bluuebunny/crossref_metadata_2025 huggingface dataset:
Sleep in Psychotic Disorders: Results From Nationwide SUPER Finland Study
Authors: Cederlöf Erik , Holm Minna , Lähteenvuo Markku , Haaki Willehard , Hietala Jarmo , Häkkinen Katja , Isometsä Erkki , Jukuri Tuomas , Kajanne Risto , Kampman Olli , Kieseppä Tuula , Lahdensuo Kaisla , Lönnqvist Jouko , Männynsalo Teemu , Niemi-Pynttäri Jussi , Suokas Kimmo , Suvisaari Jaana , Tiihonen Jari , Turunen Hannu , Wegelius Asko , Veijola Juha , Palotie Aarno , Paunio Tiina
Published: January 2022

Objective

Characterizing sleep in patients with schizophrenia, schizoaffective disorder, bipolar disorder, and psychotic depression.

Methods

This cross-sectional questionnaire study is based on the SUPER study sample, which is part of the Stanley Global Neuropsychiatric Genomics Initiative. The study is a multicentre, nationwide Finnish study consisting of patients (N = 8 623) both in primary and specialized health care. The main measurements were sleep duration, difficulties initiating sleep, early morning awakenings, and fatigue. These results were compared with a nationally representative sample of the Finnish population from the Health 2000 survey (N = 7 167) with frequency and logistic regression analyses.

Results

Patients had more sleep problems compared with the general population, especially young and middle-aged patients (Difficulties initiating sleep in young patients odds ratio = 12.3, 95% CI 9.8–15.4). Long sleep duration was the most deviating property of the sleep characteristics, being particularly common among young patients with schizophrenia (odds ratio = 27.9, 95% CI 22.1–35.2, 47.4% vs 3.3% prevalence). All sleep problems were associated with worse subjective health. We also conducted a latent class analysis, resulting in a cluster relatively free of sleep problems (58% of patients), an insomnia symptom cluster (26%), and a hypersomnia symptom cluster (15%).

Conclusions

In our sample, patients with psychotic disorders have more sleep problems—especially long sleep duration but also insomnia symptoms—compared with the general population. The patients can in a latent class analysis of their sleep symptoms be divided into groups with differing sleep profiles.
What Gender Values Do Muslims Resist? How Religiosity and Acculturation Over Time Shape Muslims’ Public-Sphere Equality, Family Role Divisions, and Sexual Liberalization Values Differently
Authors: Glas Saskia
Published: January 2022

Populist voices argue that Muslim migrants’ religion would cause them to denounce all aspects of women’s equality and sexual liberalization, no matter how long migrants have lived in Western Europe. Previous quantitative studies have refuted claims that Islamic religiosity necessarily begets gender traditionalism and that migrants would not become more progressive over time. However, existing studies have not yet addressed the assumption of uniformity in “gender egalitarianism.” The present study argues that individuals’ religiosity and acculturation over time shape support for public-sphere equality, progressive family role divisions, and sexual liberalization in different ways. EURISLAM data on 4,000 Muslim migrants show that different gender values are indeed driven by varying mechanisms and develop differently. Over time and generations, Muslim migrants’ support for public-sphere equality and sexual liberalization swell, but their support for progressive family roles dwindles. Religiosity hardly reduces support for public-sphere equality, more strongly curbs progressive family roles, and most strongly stifles sexual liberalization. These differences magnify over the years after migration; religiosity’s already weak and inconsistent obstruction to public-sphere equality further dulls, while its stronger opposition to sexual liberalization intensifies. Altogether, varying gender values differ to such an extent that any conclusion on “the gender traditionalism” of Muslim migrants should be viewed suspiciously.
Quercetin ameliorates Di (2-ethylhexyl) phthalate-induced nephrotoxicity by inhibiting NF-κB signaling pathway
Authors: Ashari Sorour , Karami Mohammad , Shokrzadeh Mohammad , Bagheri Abouzar , Ghandadi Morteza , Ranaee Mohammad , Dashti Ayat , Mohammadi Hamidreza
Published: January 2022

This study aimed to evaluate the possible protective effects of quercetin, a natural flavonoid, against nephrotoxicity induced by Di (2-ethylhexyl) phthalate (DEHP) in kidney tissue of rats and human embryonic kidney (HEK) 293 cell line. The HEK-293 cells were treated with different concentrations of quercetin 24 h before treatment with monoethylhexyl phthalate (MEHP). Male rats were treated with 200-mg/kg DEHP, 200-mg/kg DEHP plus quercetin (50 and 100 mg/kg), and 200-mg/kg DEHP plus vitamin E (20 mg/kg) for 45 days by gavage. Quercetin treatment reduced cytotoxicity and oxidative damage inducing by MEHP in HEK-293 cells. The in vivo findings showed that 100-mg/kg quercetin significantly suppressed DEHP-induced kidney damage. For exploring the involved mechanisms, the expressions of nuclear factor E2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), nuclear factor kappa B (NFκB), and tumor necrosis factor alpha (TNFα) genes were determined via real-time Polymerase chain reaction (PCR) assay. High dose of quercetin significantly decreased the gene expressions of NF-κB and TNFα, whereas the alternations of Nrf2 and HO-1 gene expressions were not significant in quercetin groups in compared with DEHP group. These findings suggested that the suppression of DEHP-induced nephrotoxicity via quercetin is correlated, at least in part, with its potential to regulate NF-κB signaling pathway.
Strong selection and high mutation supply characterize experimental Chlorovirus evolution
Authors: Retel Cas , Kowallik Vienna , Becks Lutz , Feulner Philine G D
Published: January 2022

Characterizing how viruses evolve expands our understanding of the underlying fundamental processes, such as mutation, selection and drift. One group of viruses whose evolution has not yet been extensively studied is the Phycodnaviridae, a globally abundant family of aquatic large double-stranded (ds) DNA viruses. Here we studied the evolutionary change of Paramecium bursaria chlorella virus 1 during experimental coevolution with its algal host. We used pooled genome sequencing of six independently evolved populations to characterize genomic change over five time points. Across six experimental replicates involving either strong or weak demographic fluctuations, we found single nucleotide polymorphisms (SNPs) at sixty-seven sites. The occurrence of genetic variants was highly repeatable, with just two of the SNPs found in only a single experimental replicate. Three genes A122/123R, A140/145R and A540L showed an excess of variable sites, providing new information about potential targets of selection during Chlorella–Chlorovirus coevolution. Our data indicated that the studied populations were not mutation-limited and experienced strong positive selection. Our investigation highlighted relevant processes governing the evolution of aquatic large dsDNA viruses, which ultimately contributes to a better understanding of the functioning of natural aquatic ecosystems.
Devising a Missing Data Rule for a Quality of Life Questionnaire—A Simulation Study
Authors: Jacoby Peter , Whitehouse Andrew , Leonard Helen , Saldaris Jacinta , Demarest Scott , Benke Tim , Downs Jenny
Published: January 2022

Objective:

The aim of this study was to devise an evidence-based missing data rule for the Quality of Life Inventory-Disability (QI-Disability) questionnaire specifying how many missing items are permissible for domain and total scores to be calculated using simple imputation. We sought a straightforward rule that can be used in both research and clinical monitoring settings.

Method:

A simulation study was conducted involving random selection of missing items from a complete data set of questionnaire responses. This comprised 520 children with intellectual disability from 5 diagnostic groups. We applied a simple imputation scheme, and the simulated distribution of errors induced by imputation was compared with the previously estimated standard error of measurement (SEM) for each domain.

Results:

Using a stringent criterion, which requires that the 95th percentile of absolute error be less than the SEM, 1 missing item should be permitted for 2 of the 6 QI-Disability subdomain scores to be calculated and 1 missing item per domain for the total score to be calculated. Other, less stringent criteria would allow up to 2 missing items per domain.

Conclusion:

Empirical evidence about the impact of imputing missing questionnaire responses can be gathered using simulation methods applied to a complete data set. We recommend that such evidence be used in devising a rule that specifies how many items can be imputed for a valid score to be calculated.
Unusual Cases of Hairy Cell Leukemia With Uncommon Immunophenotypes: A Diagnostic Challenge
Authors: Liu Ying , Vali-Betts Elham , Ku Nam K.
Published: January 2022

Hairy cell leukemia (HCL) is a rare indolent B-cell neoplasm with distinct morphologic and immunophenotypic features. Immunophenotypically, the neoplastic cells in HCL are strongly positive for B-cell markers, such as CD19, CD20, and CD22. They also characteristically express CD11c, CD25, CD103, and CD123, but lack CD5, CD10, and CD23. Uncommon immunophenotypes of HCL can pose diagnostic challenges. Here, we report 2 unusual cases of CD5-positive and CD10-positive HCL.
Granulomatous Slack Skin T-Cell Lymphoma Manifesting as Ulcerative and Gangrenous Lesions With a Fatal Outcome: A Case Report and Review of the Literature
Authors: Su Ruijun Jeanna , Said Jonathan , Kallen Michael E. , Jumniensuk Chayanit , Pullarkat Sheeja
Published: January 2022

Granulomatous slack skin is an extremely rare cutaneous T-cell lymphoma, which often pursues an indolent disease course. Clinically, it is characterized by areas of redundant and lax skin in flexural areas, with variable erythema. Histologic findings include granulomatous T-cell infiltrates with loss of elastic fibers and poikilodermic change. In this article, we report a patient with unusual rapidly progressive ulcerative and gangrenous skin lesions, leading to amputation and ultimately demise. We also review the literature on granulomatous slack skin with similarly aggressive clinical course and discuss the differential diagnosis.
Unclassifiable Myelodysplastic/Myeloproliferative Neoplasm With Hypocellularity: A Classification Conundrum
Authors: Hittman Jamie , Nageshwar Monika , Duong Vu H. , Lee Seung T. , Koka Rima , Singh Zeba , Kallen Michael E.
Published: January 2022

Myelodysplastic/myeloproliferative neoplasm (MPN), unclassifiable (MDS/MPN-U), has clinical and morphologic features of both myelodysplastic syndrome (MDS) and myeloproliferative neoplasms (MPNs), and does not meet diagnostic criteria for any other specific entity within MDS, MPN, or MPN, including therapy-related myeloid neoplasms, and cases evolving from a prior MDS or MPN. Diagnostic criteria for MDS/MPN-U include, among other specifications, a platelet count of greater than or equal to 450 × 10E9/L associated with bone marrow megakaryocytic proliferation. We present the case of a young adult patient with a several-year reported history of cytopenias, found to have thrombocytosis and 5% circulating blasts. Surprisingly, his bone marrow biopsy demonstrated hypocellularity (10%), with 5% to 10% blasts, myeloid hypoplasia, minimal fibrosis, and focal megakaryocytic dyspoiesis but no hyperplasia. The constellation of morphologic and clinical features presents a challenging differential diagnosis between MDS/MPN-U and MDS with excess blasts (as well as thrombocytosis). Molecular testing interestingly demonstrated an SF3B1 mutation, although no increased ring sideroblasts were found by iron staining. Cases such as these may prove instructive in refining our understanding of the MDS/MPN category, as well as its relationship to myelodysplasia and the complex molecular genetic landscape underlying myeloid neoplasia.
Consensus Recommendations on the Use of Hyaluronic Acid–Based Fillers for Nonsurgical Nasal Augmentation in Asian Patients
Authors: Trevidic Patrick , Kim Hee-Jin , Harb Ayad , Ho Wilson W. S. , Liew Steven
Published: January 2022

Background:

Nonsurgical nasal augmentation using dermal fillers such as hyaluronic acid is increasing in popularity because of its less invasive nature and shorter downtime compared with traditional surgery. However, the complexity of the nasal vasculature makes it a high-risk procedure without proper training. Appropriate patient and product selection and safer standardized injection techniques are warranted to minimize complications and to achieve reproducible aesthetic results. In this article, recommendations for nonsurgical nasal augmentation using hyaluronic acid fillers are outlined, with focus on the dorsum, tip, and columella.

Methods:

A consensus meeting was conducted to develop recommendations on nonsurgical nasal augmentation in Asian patients using hyaluronic acid–based fillers. Literature review was performed using PubMed and Google Scholar. Relevant studies were included to formulate recommendations. Consensus statements were graded using the criteria outlined by the Grading of Recommendations Assessment, Development and Evaluation Working Group.

Results:

Nonsurgical nasal augmentation is an advanced procedure that warrants in-depth knowledge of the nasal anatomy. The panel recommends thorough preinjection assessment and counseling to fully align the patient’s expectations with aesthetic goals. Injections must be deep and at the level of the periosteum or perichondrium to minimize risk of intravascular injection. Aliquots of hyaluronic acid must be introduced using slow, low-pressure, and low-volume injections. Optimal aesthetic effect is achieved with hyaluronic acid dermal fillers that are highly elastic, cohesive, and with good adaptability to their environment.

Conclusions:

Hyaluronic acid injections are safe and effective in nonsurgical nasal augmentation. In-depth knowledge of vascular anatomy and proper injection techniques using suitable products are necessary to achieve aesthetic goals safely.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, V.
Task-Specific Patient Preferences for Shared Decision-Making in Hand Surgery
Authors: Cho Hoyune E. , Baxter Natalie B. , Billig Jessica I. , Kotsis Sandra V. , Haase Steven C. , Chung Kevin C.
Published: January 2022

Background:

Shared decision-making for surgery can increase patient engagement, satisfaction, and clinical outcomes. However, the level of involvement that patients desire at each step of the decision-making process is unknown.

Methods:

The authors surveyed patients at an academic hand surgery clinic to examine the preferred role in decision-making using validated questionnaires (i.e., Control Preference Scale, Problem-Solving Decision-Making Scale, and General Self-Efficacy Scale). The Control Preference Scale assesses general treatment preferences, whereas the Problem-Solving Decision-Making Scale distinguishes between problem-solving tasks (e.g., making diagnoses, calculating risks/benefits) and decision-making tasks. Patients’ self-beliefs and perceived ability to handle difficult situations were assessed with the General Self-Efficacy Scale. The authors used linear regression models and ordinal logistic regression to examine the relationship between self-efficacy and patients’ preferred role in treatment decision-making.

Results:

Patients overall preferred an equal share of decision-making responsibility with the surgeon (mean Control Preference Scale score, 3.3 ± 0.7). Specifically, for problem-solving tasks, however, 81 percent of patients wanted to “hand over” the responsibility and 19 percent preferred shared decision-making. In contrast, for decision-making tasks, 54 percent of patients preferred shared decision-making. Each point increase in General Self-Efficacy Scale score correlated with 12 percent greater odds of preferring to retain the responsibility (OR, 1.12; 95 percent CI, 1.05 to 1.21; p = 0.001). However, self-efficacy did not show a significant effect for problem-solving tasks.

Conclusions:

The authors found that patients prefer surgeons to provide expert knowledge for problem-solving tasks but desire equal share of responsibility in decision-making tasks. The authors’ findings support the current shift away from the paternalistic model of surgical decision-making, and provide an effective strategy to tailor shared decision-making to align care delivery with patient preferences.
Comparison of Presurgical Anthropometric Measures of Right and Left Complete Unilateral Cleft Lip and/or Palate
Authors: Chong David K. , Somasundaram Mithila , Ho Emily , Dhooghe Nicolas S. , Fisher David M.
Published: January 2022

Background:

Left clefts occur twice as frequently as right ones. The sidedness has been suggested to influence certain outcomes. Some surgeons consider a right cleft more challenging to repair. This is often attributed to their reduced prevalence. The authors question whether this may be caused by morphologic differences. The authors’ hypothesis is that there are anthropometric differences between left and right complete cleft lips.

Methods:

Patients with complete unilateral cleft lip, with or without cleft palate, operated on at the age of 3 to 6 months, between 2000 and 2018, by a single surgeon, were included. Eight standardized anthropometric measurements of the cleft lip, collected just before cleft lip repair, compare lip and vermillion dimensions and ratios between left and right clefts.

Results:

One hundred thirty-nine left and 80 right unilateral cleft lips were compared. A significant difference was found between left and right clefts for cleft-side to non–cleft-side ratios comparing the lateral lip element vertical heights and vermillion heights.

Conclusions:

Patients with right cleft lips have a greater degree of lateral lip element hypoplasia, demonstrating greater deficiencies of lateral lip element vertical height and vermillion height when compared to patients with left clefts. This has clinical implications for preoperative assessment, choice of surgical technique, and postoperative and long-term outcomes.
Impact of Incision Placement on Ischemic Complications in Microsurgical Breast Reconstruction
Authors: Tevlin Ruth , Griffin Michelle , Karin Mardi , Wapnir Irene , Momeni Arash
Published: January 2022

Background:

Nipple-sparing mastectomy is associated with greater patient satisfaction than non–nipple-sparing approaches. Although various nipple-sparing mastectomy incisions have been described, the authors hypothesized that incision location would impact the rate and location of ischemic complications to the mastectomy skin flap.

Methods:

A prospectively maintained database was queried to identify patients who underwent nipple-sparing mastectomy with immediate microsurgical reconstruction with a minimum postoperative follow-up of 12 months. The impact of incision location on postoperative ischemic complications was investigated. Major complications were defined as those that required reexploration in the operating room or inpatient management; minor complications were amenable to outpatient management. Multivariable logistic and linear regression were performed to investigate risk factors for postoperative complications following breast reconstruction.

Results:

Eighty-seven patients met inclusion criteria. The following nipple-sparing mastectomy incisions were used: radial with a periareolar extension (39 percent), inframammary fold (31 percent), vertical with a periareolar extension (22 percent), vertical (6 percent), and radial (2 percent). Seven patients (8 percent) had major complications, whereas twenty-six patients (29.9 percent) developed minor postoperative complications. Inframammary fold incisions were associated with significantly greater rates of mastectomy skin flap necrosis (p = 0.002), whereas periareolar incisions were associated with significantly greater rates of postoperative nipple-areola complex necrosis (p = 0.04).

Conclusions:

The authors report a significant association between incision location and ischemic complications to the breast skin envelope in microsurgical breast reconstruction. The authors observed a significant association of inframammary fold and periareolar incisions with mastectomy skin flap and nipple-areola complex necrosis, respectively.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Harvesting Composite Arterial and Vein Grafts from Deep Inferior Epigastric Artery and Vein: A Safe Five-Step Method of Preparation
Authors: Cho Min-Jeong , Haddock Nicholas T. , Teotia Sumeet S.
Published: January 2022

Background:

As the use of stacked flaps and options for autologous breast reconstruction increase, the level of complexity in autologous breast reconstruction has risen. Frequently, these reconstruction types present technical challenges such as vessel mismatches and short pedicle length. In this study, the authors introduce their five steps of harvesting composite deep inferior epigastric artery (DIEA) and deep inferior epigastric vein (DIEV) grafts to overcome such challenges.

Methods:

The authors performed a retrospective review of patients who underwent microvascular reconstruction using DIEA/DIEV grafts from 2012 to 2020. The grafts were harvested using the five steps, as follows: step 1, a transverse, paramedian skin incision was made at the level of suprapubic crease; step 2, an oblique fasciotomy was made on the lateral rectus border; step 3, DIEA/DIEV vessels were identified and exposed past the confluence of two venae comitantes; step 4, DIEA/DIEV grafts were harvested while sparing motor nerves; and step 5, fascial closure was performed.

Results:

A total of 40 DIEA/DIEV grafts were used in 25 patients (lumbar artery perforator flaps, n = 25; lateral thigh flaps, n = 1; superficial inferior epigastric artery flaps, n = 12; and flap salvage, n = 2) for breast reconstruction. The average time of harvest was 28 minutes, and there were two flap losses.

Conclusions:

In the authors’ experience, DIEA/DIEV grafts can be safely harvested and used in flaps with short pedicles and small vessel size. Although the authors’ experience was limited to breast reconstruction, the DIEA/DIEV grafts can be used for other types of reconstruction, especially for head and neck reconstruction.
Utility of Ultrasonography and Significance of Surgical Anatomy in the Management of de Quervain Disease: A Systematic Review and Meta-Analysis
Authors: Abi-Rafeh Jad , Mojtahed Jaberi Mehrad , Kazan Roy , Alabdulkarim Abdulaziz , Boily Mathieu , Thibaudeau Stephanie
Published: January 2022

Background:

The role of ultrasound in plastic surgery practice has grown significantly over the past decade, with notable applications for conditions of the upper extremity. Its utility for the management of de Quervain disease, however, remains to be established, and the prevalence of first dorsal compartment anatomical variations needs to be adequately assessed.

Methods:

A systematic review was performed to evaluate the role of ultrasound in the diagnosis, anatomical characterization, and clinical management of de Quervain disease. A meta-analysis was conducted to establish the prevalence of first dorsal compartment anatomical variations in the de Quervain disease and general population, along with the diagnostic accuracy of ultrasound for their detection. Outcomes were documented and compared to alternative treatment options.

Results:

Extensor retinaculum thickening, tendon sheath swelling, peritendinous edema, and tendon enlargement were the most common sonographic features of de Quervain disease. The prevalence of an intercompartmental septum in the de Quervain disease surgical population was shown to be significantly greater than in the general cadaveric population (67 percent versus 35 percent, respectively). Although the efficacy of energy-based therapeutic ultrasound remains elusive, ultrasound-guided corticosteroid injections were shown to be more accurate than manual injections (90 to 100 percent versus 40 to 100 percent), and to confer significantly better treatment outcomes (73 to 100 percent versus 59 to 83 percent success rates, respectively).

Conclusions:

Ultrasound use is essential to achieve the best evidence-based outcomes in the management of de Quervain disease. The varied prevalence of first dorsal compartment anatomical variations and high accuracy of ultrasound for their detection carry significant prognostic implications.
Induction of Endotoxin Tolerance Delays Acute Rejection in a Hindlimb Transplantation Model in Rats
Authors: Rubio Yanchuck Mónica , Toledano Víctor , Bonastre Jorge , Diez Jesús , Aguirre Luis , López-Collazo Eduardo
Published: January 2022

Background:

Acute rejection is seen in 85 percent of composite vascular allogeneic transplants despite long-term immunosuppression. Recently, it was reported that the induction of endotoxin tolerance prolonged heart allograft survival in mice. However, it produced side effects in all the animals secondary to the inflammatory reaction. Galactomannan has shown endotoxin tolerance without this side effect in vitro. The authors hypothesized that galactomannan-induced endotoxin tolerance delays acute rejection in vascular allogeneic transplantation without the side effects produced by lipopolysaccharide.

Methods:

Twenty-four rat hindlimb transplants were divided into four groups according to the preconditioning received: control, lipopolysaccharide (0.16 ml/kg), galactomannan 72 hours before (galactomannan-72) (8 ml/kg), and galactomannan 24 hours before (galactomannan-24) (8 ml/kg). Median acute rejection time, weight loss, and diarrheal episodes were monitored. Blood samples were collected at 0, 7, 21, 30, 45, and 60 days. Plasma cytokines (i.e., tumor necrosis factor alpha, interferon gamma), peripheral chimerism, and lymphocyte percentages were analyzed.

Results:

Median allograft survival was 40 days (range, 40 to 44 days) in the control group, 68 days (range, 61 to 71 days) in the lipopolysaccharide group, and 70 days (range, 69 to 73 days) in both galactomannan groups (p = 0.001). Weight loss was higher in the lipopolysaccharide group (p < 0.001), as was the 83.3 percent rate of diarrheal episodes (control, 0 percent, p = 0.015; galactomannan-72, 0 percent, p = 0.015; and galactomannan-24, 16.7 percent, p = 0.02). Preconditioned rats had higher peripheral blood chimerism (lipopolysaccharide, 2.30 ± 0.13 percent; galactomannan-72, 2.63 ±1.46 percent; and galactomannan-24, 2.47 ± 0.19 percent) compared to the control group (2.06 ± 0.36 percent) (lipopolysaccharide, p = 0.04; galactomannan-72, p = 0.002; and galactomannan-24, p = 0.002).

Conclusions:

Induction of endotoxin tolerance delays acute rejection in the rat hindlimb transplantation model. Galactomannan preconditioning has no lipopolysaccharide side effects and was equally effective in delaying acute rejection.

Clinical Relevance Statement:

The contributions of this experimental work are very incipient. Although the use of galactomannan in clinical practice requires more studies to assess its safety, there is no doubt that immunomodulation may be one of the responses that solve the problem of long-term immunosuppression.
Flavobacterium coralii sp. nov., a marine bacterium isolated from coral culture seawater
Authors: Sun Hao , Zheng Huina , Wang Xiaolei , Jiang Yiwei , Liao Baolin , Li Aihua , Xiao Baohua
Published: January 2022

A Gram-stain-negative, non-motile, strictly aerobic, rod-shaped bacterium, with one polar flagellum and named D11R37T, was isolated from coral culture seawater of Acropora digitifera. Strain D11R37T grew with 0–6 % (w/v) NaCl (optimum, 0.5%), at 10–41 °C (optimum, 28 °C) and at pH 6.0–7.0 (optimum, 7.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D11R37T formed a lineage within the genus

Flavobacterium

, and it was distinct from the most closely related species

Flavobacterium suzhouense

XIN-1T and

Flavobacterium suaedae

G16-7T with 16S rRNA gene sequences similarities of 95.97% and 95.48 %. The major respiratory quinone was menaquinone-6. The polar lipids comprised one phosphatidylethanolamine, two aminolipids and one unknown polar lipid. The predominant fatty acids (more than 10 % of total fatty acids) were iso-C15 : 0 (18.0%), iso-C17 : 0 3-OH (11.9 %) and summed feature 3 (10.9 %). The DNA G+C content was 41.3 mol%. Based on polyphasic taxonomic data, strain D11R37T is considered to represent a novel species within the genus

Flavobacterium

, for which the name Flavobacterium coralii sp. nov. is proposed. The type strain is D11R37T (=KCTC 82968T=MCCC 1K06440T).
A Tar aspartate receptor and Rubisco-like protein substitute biotin in the growth of rhizobial strains
Authors: Vargas-Lagunas Carmen , Mora Yolanda , Aguilar Alejandro , Reyes-González Alma Ruth , Arteaga-Ide Alejandra , Dunn Michael F. , Encarnación Sergio , Girard Lourdes , Peralta Humberto , Mora Jaime
Published: January 2022

Biotin is a key cofactor of metabolic carboxylases, although many rhizobial strains are biotin auxotrophs. When some of these strains were serially subcultured in minimal medium, they showed diminished growth and increased excretion of metabolites. The addition of biotin, or genetic complementation with biotin synthesis genes resulted in full growth of

Rhizobium etli

CFN42 and

Rhizobium phaseoli

CIAT652 strains. Half of rhizobial genomes did not show genes for biotin biosynthesis, but three-quarters had genes for biotin transport. Some strains had genes for an avidin homologue (rhizavidin), a protein with high affinity for biotin but an unknown role in bacteria. A CFN42-derived rhizavidin mutant showed a sharper growth decrease in subcultures, revealing a role in biotin storage. In the search of biotin-independent growth of subcultures, CFN42 and CIAT652 strains with excess aeration showed optimal growth, as they also did, unexpectedly, with the addition of aspartic acid analogues α- and N-methyl aspartate. Aspartate analogues can be sensed by the chemotaxis aspartate receptor Tar. A tar homologue was identified and its mutants showed no growth recovery with aspartate analogues, indicating requirement of the Tar receptor in such a phenotype. Additionally, tar mutants did not recover full growth with excess aeration. A Rubisco-like protein was found to be necessary for growth as the corresponding mutants showed no recovery either with high aeration or aspartate analogues; also, diminished carboxylation was observed. Taken together, our results indicate a route of biotin-independent growth in rhizobial strains that included oxygen, a Tar receptor and a previously uncharacterized Rubisco-like protein.
Somatic mutations in both blood cells and vascular endothelium from patients with severe coronary artery diseases
Authors: Zhang Haotian , Tannous Henry , Mazzeo Christopher , Zheng Haoyi , Zhan Huichun
Published: January 2022

Individuals with clonal hematopoiesis of indeterminate potential (CHIP) is associated with a 2-4 fold increase in cardiovascular diseases (CVDs). While most studies focus on mutant blood cells, we propose that a better insight into the CHIP-CVD connection can be obtained by examining the genetic mutations in both the vascular endothelium and peripheral blood samples from the same patient. In this study, we examined somatic mutations by whole exome sequencing in paired blood and vascular samples from 4 patients with severe coronary artery disease who underwent coronary artery bypass graft surgery. We found that blood and endothelium can acquire the same mutations during aging and CHIP-associated mutations are not uncommon in vascular endothelium in patients with severe CVDs. Since vascular endothelial cells have critical roles in the regulation of cardiovascular function, mutant vascular endothelium offers an opportunity for further investigations to improve our diagnosis and management of individuals with CHIP.
Quantitative proteomics and phosphoproteomics of urinary extracellular vesicles define diagnostic biosignatures for Parkinson’s Disease
Authors: Hadisurya Marco , Li Li , Kuwaranancharoen Kananart , Wu Xiaofeng , Lee Zheng-Chi , Alcalay Roy N. , Padmanabhan Shalini , Tao W. Andy , Iliuk Anton
Published: January 2022

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene have been recognized as genetic risk factors for both familial and sporadic forms of Parkinson’s disease (PD). However, compared to cancer, overall lower genetic mutations contribute to the cause of PD, propelling the search for protein biomarkers for early detection of the disease. Utilizing 141 urine samples from four groups, healthy individuals (control), healthy individuals with G2019S mutation in the LRRK2 gene (non-manifesting carrier/NMC), PD individuals without G2019S mutation (idiopathic PD/iPD), and PD individuals with G2019S mutation (LRRK2 PD), we applied a proteomics strategy to determine potential diagnostic biomarkers for PD from urinary extracellular vesicles (EVs). After efficient isolation of urinary EVs through chemical affinity followed by mass spectrometric analyses of EV peptides and enriched phosphopeptides, we identified and quantified 4,480 unique proteins and 2,682 unique phosphoproteins. We detected multiple proteins and phosphoproteins elevated in PD EVs that are known to be involved in important PD pathways, in particular the autophagy pathway, as well as neuronal cell death, neuroinflammation, and formation of amyloid fibrils. Our data revealed that LRRK2 and its Rab substrates are altered but not significant PD biomarkers. We established two panels of proteins and phosphoproteins as novel candidates for disease and risk biomarkers, and substantiated using ROC, machine learning, clinical correlation, and in-depth network analysis. Several disease biomarkers were further validated in patients with PD using parallel reaction monitoring (PRM) and immunoassay for targeted quantitation. These findings demonstrate a general strategy of utilizing biofluid EV proteome/phosphoproteome as an outstanding and non-invasive source for a wide range of disease exploration.
SARS-CoV-2 Omicron variant virus isolates are highly sensitive to interferon treatment
Authors: Bojkova Denisa , Rothenburger Tamara , Ciesek Sandra , Wass Mark N. , Michaelis Martin , Cinatl Jindrich
Published: January 2022

Recently, we have shown that SARS-CoV-2 Omicron virus isolates are less effective at inhibiting the host cell interferon response than Delta viruses. Here, we present further evidence that reduced interferon-antagonising activity explains at least in part why Omicron variant infections are inherently less severe than infections with other SARS-CoV-2 variants. Most importantly, we here also show that Omicron variant viruses display enhanced sensitivity to interferon treatment, which makes interferons promising therapy candidates for Omicron patients, in particular in combination with other antiviral agents.
A Machine-Learning Based Objective Measure for ALS Disease Severity
Authors: Vieira Fernando G. , Venugopalan Subhashini , Premasiri Alan S. , McNally Maeve , Jansen Aren , McCloskey Kevin , Brenner Michael P. , Perrin Steven
Published: January 2022

Amyotrophic Lateral Sclerosis (ALS) disease severity is usually measured using the subjective, questionnaire-based revised ALS Functional Rating Scale (ALSFRS-R). An objective measure for tracking disease severity and progression would be a powerful tool for evaluating real-world drug effectiveness, efficacy in clinical trials, as well as identifying participants for cohort studies. Here we develop a machine learning (ML) based objective measure for ALS disease severity, based on voice samples and accelerometer measurements from a longitudinal dataset collected by the ALS Therapy Development Institute (ALS-TDI) over four years. 584 people living with ALS consented and carried out prescribed speaking and limb-based tasks. 542 participants contributed 5814 voice recordings, and 350 contributed 13009 accelerometer samples, while simultaneously measuring ALSFRS-R scores. Using the data from 475 participants, we trained machine learning (ML) models to predict bulbar-related FRS scores from speech, and limb-related scores from accelerometer samples. On the test set (n=109 participants) the voice models achieved a multiclass AUC of 0.86 (95% CI, 0.85-0.88) on speech FRS prediction, whereas the accelerometer models achieved a median multiclass AUC of 0.73 on 6 limb-related functions. Further, the correlation (and inverse correlations) across different bulbar and limb functions observed in the self-reported ALSFRS-R scores are preserved in the ML-derived scores. Next, we used these models and self-reported ALSFRS-R scores to evaluate the real-world effects of edaravone, a drug recently approved for use in ALS. In the cohort of 54 test participants who received edaravone as part of their usual care, the ML-derived objective scores were consistent with the self-reported ALSFRS-R scores, and both showed highly variable outcomes from edaravone treatment from person to person. At the individual level, the continuous ML-derived score is able to capture a gradual change that is absent in the integer ALSFRS-R scores. This demonstrates the value of these tools for assessing both disease severity and potentially drug effects.
A bite force database of 654 insect species
Authors: Rühr Peter Thomas , Edel Carina , Frenzel Melina , Blanke Alexander
Published: January 2022

Bite force is a decisive performance trait in animals because it plays a role for numerous life history components such as food consumption, inter- and intraspecific interactions, and reproductive success. Bite force has been studied across a wide range of vertebrate species, but only for 20 species of insects, the most speciose animal lineage. Here we present the insect bite force database with bite force measurements for 654 insect species covering 111 families and 13 orders with body lengths ranging from 4.2 - 180.1 mm. In total we recorded 1906 bite force series from 1290 specimens, and, in addition, present basal head, body, and wing metrics. As such, the database will facilitate a wide range of studies on the characteristics, predictors, and macroevolution of bite force in the largest clade of the animal kingdom and may serve as a basis to further our understanding of macroevolutionary processes in relation to bite force across all biting metazoans.
Host Chitinase 3-like-1 is a Universal Therapeutic Target for SARS-CoV-2 Viral Variants in COVID 19
Authors: Kamle Suchitra , Ma Bing , Lee Chang Min , Schor Gail , Zhou Yang , Lee Chun Geun , Elias Jack A.
Published: January 2022

COVID 19 is the disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2; SC2) which has caused a world-wide pandemic with striking morbidity and mortality. Evaluation of SC2 strains demonstrated impressive genetic variability and many of these viral variants are now defined as variants of concern (VOC) that cause enhanced transmissibility, decreased susceptibility to antibody neutralization or therapeutics and or the ability to induce severe disease. Currently, the delta (δ) and omicron (o) variants are particularly problematic based on their impressive and unprecedented transmissibility and ability to cause break through infections. The delta variant also accumulates at high concentrations in host tissues and has caused waves of lethal disease. Because studies from our laboratory have demonstrated that chitinase 3-like-1 (CHI3L1) stimulates ACE2 and Spike (S) priming proteases that mediate SC2 infection, studies were undertaken to determine if interventions that target CHI3L1 are effective inhibitors of SC2 viral variant infection. Here we demonstrate that CHI3L1 augments epithelial cell infection by pseudoviruses that express the alpha, beta, gamma, delta or omicron S proteins and that the CHI3L1 inhibitors anti-CHI3L1 and kasugamycin inhibit epithelial cell infection by these VOC pseudovirus moieties. Thus, CHI3L1 is a universal, VOC-independent therapeutic target in COVID 19.
‘Holey’ niche! Finding holes in niche hypervolumes using persistence homology
Authors: Conceição Pedro , Morimoto Juliano
Published: January 2022

Hutchinson’s niche hypervolume concept has enabled significant progress in our understanding of species’ ecological needs and distributions across environmental gradients. Nevertheless, the properties of Hutchinson’s n-dimensional hypervolumes can be challenging to calculate and several methods have been proposed to extract meaningful measurements of hypervolumes’ properties (e.g., volume).

One key property of hypervolumes are holes, which provide important information about the ecological occupancy of species. However, to date, current methods rely on volume estimates and set operations to identify holes in hypervolumes. Yet, this approach can be problematic because in high-dimensions, the volume of region enclosing a hole tends to zero.

Here, we propose the use of the topological concept of persistence homology (PH) to identify holes in hypervolumes and in ecological datasets more generally. PH allows for the estimates of topological properties in n-dimensional niche hyper-volumes and is independent of the volume estimates of the hypervolume. We demonstrate the application of PH to canonical datasets and to the identification of holes in the hypervolumes of five vertebrate species with diverse niches, highlighting the potential benefits of this approach to gain further insights into animal ecology.

Overall, our approach enables the study of an yet unexplored property of Hutchinson’s hypervolumes (i.e., holes), and thus, have important implications to our understanding of animal ecology.
Border closure and travel restrictions to control the spread of COVID-19: an update to a Cochrane review
Authors: Abou-Setta Ahmed M. , Lam Otto LT , Kasireddy Viraj , Askin Nicole , Tricco Andrea C.
Published: January 2022

Background

COVID-19 has proven to be more difficult to manage for many reasons including its high infectivity rate. One of the potential ways to limit its spread is by limiting free travel across borders, including via air travel. The objective of this systematic review is to identify, critically-appraise and summarize evidence on border closures and travel restrictions.

Methods

This review is based on the Cochrane review: “International travel-related control measures to contain the COVID-19 pandemic” and followed the same methodology. In brief, we searched for clinical and modelling studies in general health and COVID-19-specific bibliographic databases. The primary outcome categories were (i) cases avoided, (ii) cases detected, and (iii) a shift in epidemic development. Secondary outcomes were other infectious disease transmission outcomes, healthcare utilisation, resource requirements and adverse effects if identified in studies assessing at least one primary outcome.

Results

We included 43, mostly modelling, studies that met our inclusion criteria. Fourteen new studies were identified in the updated search, as well as updated companions (e.g., peer-reviewed publications that were previously only available as pre-prints). Most studies were of moderate to high quality. The added studies did not change the main conclusions of the Cochrane review nor the quality of the evidence (very low to low certainty). However, it did add to the evidence base for most outcomes.

Conclusions

Weak evidence supports the use of border closures to limit the spread of COVID-19 via air travel. Real-world studies are required to support these conclusions.
Segmentation stability of human head and neck cancer medical images for radiotherapy applications under de-identification conditions: benchmarking data sharing and artificial intelligence use-cases
Authors: Sahlsten Jaakko , Wahid Kareem A. , Glerean Enrico , Jaskari Joel , Naser Mohamed A. , He Renjie , Kann Benjamin H. , Mäkitie Antti , Fuller Clifton D. , Kaski Kimmo
Published: January 2022

Background

Demand for head and neck cancer (HNC) radiotherapy data in algorithmic development has prompted increased image dataset sharing. Medical images must comply with data protection requirements so that re-use is enabled without disclosing patient identifiers. Defacing, i.e., the removal of facial features from images, is often considered a reasonable compromise between data protection and re-usability for neuroimaging data. While defacing tools have been developed by the neuroimaging community, their acceptability for radiotherapy applications have not been explored. Therefore, this study systematically investigated the impact of available defacing algorithms on HNC organs at risk (OARs).

Methods

A publicly available dataset of magnetic resonance imaging scans for 55 HNC patients with eight segmented OARs (bilateral submandibular glands, parotid glands, level II neck lymph nodes, level III neck lymph nodes) was utilized. Eight publicly available defacing algorithms were investigated: afni_refacer, DeepDefacer, defacer, fsl_deface, mask_face, mri_deface, pydeface, and quickshear. Using a subset of scans where defacing succeeded (N=29), a 5-fold cross-validation 3D U-net based OAR auto-segmentation model was utilized to perform two main experiments: 1.) comparing original and defaced data for training when evaluated on original data; 2.) using original data for training and comparing the model evaluation on original and defaced data. Models were primarily assessed using the Dice similarity coefficient (DSC).

Results

Most defacing methods were unable to produce any usable images for evaluation, while mask_face, fsl_deface, and pydeface were unable to remove the face for 29%, 18%, and 24% of subjects, respectively. When using the original data for evaluation, the composite OAR DSC was statistically higher (p ≤ 0.05) for the model trained with the original data with a DSC of 0.760 compared to the mask_face, fsl_deface, and pydeface models with DSCs of 0.742, 0.736, and 0.449, respectively. Moreover, the model trained with original data had decreased performance (p ≤ 0.05) when evaluated on the defaced data with DSCs of 0.673, 0.693, and 0.406 for mask_face, fsl_deface, and pydeface, respectively.

Conclusion

Defacing algorithms may have a significant impact on HNC OAR auto-segmentation model training and testing. This work highlights the need for further development of HNC-specific image anonymization methods.