bluuebunny/crossref_metadata_2025 huggingface dataset:
Congenital factor V deficiency from compound heterozygous mutations with a novel variant c.2426del (p.Pro809Hisfs∗2) in the F5 gene
Authors: Park Chang-Hun , Park Min-Seung , Lee Ki-O , Kim Sun-Hee , Park Young Shil , Kim Hee-Jin
Published: January 2020

Introduction:

Congenital factor V deficiency (FVD) is a rare bleeding disorder characterized by low or undetectable plasma factor V (FV) levels leading to mild to severe bleeding symptoms. Currently, more than 100 mutations have been reported in F5. We herein report a patient with FVD from mutations in the F5 gene.

Patient concerns:

A 52-year-old man with prolonged prothrombin time and activated partial thromboplastin time corrected by mixing test on preoperative screening. His past medical or family history was not remarkable.

Diagnosis:

Factor assays revealed a markedly reduced FV activity at 7%. Other factors were not decreased. DNA sequencing analysis to detect F5 gene mutations showed the patient was compound heterozygous for c.286G>C (p.Asp96His) and c.2426del (p.Pro809Hisfs∗2). Asp96His was previously described missense mutation and Pro809Hisfs∗2 was a novel deleterious mutation.

Interventions:

Fresh-frozen plasma was administered to supplement FV before surgery.

Outcomes:

Subsequent factor assays revealed temporarily increased FV activity at 33%.

Conclusion:

As was the case in our patient, genotype-phenotype correlations are poor in FVD, and molecular genetic test is necessary to confirm the diagnosis.
Sedative reduction method for children with intussusception
Authors: Doo Jin Woong , Kim Soon Chul
Published: January 2020

Intussusception is common emergency condition in children. Pneumatic or hydrostatic reduction (HR) is considered the first-choice management strategy in cases lacking indications for surgical intervention. Generally, sedatives are not used in children undergoing interventional radiology procedures. Surgical management is associated with long hospitalization durations and high costs, unlike nonsurgical reduction. To avoid surgery, reduction procedures are repeated despite initial treatment failure. However, in cases involving repeated failures, children should be referred for surgery.

To ensure good response to reduction, we planned HR under sedation during the third reduction attempt. Sedative reduction (SR) was performed with the administration of ketamine, midazolam, and atropine. All patients with contraindications against HR underwent laparoscopic reduction (LR) without HR.

During 3 years, SR was performed in 43 patients, and in 28 (65.1%), the treatment was successful. Among the 15 patients in whom the procedure failed, 14 underwent LR without intestinal resection. There was no significant risk factor contributing to failed reduction under sedation.

During the second or third HR attempt, successful reduction may be ensured with the SR procedure with intravenous ketamine, midazolam, and atropine; this procedure may further reduce surgery rates in pediatric intussusception.
Percutaneous coronary intervention for congenital absence of the right coronary artery with acute myocardial infarction
Authors: Liu Wei-Chao , Qi Qiang , Geng Wei , Tian Xiang
Published: January 2020

Rationale:

Congenital absence of the right coronary artery with acute myocardial infarction (AMI) is a rare clinical situation that may lead to death. We report a case of successful percutaneous coronary intervention for congenital absence of the right coronary artery with AMI.

Patient concerns:

A 53-year-old woman had a 7-day history of chest discomfort that had worsened over 10 hours. She was diagnosed as having myocardial infarction and was admitted to hospital.

Diagnosis:

Coronary angiography showed absence of the right coronary artery; the left anterior descending (LAD) branch sent out the right ventricular branch and the posterior descending branch. The LAD branch was occluded and there was diffuse stenosis of the middle right ventricular branch and severe stenosis of the distal circumflex branch.

Interventions:

Percutaneous coronary intervention was performed. One stent was implanted in the LAD branch and another implanted in the right ventricular branch.

Outcomes:

The patient was discharged 3 weeks after surgery. The follow-up showed that the patient was asymptomatic without recurrence.

Lessons:

Although absence of the right coronary artery with AMI is a fatal condition, percutaneous coronary intervention remains an effective treatment.
Occipitocervical fusion combined with 3-dimensional navigation and 3-dimensional printing technology for the treatment of atlantoaxial dislocation with basilar invagination
Authors: Yuan Tianyang , Jia Guoliang , Yang Lili , Xu Derui , Zhang Jun , Liu Qinyi
Published: January 2020

Introduction:

Basilar invagination (BI) is a common deformity in the occipitocervical region. The traditional surgical method of BI is direct transoral decompression followed by posterior decompression and fixation. Posterior-only decompression and fixation have achieved good efficacy in the treatment of BI in recent years, but complications are common due to the operation in the upper cervical vertebra and the medulla oblongata region. Moreover, posterior-only occipitocervical fusion combined with an intraoperative 3-dimensional (3D) navigation system is relatively rare, and reports of this procedure combined with 3D printing technology have not been published. We present a case of BI treated with posterior-only occipitocervical fusion combined with 3D printing technology and 3D navigation system to reduce the risk of surgical complications.

Patient Concerns:

A 55-year-old patient with a history of neck pain and numbness of the extremities for 6 years developed a walking disorder for 1 year.

Diagnoses:

Atlantoaxial dislocation with BI.

Interventions:

The patient underwent posterior-only occipitocervical fusion combined with intraoperative 3D navigation system and 3D printing technology.

Outcomes:

The patient's walking disorder was resolved and he was able to walk approximately 100 m by himself when he was allowed to get up and move around with the help of a neck brace. At 6 months postoperatively, the patient reported that the numbness of the limbs was reduced, and he could walk >500 m by himself.

Conclusion:

Occipitocervical fusion is one of the established techniques for the treatment of BI. The biggest advantage of the 2 technologies was that it ensured precise implant placement. The advantages of intraoperative 3D navigation systems are as follows: real-time intraoperative monitoring of the angle and depth of implant placement; the best nailing point can be determined at the time of implantation, rather than according to the operator's previous experience; and the extent of screw insertion is visible to the naked eye, rather than being dependent on the “hand feel” of the surgeon. At the same time, the 3D printing technology can be applied to clarify the relationship between blood vessels and bone around the implant to minimize injury to important structures during implantation.
Effects of lung protective ventilation on postoperative pulmonary outcomes for prolonged oral cancer combined with free flap surgery
Authors: Cheng Chia-Dan , Lin Wei-Lin , Chen Yuan-Wu , Cherng Chen-Hwan
Published: January 2020

The intraoperative lung protective ventilation with low tidal volume, positive end expiratory pressure (PEEP) and intermittent lungs recruitment was found to decrease postoperative pulmonary complications. In this retrospective medical records study, we investigated the effects of lung protective ventilation on postoperative pulmonary outcomes among the patients received prolonged oral cancer combined with free flap surgery.

We collected the medical records of the patients received oral cancer surgery with the operation time more than 12 hours from January 2011 to December 2015. We recorded

Fifty nine cases were included. Thirty cases received the lung protective ventilation and 29 cases received conventional ventilation. Compared to the patients received conventional ventilation, the patients received intraoperative lung protective ventilation showed

In conclusion, for the prolonged oral cancer combined with free flap surgery, the intraoperative lung protective ventilation improves postoperative pulmonary outcomes and decreases the duration of ICU stay.
Nondrug therapies for hypertensive patients complicated with cervical spondylosis
Authors: Wang Xinyi , Ju Jianqing , Xu Hao
Published: January 2020

Purpose:

The aim of this study was to systematically evaluate the efficacy and safety of nondrug therapies for hypertensive patients complicated with cervical spondylosis.

Methods:

Randomized controlled trials (RCTs) concerned with nondrug therapies for hypertensive patients complicated with cervical spondylosis were identified by searching 5 English and Chinese databases. Study selection, data extraction, and risk of bias assessment were conducted independently by 2 authors. RevMan 5.3 software was used for meta-analysis with effect estimate presented as relative risk (RR) and mean difference (MD) with a 95% confidence interval (CI).

Results:

A total of 13 studies involving 929 patients were included. The majority of the included trials were assessed to be of high clinical heterogeneity and high risk of bias. The results of meta-analysis showed that there was a significant improvement in the effectiveness rate of cervical vertebra symptoms (RR = 1.67, 95% CI [1.33, 2.10], P < .0001), effectiveness rate of blood pressure lowering (RR = 1.35, 95% CI [1.06, 1.71], P = .02), systolic blood pressure reduction (MD = −11.05, 95% CI [−14.12, −7.98] mmHg, P < .0001), and diastolic blood pressure reduction (MD = −6.96, 95% CI [−8.89, −5.04] mmHg, P < .00001). Nondrug therapies had no significant difference compared with drugs in the effectiveness rate of overall improvement (RR = 1.3, 95% CI [0.93, 1.82], P = .12). There were no serious adverse effects related to nondrug therapies in the included trials.

Conclusion:

The results show sound advantages of nondrug therapies over conventional medicine or sham procedure in efficacy. However, the evidence remains weak because of the high clinical heterogeneity and high risk of the included trials. Therefore, further thorough investigation, large-scale, proper-designed, randomized trials of nondrug therapies for hypertension complicated with cervical spondylosis are warranted.

Prospero registration number:

CRD2019123175.
Prognostic value of 18F-FET PET/CT in newly diagnosed WHO 2016 high-grade glioma
Authors: Dissaux Gurvan , Basse Victor , Schick Ulrike , EL Kabbaj Osman , Auberger Benjamin , Magro Elsa , Kassoul Aboubakr , Abgral Ronan , Salaun Pierre-Yves , Bourhis David , Querellou Solène
Published: January 2020

O-(2-[18F]fluoroethyl)-l-tyrosine positron-emission tomography/computed tomography (18F-FET PET/CT) is well known in brain tumor management. Our study aimed to identify the prognostic value of 18F-FET PET/CT in high-grade gliomas (HGG) according the current 2016 World Health Organization (WHO) classification.

Patients with histologically proven WHO 2016 HGG were prospectively included. A dynamic 18F-FET PET/CT was performed allowing to obtain 2 static PET frames (static frame 1: 20–40 minutes and static frame 2: 2–22 minutes). We analyzed static parameters (standard uptake value [SUV]max, SUVmean, SUVpeak, TBRmax, TBRmean, tumoral lesion glycolysis, and metabolic tumoral volume) for various isocontours (from 10% to 90%). PET parameters, clinical features, and molecular biomarkers were compared with progression-free survival (PFS) and overall survival (OS) in univariate and multivariate analysis.

Twenty-nine patients were included (grade III n = 3, grade IV n = 26). Mean PFS and OS were, respectively, 8.8 and 13.9 months. According to univariate analysis, SUVmean, SUVpeak, TBRmax, and TBRmean were significantly correlated with OS. In static 1 analysis, TBRmax seemed to be the best OS prognostic parameter (P = .004). In static 2 analysis, TBRmean was the best parameter (P = .01). In static 1 analysis, only SUVpeak was significant (P = .05) for PFS. Good performance status (PS < 2; P < .0001) and extent of resection (P = .019) identified the subgroup of patients with the best OS. Only TBRmax (P = .026) and extent of resection (P = .025) remained significant parameters in multivariate analysis.

Our data suggested that high TBRmax seemed to be the most significant OS independent prognostic factor in patients with newly diagnosed HGG.
Shallow periorbital injection of triamcinolone acetonide in treatment of lower eyelid entropion related to thyroid-associated ophthalmopathy
Authors: Mo Fei , Xu Dongdong , Xu Haiyan , Li Gang , Gao Yizhuo , Li Hui
Published: January 2020

Introduction:

Entropion and secondary trichiasis can lead to irritative symptoms and essential damage of ocular surface. There is no literature reporting the lower eyelid entropion related to thyroid-associated ophthalmopathy (TAO), let alone the treatment. Treatment based on etiology may yield effective and sustained results. We report 3 case reports of lower eyelid entropion associated with TAO, and provide an effective and persistent alternative to cure this entropion via the administration of shallow periorbital injections of triamcinolone acetonide (TA).

Patient concerns:

Three patients presented irritative symptoms of ocular surface and diplopia.

Diagnosis:

According to thyroid dysfunction, physical examination, and imaging findings of extraocular muscle involvement, TAO and unilateral or bilateral lower eyelid entropion were diagnosed.

Interventions:

We administered shallow periorbital injections of TA to the affected eye at 3- to 4-week intervals depending on clinical response.

Outcomes:

All patients underwent complete correction of the lower eyelid entropion and no recurrence was found.

Conclusion:

The cause of lower eyelid entropion related to TAO might be the immunoinflammatory reaction of the lower eyelid retractors, enhancing the traction of pulling the lower eyelid inferoposteriorly. This condition can be treated with shallow periorbital injections of TA. Histopathological evidence and randomized controlled trials are expected to confirm our hypothesis.
Study of the rational dose of propofol in elderly patients under bispectral index monitoring during total intravenous anesthesia
Authors: Jia Lina , Hou Jiachen , Zheng Haibo , Sun Lihua , Fan Yingying , Wang Xu , Hao Mingyue , Li Yue , Yang Tongwei
Published: January 2020

Background:

Propofol has been used widely as an anesthetic for elderly patients; however, the drug instructions only indicate that the need for maintenance of general anesthesia in elderly patients is reduced, and not the extent of the reduction. This study has summarized the usage of propofol in total intravenous anesthesia under bispectral index (BIS) monitoring and determined the optimum dosage of propofol for elderly patients.

Methods:

The study comprised 156 patients undergoing elective surgery under general anesthesia divided into 2 groups according to their age: the elderly group (O group) and nonelderly group (Y group). BIS monitoring was used in both groups during the operation, and propofol and remifentanil were used to maintain anesthesia. The preoperative special conditions, intraoperative maintenance of propofol, remifentanil, fentanyl, cis-atracurium, vasoactive drug use, and hemodynamic changes were summarized.

Results:

Propofol maintenance in the O group was 3.372 ± 0.774 mg/(kg h), which was significantly lesser than that in Y group (P < 0.05). The incidence of cardiovascular and cerebrovascular diseases and the use rate of vasoactive drugs in the O group were significantly higher than in the Y group (P < 0.05).

Conclusion:

Propofol maintenance in the O group was significantly lower than that in the nonelderly group; this indicates that the anesthetic drug delivery rate for elderly patients should be reduced.
Normative values for Glazer Protocol in the evaluation of pelvic floor muscle bioelectrical activity
Authors: Oleksy Łukasz , Wojciechowska Małgorzata , Mika Anna , Antos Elżbieta , Bylina Dorota , Kielnar Renata , Pruszczyński Błażej , Stolarczyk Artur
Published: January 2020

The aim of the study was to evaluate pelvic floor muscle bioelectrical activity in healthy, young, and nulliparous women, and to present normative values for all phases and parameters measured with the Glazer Protocol.

In this study, 96 healthy, young, nulliparous women (age 22–27 years; 168.6 ± 5.1 cm; 57.1 ± 11.8 kg) were tested. The bioelectrical activity of the pelvic floor muscles was collected using an endovaginal electrode with the Glazer Protocol, which included the following series of muscles contractions and relaxations: pre-baseline rest, phasic contractions, tonic contractions, isometric contractions for muscle endurance evaluation, and post-baseline rest.

The following normative values of the bioelectrical signal for all phases of the Glazer Protocol were calculated: mean, minimal, and maximal values, 95% confidence interval, standard deviation, 95% standard deviation confidence interval, variance, coefficient of variation, and standard error of measurement. Average Mean Amplitude (μV) was as follows: pre-baseline rest (6.26 ± 3.33 μV), phasic contractions (49.76 ± 26.44 μV), tonic contractions (37.05 ± 25.99 μV), endurance contraction (16.10 ± 6.68 μV), and post-baseline rest (6.93 ± 3.99 μV).

This study was the first in which normative values for all phases of the Glazer Protocol were reported. This protocol is very often used in electromyography devices as a tool for pelvic floor muscle assessment. Due to the fact that the interpretation of the pelvic floor muscle evaluation is complex and difficult, the authors believe that the normative values proposed in this study allow for comprehensive interpretation of this test (both qualitatively and quantitatively) and provide a reference point for parameters measured in women with different pelvic floor dysfunctions.
Correlation between the caries status of the first permanent molars and the overall DMFT Index
Authors: Pontigo-Loyola América Patricia , Márquez-Corona María de Lourdes , Minaya-Sánchez Mirna , Lucas-Rincón Salvador Eduardo , Casanova-Rosado Juan Fernando , Robles-Minaya José Luis , Casanova-Sarmiento Juan Alejandro , Casanova-Rosado Alejandro José , Mendoza-Rodriguez Martha , Medina-Solís Carlo Eduardo
Published: January 2020

To analyze whether a correlation exists between the caries status (Decayed, Missing and Filled Teeth, DMFT Index) of the first permanent molars (FPMs) and that of the full permanent dentition of Mexican adolescents, and to propose its use in large epidemiological studies of dental caries.

We conducted a cross-sectional study of 1538 adolescents from 12 to 15 years old. Based on a clinical oral examination, we determined the DMFT Indices of their FPMs (FPM-DMFT) and of their full permanent dentition (comprehensive DMFT Index). We explored each FPM to determine whether it was with or without caries, filled, missing or sealed. For our statistical analysis, we used Fisher exact test and Spearman correlation in Stata software.

After examining a total of 6157 FPMs, we found that 56.8% of our sample of adolescents had no caries in their 4 FPMs whereas 4.9% experienced caries in all 4. No significant differences emerged by sex (P > .05); however, by age, the older adolescents experienced greater FPM-DMFT (P < .05). Analysis yielded a correlation of r = 0.8693 between the FPM-DMFT and comprehensive DMFT scores (P < .0001) of participants. The underestimation of caries prevalence (DMFT > 0) was 5.4% (48.6% vs 43.2%), while the DMFT Index was underestimated at 0.34 (1.15 vs 0.81).

The strong correlation between the FPM-DMFT and comprehensive DMFT Indices suggests that overall caries status can be inferred on the basis of FPM caries status. This evidence is useful when conducting large epidemiological studies such as national surveys.
Medicaid Expansion Reduced Emergency Department Visits by Low-income Adults Due to Barriers to Outpatient Care
Authors: Chou Shih-Chuan , Gondi Suhas , Weiner Scott G. , Schuur Jeremiah D. , Sommers Benjamin D.
Published: January 2020

Background:

Prior studies have found conflicting effects of Medicaid expansion on emergency department (ED) utilization but have not studied the reasons patients go to EDs.

Objectives:

Examine the changes in reasons for ED use associated with Medicaid expansion.

Research Design:

Difference-in-difference analysis.

Subjects:

We included sample adults from the 2012 to 2017 National Health Interview Survey who were US citizens and reported a total family income below 138% federal poverty level (n=30,259).

Measures:

We examined changes in the proportion of study subjects reporting: (1) any ED visits; (2) ED visits due to perceived illness severity; (3) office not open; and (4) barriers to outpatient care, comparing expansion and nonexpansion states.

Results:

Overall, 30.6% of low-income adults reported ED use in the past year, of which 74.1% reported illness acuity, 12.4% reported office not open, 9.5% reported access barriers, and 4.0% did not report any reason. Medicaid expansion was not associated with statistically significant changes in overall ED use [−2.2% (95% confidence interval—CI), −5.5% to 1.2%), P=0.21], ED visits due to perceived illness severity [0.5% (95% CI, −2.4% to 3.5%), P=0.73], or office not open [−0.9% (95% CI, −2.3% to 0.5%); P=0.22], but was associated with significant decrease in ED visits due to access barriers [−1.4% (95% CI, −2.6% to −0.2%), P=0.022].

Conclusions:

Medicaid expansion was associated with a decrease in low-income adults who reported outpatient care barriers as reasons for ED visits. There were no significant changes in overall ED utilization, likely because the majority of respondent reported ED use due to concerns with illness severity or outpatient office was closed.
Shared Decision-Making
Authors: Treiger Teresa M.
Published: January 2020

Purpose/Objectives:

Despite improved access to information, many people are neither engaged in their health care nor in the decision-making process. As the hub of care coordination, case managers are perfectly positioned to participate in and support shared decision-making (SDM) efforts. This article addresses SDM from a case management perspective.

The objectives are to

Primary Practice Setting(s):

Applicable to all health care sectors where professional case management is practiced.

Findings/Conclusions:

Communication skill is an essential case management competency. Shared decision-making is a communication process in which a case manager and a client collaborate to make the best health care decisions based on what matters most to the client. Case managers must undertake education and training to become fluent in shared decision-making as a core feature of person-centered, professional practice.

Implications for Professional Case Management Practice:

Professional case managers must understand the concept and principles of shared decision-making as applies in their practice as well as their responsibilities to support care team colleagues using shared decision-making concepts. Organizations should incorporate shared decision-making language in program descriptions, individual performance plans, satisfaction surveys, and department/organization goals.
Systematic Review on the Influencing Factors of Nurses' and Nursing Students' Attitudes Toward Hospice and Palliative Care
Authors: Jeong Sung Hoon , Lee So Jeong , Cho Seul Min , Cho Hyun
Published: January 2020

Identifying the degree of attitudes has a critical effect on the application of hospice and palliative care. However, studies on hospice and palliative care attitudes highlight only statistically significant outcomes and do not propose comprehensive conclusions or generalizations about attitudes. Therefore, we conducted a systematic review to synthesize and appraise articles that analyzed nurses' attitudes regarding palliative care services. After compiling, the finally selected 13 articles indicated that influencing factors on nurses' attitudes were experience in caring for the dying, career or education level, knowledge and education toward hospice and palliative care, religious belief, death (education and anxiety), and age. Most nurses and nursing students displayed positive cognition and attitudes, yet a low level of knowledge. These results show that an introduction of hospice and palliative care education and practical training in nursing curricula is necessary. And such implementation should take place within sanatoriums as well, where attending the terminally ill takes place at all times. Because hospice and palliative care is usually provided by a multidisciplinary team, it is necessary to identify which factors influence each member of the team likewise. It is anticipated this study will become a preliminary basis for such research.
Food Waste, Healthy Diets, and Environmental Sustainability
Authors: Conrad Zach
Published: January 2020

Food is wasted at various points in the US food system, but the greatest amount of food waste occurs at the consumer level. Emerging research now shows a connection between consumer food waste, healthy diets, and environmental impacts, with implications for food security and hunger. In the United States, the average consumer wastes nearly 1 lb of food every day—approximately one-quarter of edible food purchased. Those who consume healthier diets waste more food than people who consume diets that are less healthy. This food waste accounts for vast amounts of wasted cropland, irrigation water, fertilizers, pesticides, and energy, as well as greenhouse gas emissions and other environmental impacts. These inefficiencies can reduce agricultural productivity and undermine efforts to feed an expanding global population and reduce food insecurity in the United States and globally. Nutrition professionals can help move consumers toward healthier diets and reduce food waste simultaneously.
Sclerotherapy With OK-432 for the Treatment of Symptomatic Lymphocele After Lymph Node Dissection
Authors: Uyulmaz Semra , Puippe Gilbert , Büyükakyüz Nilgün , Giovanoli Pietro , Pfammatter Thomas , Lindenblatt Nicole
Published: January 2020

Objective

This study aimed to determine the benefits of sclerotherapy with OK-432 for the treatment of postoperative chronic lymphocele.

Background

Postoperative chronic lymphocele formation is common and accounts for a high postoperative morbidity. Nonsurgical strategies comprise repetitive percutaneous fluid aspiration or percutaneous sclerotherapy. OK-432 has been used to treat congenital lymphatic malformations with several reports of promising results. We hypothesized that it is more beneficial than repetitive percutaneous fluid aspiration for the treatment of symptomatic lymphocele.

Methods

Two cohorts of melanoma patients who developed recurrent lymphocele after lymph node dissection from January 2013 to August 2017 were compared. The first cohort was treated with repetitive percutaneous fluid aspiration (n = 20). The second cohort received OK-432 sclerotherapy (n = 20). Primary end points were overall treatment duration, number of treatment sessions, and the clinical success in both cohorts. Secondary end points were surgical site infection rate, need for additional antibiotic treatment, wound healing disorders, and the need for revision surgery.

Results

Mean overall duration of treatment with sclerotherapy was significantly shorter than with repetitive aspiration (9.4 ± 7.2 vs 47.5 ± 31.9 days, P < 0.01). Mean number of sclerotherapy treatment sessions were 2.5 ± 1.2. Clinical success with OK-432 was 19 of 20, and that with repeated aspiration was 7 of 20 (χ2 = 15.82, P < 0.001). No surgical site infection occurred in the sclerotherapy cohort, which was significantly lower than those treated with repetitive aspiration (P < 0.03). Surgical revision was mandatory in 12 of 20 patients who were treated with repetitive aspiration, and only 1 of 20 patients in the sclerotherapy cohort.

Conclusion

Sclerotherapy with OK-432 for the treatment of postoperative lymphocele is highly beneficial with a significant reduction of morbidity and the overall treatment time compared with repetitive aspiration.
Shewanella polaris sp. nov., a psychrotolerant bacterium isolated from Arctic brown algae
Authors: Cha Qian-Qian , Ren Xue-Bing , Sun Yuan-Yuan , He Xiao-Yan , Su Hai-Nan , Chen Xiu-Lan , Zhang Yu-Zhong , Xie Bin-Bin , Zhao Long-Sheng , Song Xiao-Yan , Zhang Xi-Ying
Published: January 2020

A Gram-stain-negative, facultatively anaerobic, flagellated and rod-shaped bacterium, designated strain SM1901T, was isolated from a brown algal sample collected from Kings Bay, Svalbard, Arctic. Strain SM1901T grew at −4‒30 °C and with 0–7.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed DNA and Tween 80. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SM1901T was affiliated with the genus

Shewanella

, showing the highest sequence similarity to the type strain of

Shewanella litoralis

(97.5%), followed by those of

Shewanella vesiculosa

,

Shewanella livingstonensis

and

Shewanella saliphila

(97.3 % for all three). The major cellular fatty acids were summed feature 3 (C16 : 1
ω7с and/or C16 : 1
ω6с), C16 : 0, C18 : 0, iso-C15 : 0 and C17 : 1
ω8с and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The respiratory quinones were ubiquinones Q-7, Q-8, menaquinones MK-7(H) and MK-8. The genome of strain SM1901T was 4648537 nucleotides long and encoded a variety of cold adaptation related genes, providing clues for better understanding the ecological adaptation mechanisms of polar bacteria. The genomic DNA G+C content of strain SM1901T was 40.5 mol%. Based on the polyphasic evidence presented in this paper, strain SM1901T was considered to represent a novel species, constituting a novel psychrotolerant lineage out of the known SF clade encompassed by polar

Shewanella

species, within the genus

Shewanella

, for which the name Shewanella polaris sp. nov. is proposed. The type strain is SM1901T (=KCTC 72047T=MCCC 1K03585T).
The neoantigen landscape of mycosis fungoides
Authors: Sivanand A , Hennessey D , Iyer A , O’Keefe S , Surmanowicz P , Vaid G , Gniadecki R
Published: January 2020

Background

Mycosis fungoides (MF), the most common type of cutaneous T-cell lymphoma, has a dismal prognosis in advanced stages. Treatments for advanced disease are mostly palliative and MF remains incurable. Although MF is a known immunogenic neoplasm, immunotherapies such as interferons and the immune checkpoint inhibitors yield inconsistent results. Since the number, HLA-binding strength and subclonality of neoantigens are correlated with the therapeutic responses, we aimed here to characterize the landscape of neoantigens in MF.

Methods

We conducted whole exome and whole transcriptome sequencing of 24 MF samples (16 plaque, 8 tumour) from 13 patients. Bioinformatic pipelines (Mutect2, OptiType, MuPeXi) were used forin silicomutation calling, HLA typing, and neoantigen prediction. Phylogenetic analysis was used to subdivide the malignant cell population into stem and clades (subclones). Clonality of neaontigens was determined by matching neoantigens to the stem and clades of the phylogenetic tree of each MF sample.

Results

MF has a high mutational load (median 3217 non synonymous mutations), resulting in a significant number of total neoantigens (median 1309 per sample) and high-affinity neoantigens (median 328). In stage I disease most neoantigens were clonal but with progression to stage II, subclonal neoantigens comprised >50% of the total. There was very little overlap in neoantigens across patients or between different lesions on the same patient, indicating a high degree of genetic heterogeneity.

Conclusions

Analysis of the neoantigen landscape of MF revealed a very high neoantigen load and thus a significant immunogenic potential of this lymphoma. However, neoantigenic heterogeneity and significant subclonality might limit the efficacy of immunotherapy. We hypothesize that neoantigen number and subclonality might be useful biomarkers determining sensitivity to immunotherapeutic strategies.
The Atlas of Inflammation-Resolution (AIR)
Authors: Serhan Charles N. , Gupta Shailendra , Perretti Mauro , Godson Catherine , Brennan Eoin , Li Yongsheng , Soehnlein Oliver , Shimizu Takao , Werz Oliver , Chiurchiù Valerio , Azzi Angelo , Dubourdeau Marc , Gupta Suchi Smita , Schopohl Patrick , Hoch Matti , Gjorgevikj Dragana , Khan Faiz M. , Brauer David , Tripathi Anurag , Cesnulevicius Konstantin , Lescheid David , Schultz Myron , Repsilber Dirk , Kruse Robert , Sala Angelo , Haeggström Jesper Z. , Levy Bruce D. , Filep János G. , Wolkenhauer Olaf
Published: January 2020

Acute inflammation is a protective reaction by the immune system in response to invading pathogens or tissue damage. Ideally, the response should be localized, self-limited, and returning to homeostasis. If not resolved, acute inflammation can result in organ pathologies leading to chronic inflammatory phenotypes. Acute inflammation and inflammation resolution are complex coordinated processes, involving a number of cell types, interacting in space and time. The biomolecular complexity and the fact that several biomedical fields are involved, make a multi and interdisciplinary approach necessary.

This Atlas of Inflammation Resolution (AIR) is a web-based resource capturing the state-of-the-art in acute inflammation and inflammation resolution research. The AIR provides an interface for users to search thousands of interactions, arranged in inter-connected multi-layers of process diagrams, covering a wide range of clinically relevant phenotypes. The AIR serves as an open access knowledgebase, including a gateway to numerous public databases. It is furthermore possible for the user to map experimental data onto the molecular interaction maps of the AIR, providing the basis for bioinformatics analyses and systems biology approaches. By mapping experimental data onto the Atlas, it can be used to elucidate drug action as well as molecular mechanisms underlying different disease phenotypes. For the visualization and exploration of information, the AIR uses the Minerva platform, which is a well-established tool for the presentation of disease maps. The molecular details of the AIR are encoded using international standards.

The Atlas of Inflammation Resolution was created as a freely accessible resource, supporting research and education in the fields of acute inflammation and inflammation resolution. The AIR connects research communities, facilitates clinical decision making, and supports research scientists in the formulation and validation of hypotheses.
Extensive fragmentation and re-organization of gene co-expression patterns underlie the progression of Systemic Lupus Erythematosus
Authors: Ntasis Vasilis F. , Panousis Nikolaos I. , Tektonidou Maria G. , Dermitzakis Emmanouil T. , Boumpas Dimitrios T. , Bertsias George K. , Nikolaou Christoforos
Published: January 2020

Systemic Lupus Erythematosus (SLE) is the prototype of autoimmune diseases, characterized by extensive gene expression perturbations in peripheral blood immune cells. Circumstantial evidence suggests that these perturbations may be due to altered epigenetic profiles and chromatin accessibility but the relationship between transcriptional deregulation and genome organization remains largely unstudied. We developed a genomic approach that leverages patterns of gene coexpression from genome-wide transcriptome profiles in order to identify statistically robust Domains of Co-ordinated gene Expression (DCEs). By implementing this method on gene expression data from a large SLE patient cohort, we identify significant disease-associated alterations in gene co-regulation patterns, which also correlate with the SLE activity status. Low disease activity patient genomes are characterized by extensive fragmentation leading to DCEs of smaller size. High disease activity genomes display excessive spatial redistribution of co-expression domains with expanded and newly-appearing (emerged) DCEs. Fragmentation and redistribution of gene coexpression patterns correlate with SLE-implicated biological pathways and clinically relevant endophenotypes such as kidney involvement. Notably, genes lying at the boundaries of split DCEs of low activity genomes are enriched in the interferon and other SLE susceptibility signatures, suggesting the implication of DCE fragmentation at early disease stages. Interrogation of promoter-enhancer interactions from various immune cell subtypes shows that a significant percentage of nested connections are disrupted by a DCE split or depletion in SLE genomes. Collectively, our results underlining an important role for genome organization in shaping gene expression in SLE, could provide valuable insights into disease pathogenesis and the mechanisms underlying disease flares.

Significance

Although widespread gene expression changes have been reported in Systemic Lupus Erythematosus (SLE), attempts to link gene deregulation with genome structure have been lacking. Through a computational framework for the segmentation of gene expression data, we reveal extensive fragmentation and reorganization of gene co-regulation domains in SLE, that correlates with disease activity states. Gene co-expression domains pertaining to biological functions implicated in SLE such as the interferon pathway, are being disrupted in patients, while others associated to severe manifestations such as nephritis, emerge in previously uncorrelated regions of the genome. Our results support extensive genome re-organization underlying aberrant gene expression in SLE, which could assist in the early detection of disease flares in patients that are in remission.

Graphical Abstract
Structural analysis of Sub16 sedolisin ofTrichophyton rubrumreveals a flexible nature of its pro domain
Authors: Latka Chitra , Bikshapathi Jagga , Aggarwal Priyanka , Bhavesh Neel Sarovar , Chakraborty Rahul , Khan Sabab Hasan , Taneja Bhupesh
Published: January 2020

Trichophyton rubrumis one of the leading causes of superficial skin infections worldwide. It is a keratinolytic fungus specialized in colonization of keratinized tissue of skin, hair and nails for long periods of time. The fungus encodes a wide repertoire of secreted proteases in its genome that not only aid in nutrient acquisition but also establishment of infection on the host. The proteases are synthesized in ‘prepro’ form that requires removal of the prosegment for activation. In order to gain insights into the structural association of the pro domain with the catalytic domain, we investigate the structural features of the pro domain of the secreted sedolisin member Sub16 ofT. rubrum. Our results show that the pro domain of Sub16 may have inherent flexibility in the absence of the associated catalytic domain which is stabilized in complex with catalytic domain. This is the first report of structural investigation on a stand-alone pro domain of sedolisin family of subtilases that will help in design of further structural studies of this protein.
Modeling metabolic variation with single-cell expression data
Authors: Zhang Yuanchao , Kim Man S. , Nguyen Elizabeth , Taylor Deanne M.
Published: January 2020

Cellular metabolism encompasses the biochemical reactions and transportation of various metabolites in cells and their surroundings, which are integrated at all levels of cellular functions. We developed a method to systematically simulate cellular metabolism using single-cell RNA-seq (scRNA-seq) data through constraint-based context specific metabolic modeling. We simulated the NAD+biosynthesis activity in 7 different mouse tissues, and the simulated NAD+biosynthesis flux levels showed significant linear correlation with experimental measurements in previous research. We also show that the simulated NAD+biosynthesis fluxes are reproducible using two additional scRNA-seq datasets.
Phylogenetic signal is associated with the degree of variation in root-to-tip distances
Authors: Vankan Mezzalina , Ho Simon Y.W. , Pardo-Diaz Carolina , Duchêne David A.
Published: January 2020

The phylogenetic information contained in sequence data is partly determined by the overall rate of nucleotide substitution in the genomic region in question. However, phylogenetic signal is affected by various other factors, such as heterogeneity in substitution rates across lineages. These factors might be able to predict the phylogenetic accuracy of any given gene in a data set. We examined the association between the accuracy of phylogenetic inference across genes and several characteristics of branch lengths in phylogenomic data. In a large number of published data sets, we found that the accuracy of phylogenetic inference from genes was consistently associated with their mean statistical branch support and variation in their gene tree root-to-tip distances, but not with tree length and stemminess. Therefore, a signal of constant evolutionary rates across lineages appears to be beneficial for phylogenetic inference. Identifying the causes of variation in root-to-tip lengths in gene trees also offers a potential way forward to increase congruence in the signal across genes and improve estimates of species trees from phylogenomic data sets.
eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs
Authors: Kerimov Nurlan , Hayhurst James D. , Peikova Kateryna , Manning Jonathan R. , Walter Peter , Kolberg Liis , Samoviča Marija , Sakthivel Manoj Pandian , Kuzmin Ivan , Trevanion Stephen J. , Burdett Tony , Jupp Simon , Parkinson Helen , Papatheodorou Irene , Yates Andrew , Zerbino Daniel R. , Alasoo Kaur
Published: January 2020

An increasing number of gene expression quantitative trait locus (eQTL) studies have made summary statistics publicly available, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and colocalisation. However, differences between these datasets, in their variants tested, allele codings, and in the transcriptional features quantified, are a barrier to their widespread use. Consequently, target genes for most GWAS signals have still not been identified. Here, we present the eQTL Catalogue (https://www.ebi.ac.uk/eqtl/), a resource which contains quality controlled, uniformly recomputed QTLs from 21 eQTL studies. We find that for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies, enabling the integrative analysis of these data. Although mostcis-eQTLs were shared between most bulk tissues, the analysis of purified cell types identified a greater diversity of cell-type-specific eQTLs, a subset of which also manifested as novel disease colocalisations. Our summary statistics can be downloaded by FTP, accessed via a REST API, and visualised on the Ensembl genome browser. New datasets will continuously be added to the eQTL Catalogue, enabling the systematic interpretation of human GWAS associations across many cell types and tissues.
Sex ratio and sexual conflict in a collective action problem
Authors: Lindstedt C. , Gerber N. , Kokko H.
Published: January 2020

The maintenance of cooperation is difficult whenever collective action problems are vulnerable to freeriding (reaping the benefits without contributing to the maintenance of the good). We identify a novel factor that can make a system tolerate an extent of freeriding. If a population consists of discrete types with demographically distinct roles, such that the success of one type does not imply it can spread to replace other types in the population, then collective goods may persist in the presence of free-riders because they are necessarily kept in a minority role. Biased sex ratios (e.g. in haplodiploids) create conditions where individuals of one sex are a minority. We show that this can make the less common sex contribute less to a public good in a setting where the relevant life-history stage — larval group defence against predators — does not feature any current breeding opportunities that might lead to confounding reasons behind sex-specific behaviour. We test our model with haplodiploid pine sawfly larvae, showing that female larvae are the main contributors to building the antipredator defence against predators.

Significance statement

Individuals in groups can cooperate to achieve something together, but with an evolutionary difficulty: if benefits of cooperation are shared equally among all, freeriders get the same benefit as others while paying less for it. We propose a novel reason why freeriding does not automatically spread until the collectively beneficial outcome is destroyed: sometimes groups consist of individuals of distinct categories, limiting freerider spread. If, for example, there are always fewer males than females, then even if every male becomes a freerider, the whole group still survives simply because not everyone can be male. Pine sawfly larvae defend against predators by regurgitating sticky fluids, but females contribute more to this common defence, and we show this example fits our model.
Bicc1anddicerregulate left-right patterning through post-transcriptional control of the Nodal-inhibitordand5
Authors: Maerker Markus , Getwan Maike , Dowdle Megan E. , Pelliccia José L. , McSheene Jason C. , Yartseva Valeria , Minegishi Katsura , Vick Philipp , Giraldez Antonio J. , Hamada Hiroshi , Burdine Rebecca D. , Sheets Michael D. , Schweickert Axel , Blum Martin
Published: January 2020

Rotating cilia at the vertebrate left-right organizer (LRO) generate an asymmetric leftward flow, which is sensed by cells at the left LRO margin. How the flow signal is processed and relayed to the laterality-determining Nodal cascade in the left lateral plate mesoderm (LPM) is largely unknown. We previously showed that flow down-regulates mRNA expression of the Nodal inhibitor Dand5 in left sensory cells. De-repression of the co-expressed Nodal drives LPM Nodal cascade induction. Here, we identify the mechanism ofdand5downregulation, finding that its posttranscriptional repression is a central process in symmetry breaking. Specifically, the RNA binding protein Bicc1 interacts with a proximal element in the 3’-UTR ofdand5to repress translation in adicer1-dependent manner. Thebicc1/dicer1module acts downstream of flow, as LRO ciliation was not affected upon its loss. Loss ofbicc1ordicer1was rescued by parallel knockdown ofdand5, placing both genes in the process of flow sensing.