz Emily , Seah Brandon KB , Butter Falk , Nowacki Mariusz , Swart Estienne C.
Published: August 2023

Chromatin remodeling is required for essential cellular processes, including DNA replication, DNA repair, and transcription regulation. The ciliate germline and soma are partitioned into two distinct nuclei within the same cell. During a massive editing process that forms a somatic genome, ciliates eliminate thousands of DNA sequences from a germline genome copy in the form of internal eliminated sequences (IESs). Recently we showed that the chromatin remodeler ISWI1 is required for somatic genome development in the ciliateParamecium tetraurelia. Here we describe two paralogous proteins, ICOP1 and ICOP2, essential for DNA elimination. ICOP1 and ICOP2 are highly divergent from known proteins; the only domain detected showed distant homology to the WSD motif. We show that both ICOP1 and ICOP2 interact with the chromatin remodeler ISWI1. UponICOPknockdown, changes in alternative IES excision boundaries and nucleosome densities are similar to those observed forISWI1knockdown. We thus propose that a complex comprising ISWI1 and either or both ICOP1 and ICOP2 are needed for chromatin remodeling and accurate DNA elimination inParamecium.
Hyphal exploration strategies and habitat modification of an arbuscular mycorrhizal fungus in microengineered soil chips
Authors: Hammer Edith C. , Arellano-Caicedo Carlos , Mafla-Endara Paola Micaela , Kiers E. Toby , Shimizu Tom , Ohlsson Pelle , Aleklett Kristin
Published: August 2023

Arbuscular mycorrhizal fungi (AMF) are considered ecosystem engineers, however, the exact mechanisms by which they modify and influence their immediate surroundings are largely unknown and difficult to study in soil. In this study, we used microfluidic chips, simulating artificial soil structures, to study foraging strategies and habitat modification ofRhizophagus irregularisin symbiotic state associated to carrot roots. Our results suggest that AMF hyphae forage over long distances in void spaces, prefer straight over tortuous passages, anastomose and show strong inducement of branching when encountering obstacles. We observed bi-directional vesicle transport inside active hyphae and documented strategic allocation of biomass within the mycelium e.g., truncated hyphal growth and cytoplasm retraction from inefficient paths. We foundR. irregularisable to modify pore-spaces in the chips by producing irregularly shaped spores that filled up pores. We suggest that studying AMF hyphal behaviour in spatial settings can explain phenomena reported at bulk scale such as AMF modification of water retention in soils. The use of microfluidic soil chips in AMF research opens up novel opportunities to under very controlled conditions study ecophysiology and interactions of the mycelium with both biotic and abiotic factors.
Ultrafast genome-wide inference of pairwise coalescence times
Authors: Schweiger Regev , Durbin Richard
Published: August 2023

The pairwise sequentially Markovian coalescent (PSMC) algorithm and its extensions infer the coalescence time of two homologous chromosomes at each genomic position. This inference is used in reconstructing demographic histories, detecting selection signatures, studying genome-wide associations, constructing ancestral recombination graphs, and more. Inference of coalescence times between each pair of haplotypes in a large data set is of great interest, as they may provide rich information about the population structure and history of the sample. Here, we introduce a new method,Gamma-SMC, which is more than 10 times faster than current methods. To obtain this speed-up, we represent the posterior coalescence time distributions succinctly as a gamma distribution with just two parameters; in contrast, PSMC and its extensions hold these in a vector over discrete intervals of time. Thus, Gamma-SMC has constant time-complexity per site, without dependence on the number of discrete time states. Additionally, because of this continuous representation, our method is able to infer times spanning many orders of magnitude and, as such, is robust to parameter misspecification. We describe how this approach works, show its performance on simulated and real data, and illustrate its use in studying recent positive selection in the 1000 Genomes Project data set.
`Cryo-EM': electron cryomicroscopy, cryo electron microscopy or something else?
Authors: Henderson Richard , Hasnain Samar
Published: August 2023

Structural biology continues to benefit from an expanding toolkit, which is helping to gain unprecedented insight into the assembly and organization of multi-protein machineries, enzyme mechanisms and ligand/inhibitor binding. During the last ten years, cryoEM has become widely available and has provided a major boost to structure determination of membrane proteins and large multi-protein complexes. Many of the structures have now been made available at resolutions around 2 Å, where fundamental questions regarding enzyme mechanisms can be addressed. Over the years, the abbreviation cryoEM has been understood to stand for different things. We wish the wider community to engage and clarify the definition of cryoEM so that the expanding literature involving cryoEM is unified.
Crevice corrosion behavior and mechanism of laser additive manufacturing nickel-based alloy under wedge-shaped crevice by using wire beam electrode
Authors: Xi Yuchen , Wang Qinying , Wu Yafei , Zhang Xingshou , Dong Lijin , Bai ShuLin , Yang Yi
Published: August 2023

Purpose

The purpose of this study is to investigate the crevice corrosion behavior and mechanism of laser additive manufacturing (LAM) nickel-based alloy under wedge-shaped crevice.

Design/methodology/approach

First, the opening size of the wedge-shaped crevice was designed to 0.1, 0.3 and 0.5 mm by controlling the thickness of silicon rubber and the double-side adhesive tape. Then, one side of the glass sheet was stuck on the silicon strip and keep the electrodes of Rows 1 and 2 outside the crevice as a reference, and the opposite side was stuck to the wire beam electrode by silica gel.

Findings

The current density with a maximum value of 5.7 × 10−6 A/cm2 was observed at the crevice opening of 0.5 mm, while the lowest value of 9.2 × 10−7 A/cm2 was found at the crevice opening of 0.1 mm. In addition, the corrosion resistance at the inside of the crevice is higher than that at the outside and the middle of the crevice. It means that the internal width of the wedge-shaped crevice tends toward 0, which hinders the migration of ions in the corrosive medium. The generation of corrosive products further reduce the crevice size to cause the inhibition of corrosion at the inside of the crevice as well.

Originality/value

The multilayer and multipath LAM component is prepared to show the complex microstructure, which made the corrosion behavior and mechanism at wedge-shaped crevice nondeterminacy.
Who should retain the service tips? Tips retention practices and the British customers’ returning intention to the same Indian restaurants
Authors: Hosain Md. Sajjad
Published: August 2023

Purpose

Service tip is an optional gift that is given by the customers to the waiters (or any other service staffs) for their services. Although the service tips are given to the waiters or service staffs, many restaurant owners or managements take away such gifts from the service staffs. This paper aims to identify the relationship between tips retention practice (TRP) and returning intention (RI) of the British customers to the same Indian restaurants for dining once they know that such tips are retained by the owners not by the service staffs. TRP was further divided into positive TRP (service staffs retaining the tips) and negative TRP (owners or management retaining the tips). The study further used a moderating variable (Female Customers’ Role) to test the moderating effect on the direct relationship.

Design/methodology/approach

The author purposively selected 1,223 British diners who take dining services at different Indian restaurants and used a structured survey instrument to collect primary data from those selected respondents. The author used SPSS 25 for descriptive statistics and a covariance-based structural equation modeling through AMOS 25.

Findings

Based on survey responses and proper statistical analysis, it was revealed that a positive TRP has a significant positive relationship with positive RI, whereas a negative TRP also has a significant positive relationship with negative RI. The results further disclosed that such a relationship can be strengthened by the Female Customers’ Role, that is, female diners are particularly reluctant in returning to those Indian restaurants where they experience a negative TRP.

Originality/value

This is one of the few empirical research attempts that have tried to reveal the dining customers’ intention toward TRPs. The author expects that the study results will contribute to upcoming investigations focusing on TRPs and policies. The author further anticipates that the study findings will guide the Indian restaurant managements in shaping their TRPs and policies.
Thermal analysis for foreign objects in high-power wireless power transfer systems
Authors: Tiemann Myrel , Clemens Markus , Schmuelling Benedikt
Published: August 2023

Purpose

This paper aims to present a fast and modular framework implementation for the thermal analyses of foreign metal objects in the context of wireless power transfer (WPT) to evaluate whether they pose a hazard to the system. This framework serves as a decision-making tool for determining the necessity of foreign object detection in certain applications and at certain transmitted power levels.

Design/methodology/approach

To assess the necessity of implementing foreign object detection, the considered WPT system is modeled, and Arnoldi-Krylov-based model order reduction is applied to generate separate reduced models of the ground and vehicle modules of the WPT system. This enables interoperable evaluations to be conducted. Further discussion on the implementation details of the system-level simulations used to evaluate the electrical and thermal characteristics is provided. The resulting modular implementation allows for efficient evaluation of the thermal behavior of the wireless charging system at various transferred power levels and under various boundary conditions.

Findings

Based on the transferred power level, the WPT model, the relative positioning between the vehicle and the charging pad and the charging time, it may be necessary to divide the area of the charging pad into multiple regions for the purpose of implementing foreign object detection.

Originality/value

While the tools and fundamentals of thermal analysis are widely known and used, their application to high-power WPT systems for electric vehicles has not yet been thoroughly discussed in this form in the literature. The approach presented in this paper is not limited to the specific WPT model discussed but rather is directly applicable to other WPT models as well.
Benefits of IPSAS and their differences from IFRS: a discussion paper
Authors: Rompotis Gerasimos , Balios Dimitris
Published: August 2023

Purpose

This paper tries to shed light on the international progress regarding the adoption of International Public Sector Accounting Standards (IPSAS), to accentuate the benefits resulting from the application of IPSAS, and to highlight the main differences between IPSAS and IFRS.

Design/methodology/approach

A comprehensive literature review is conducted which focuses on issues concerning the factors that induce the adoption of IPSAS, the obstacles that must be overcome, the degree of IPSAS’ proliferation worldwide, the repercussions from adopting IPSAS, the benefits of IPSAS, and the differences between IPSAS and IFRS. The selection process of the cited articles focuses on journals with high rankings in the ABS list.

Findings

It is accentuated that IPSAS carry significant benefits regarding the improved quality of the financial information reported by the public sector, the enhancement of transparency and accountability, the upgrading of the decision-making process and the restored trust in public finances. However, there is more work that needs to be done toward the global proliferation of IPSAS.

Practical implications

This study provides insights regarding the implementation process of IPSAS, which should be useful to all the parties engaged in the reform of the public administration, such as national governments, local or international regulators, accounting standard setters and institutional organizations.

Originality/value

The current study clarifies whether the public sector should move from using the business focused IFRS, as it is frequently the case, to the adoption of IPSAS. In addition, this study comprehensive literature review can be used by academics and researchers as a basis for further research on the issue. More importantly, policymakers and other officials who need to make informed decisions about financial reporting issues at the government level and the public sector in general can benefit from this study.