bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlates of Expressed Emotion Among Family Members of Individuals Who Sought Treatment for Opioid Use
Authors: Ellis Jennifer D. , Resko Stella M. , Brown Suzanne , Agius Elizabeth , Kollin Rachel , Burlaka Viktor
Published: August 2020

Expressed emotion has been robustly associated with negative mental health outcomes. Understanding correlates of expressed emotion by family members of individuals with opioid use disorder is important, as this group faces high levels of stress and can play an important role in their loved ones' treatment. Thus, immediate family members of individuals who sought treatment for opioid problems (N = 195) completed a web-based survey that included measures of expressed emotion, self-stigma, social support, and demographic characteristics. Multiple linear regression analyses were conducted to examine correlates of two types of expressed emotion—criticism and emotional overinvolvement. Results indicated that higher self-stigma and lower social support were significantly associated with higher emotional overinvolvement. Higher self-stigma and having experienced debt related to a family member's opioid use were associated with higher criticism. Thus, self-stigma and financial burden may exacerbate likelihood of expressed emotion, whereas social support may buffer against expressed emotion.
Comparison of Clinical Options
Authors: Díaz Desiree A. , Anderson Mindi , Hill Peggy P. , Quelly Susan B. , Clark Kristen , Lynn Melissa
Published: August 2020

Background

Minimal evidence compares nursing student outcomes when replacing clinical hours with manikin-based high-fidelity patient simulation (HFPS) or virtual simulation.

Purpose

The study aims were to compare differences in outcomes: (1) between 2 intervention groups (HFPS or virtual simulation) when replacing 25% of pediatric/obstetrics clinical hours and (2) pass/fail for clinical practice between the intervention groups and a face-to-face clinical group (control).

Methods

A quasi-experimental study was conducted to determine differences in knowledge between intervention groups participating in 6 pediatric/obstetrics simulation scenarios.

Results

No differences in composite knowledge were found between simulation groups (P = .319). There also was no difference in clinical practice pass/fail among the groups.

Conclusions

HFPS and virtual simulation were equally effective in achieving learning goals.
Sexually Transmitted Infections in Pregnancy: A Narrative Review of the Global Research Gaps, Challenges, and Opportunities
Authors: Grant Juliana S. , Chico R. Matthew , Lee Anne CC. , Low Nicola , Medina-Marino Andrew , Molina Rose L. , Morroni Chelsea , Ramogola-Masire Doreen , Stafylis Chrysovalantis , Tang Weiming , Vallely Andrew J. , Wynn Adriane , Yeganeh Nava , Klausner Jeffrey D.
Published: August 2020

Background

Sexually transmitted infections (STI), such as chlamydial, gonorrheal, and trichomonal infections, are prevalent in pregnant women in many countries and are widely reported to be associated with increased risk of poor maternal and neonatal outcomes. Syndromic STI management is frequently used in pregnant women in low- and middle-income countries, yet its low specificity and sensitivity lead to both overtreatment and undertreatment. Etiologic screening for chlamydial, gonorrheal, and/or trichomonal infection in all pregnant women combined with targeted treatment might be an effective intervention. However, the evidence base is insufficient to support the development of global recommendations. We aimed to describe key considerations and knowledge gaps regarding chlamydial, gonorrheal, and trichomonal screening during pregnancy to inform future research needed for developing guidelines for low- and middle-income countries.

Methods

We conducted a narrative review based on PubMed and clinical trials registry searches through January 20, 2020, guidelines review, and expert opinion. We summarized our findings using the frameworks adopted by the World Health Organization for guideline development.

Results

Adverse maternal-child health outcomes of potential interest are wide-ranging and variably defined. No completed randomized controlled trials on etiologic screening and targeted treatment were identified. Evidence from observational studies was limited, and trials of presumptive STI treatment have shown mixed results. Subgroups that might benefit from specific recommendations were identified. Evidence on harms was limited. Cost-effectiveness was influenced by STI prevalence and availability of testing infrastructure and high-accuracy/low-cost tests. Preliminary data suggested high patient acceptability.

Discussion

Preliminary data on harms, acceptability, and feasibility and the availability of emerging test technologies suggest that etiologic STI screening deserves further evaluation as a potential tool to improve maternal and neonatal health outcomes worldwide.
Association Between Physicians’ Workload and Prescribing Quality in One Tertiary Hospital in China
Authors: Guan Xiaodong , Ni Bingyu , Zhang Jingyuan , Zhu Dawei , Cai Zheng , Meng Wenshuang , Shi Luwen , Ross-Degnan Dennis
Published: August 2020

Background

Alarming increasing trends in physician workload have attracted much attention in recent years. Heavy workload may compromise the quality of medication use. Previous studies have identified a series of factors contributing to inappropriate prescribing; however, there is no demonstrated evidence supporting an association between workload and the appropriateness of physicians’ prescriptions in China. This study aimed to investigate the relationship between physician workload and prescription quality in a tertiary hospital in Beijing, China.

Methods

Our study was a single-center, retrospective study, with all outpatient electronic health records extracted from hospital information system of a tertiary hospital in Beijing from July 1 to November 30, 2015. We used outpatient volume in each 5-hour shift as the measure of physician workload. The evaluation of prescribing quality was based on the Rational Drug Use System. Generalized linear models with a γ distribution and a log link were used to explore factors associated with inappropriate prescribing, and we undertook a series of robustness tests with respect to different exclusion criteria.

Results

A total of 457,784 prescriptions from 502 physicians were included in the study. Physicians had an average workload of 34.3 (±19.8) patients per shift, and the mean rate of inappropriate prescribing per shift was 14.1% (±14.6%). Higher rates of inappropriate prescribing were associated with heavier workloads (P < 0.001). Physicians who worked in the afternoon, chief physicians, those working in surgical department, males, and those with more than 20-year experience had higher rates of inappropriate prescribing with increasing workload.

Conclusions

Heavier workload was associated with higher risk of prescribing inappropriately. It requires great efforts to determine optimal physician workloads and mitigate the potential adverse effects on the prescription quality.
Clinical characteristics, risk factors, and incidence of symptomatic coronavirus disease 2019 in a large cohort of adults living with HIV: a single-center, prospective observational study
Authors: Inciarte Alexy , Gonzalez-Cordon Ana , Rojas Jhon , Torres Berta , de Lazzari Elisa , de la Mora Lorena , Martinez-Rebollar Maria , Laguno Montserrat , Callau Pilar , Gonzalez-Navarro Azucena , Leal Lorna , Garcia Felipe , Mallolas Josep , Mosquera Mar , Marcos Maria A. , Ambrosioni Juan , Miro Josep M. , Martinez Esteban , Blanco Jose L.
Published: August 2020

Background:

It is unclear how characteristics, risk factors, and incidence of coronavirus disease 2019 (COVID-19) in people living with HIV (PLWH) differ from the general population.

Methods:

Prospective observational single-center cohort study of adult PLWH reporting symptoms of COVID-19. We assessed clinical characteristics, risk factors for COVID-19 diagnosis and severity, and standardized incidence rate ratio for COVID-19 cases in PLWH cohort and in Barcelona.

Results:

From 1 March 2020 to 10 May 2020, 53 out of 5683 (0.9% confidence interval 0.7–1.2%) PLWH were diagnosed with COVID-19. Median age was 44 years, CD4+ T cells were 618/μl and CD4+/CD8+ was 0.90. All but two individuals were virologically suppressed. Cough (87%) and fever (82%) were the most common symptoms. Twenty-six (49%) were admitted, six (14%) had severe disease, four (8%) required ICU admission, and two (4%) died. Several laboratory markers (lower O2 saturation and platelets, and higher leukocytes, creatinine, lactate dehydrogenase, C reactive protein, procalcitonin, and ferritin) were associated with COVID-19 severity. No HIV or antiretroviral-related factors were associated with COVID-19 diagnosis or severity. Standardized incidence rate ratios of confirmed or confirmed/probable COVID-19 in PLWH were 38% (95% confidence interval 27–52%, P < 0.0001) and 33% (95% confidence interval 21–50%, P < 0.0001), respectively relative to the general population.

Conclusion:

PLWH with COVID-19 did not differ from the rest of the HIV cohort. Clinical presentation, severity rate, and mortality were not dependent on any HIV-related or antiretroviral-related factor. COVID-19 standardized incidence rate was lower in PLWH than in the general population. These findings should be confirmed in larger multicenter cohort studies.
Inflammation, cytomegalovirus and the growth hormone axis in HIV-exposed uninfected Zimbabwean infants
Authors: Evans Ceri , Chasekwa Bernard , Rukobo Sandra , Govha Margaret , Mutasa Kuda , Ntozini Robert , Humphrey Jean H. , Prendergast Andrew J.
Published: August 2020

Objectives:

Despite avoiding HIV infection, HIV-exposed uninfected (HEU) infants have poorer clinical outcomes than HIV-unexposed infants, including impaired growth. The growth hormone (GH) axis is an important regulator of infant growth through hepatic synthesis of insulin-like growth-factor-1 (IGF-1), and may be disrupted by chronic inflammation and acute infections, including cytomegalovirus (CMV). We tested the hypothesis that these factors lead to disruption of the GH axis in HEU infants, which might contribute to their impaired growth.

Design:

Substudy of 343 infants from the ZVITAMBO trial in Harare, Zimbabwe.

Methods:

IGF-1, growth parameters, C-reactive protein (CRP) and CMV viraemia were evaluated in 243 HEU infants and 100 HIV-unexposed infants. Univariable linear and logistic regression models were used to determine associations between IGF-1 and growth parameters, CRP and CMV.

Results:

Mean 6-week IGF-1 was significantly lower in HEU compared with HIV-unexposed infants (29.6 vs. 32.6 ng/ml; P = 0.014), and associated with subsequent linear and ponderal growth through 6 months of age. CRP was inversely correlated with IGF-1 in all infants regardless of HIV exposure status (β = −0.84; P = 0.03). CMV viral loads were inversely correlated with IGF-1 in HEU (β = −1.16; P = 0.008) but not HIV-unexposed (β = 0.21; P = 0.83) infants.

Conclusion:

Overall, we found evidence for greater disruption of the GH axis in HEU compared with HIV-unexposed infants as early as 6 weeks of age, suggesting a role for reduced IGF-1 in mediating growth impairment in HEU infants. Inflammation and coinfections may be drivers of growth impairment in HEU infants by disrupting the GH axis.
Liver steatosis and nonalcoholic fatty liver disease with fibrosis are predictors of frailty in people living with HIV
Authors: Milic Jovana , Menozzi Valentina , Schepis Filippo , Malagoli Andrea , Besutti Giulia , Franconi Iacopo , Raimondi Alessandro , Carli Federica , Mussini Cristina , Sebastiani Giada , Guaraldi Giovanni
Published: August 2020

Objective:

The aim was to investigate the contribution of liver steatosis and significant fibrosis alone and in association [nonalcoholic fatty liver disease (NAFLD) with fibrosis] to frailty as a measure of biological age in people living with HIV (PLWH).

Design:

This was a cross-sectional study of consecutive patients attending Modena HIV Metabolic Clinic in 2018–2019.

Methods:

Patients with hazardous alcohol intake and viral hepatitis coinfection were excluded. Liver steatosis was diagnosed by controlled attenuation parameter (CAP), while liver fibrosis was diagnosed by liver stiffness measurement (LSM). NAFLD was defined as presence of liver steatosis (CAP ≥248 dB/m), while significant liver fibrosis or cirrhosis (stage ≥F2) as LSM at least 7.1 kPa. Frailty was assessed using a 36-Item frailty index. Logistic regression was used to explore predictors of frailty using steatosis and fibrosis as covariates.

Results:

We analysed 707 PLWH (mean age 53.5 years, 76.2% men, median CD4+cell count 700 cells/μl, 98.7% with undetectable HIV RNA). NAFLD with fibrosis was present in 10.2%; 18.9 and 3.9% of patients were classified as frail and most-frail, respectively. Univariate analysis demonstrated that neurocognitive impairment [odds ratio (OR) = 5.1, 1.6–15], vitamin D insufficiency (OR = 1.94, 1.2–3.2), obesity (OR = 8.1, 4.4–14.6), diabetes (OR = 3.2, 1.9–5.6), metabolic syndrome (OR = 2.41, 1.47–3.95) and osteoporosis (OR = 0.37, 0.16–0.76) were significantly associated with NAFLD with fibrosis. Predictors of frailty index included steatosis (OR = 2.1, 1.3–3.5), fibrosis (OR = 2, 1–3.7), NAFLD with fibrosis (OR = 9.2, 5.2–16.8), diabetes (OR = 1.7, 1–2.7) and multimorbidity (OR = 2.5, 1.5–4).

Conclusion:

Liver steatosis and NAFLD with fibrosis were associated with frailty. NAFLD with fibrosis exceeded multimorbidity in the prediction of frailty, suggesting the former as an indicator of metabolic age in PLWH.
The effect of universal testing and treatment on HIV stigma in 21 communities in Zambia and South Africa
Authors: Stangl Anne L. , Pliakas Triantafyllos , Mainga Tila , Steinhaus Mara , Mubekapi-Musadaidzwa Constance , Viljoen Lario , Dunbar Rory , Schaap Ab , Floyd Sian , Mandla Nomtha , Bond Virginia , Hoddinott Graeme , Fidler Sarah , Hayes Richard , Ayles Helen , Bock Peter , Donnell Deborah , Hargreaves James R.
Published: August 2020

Objectives:

To assess the impact of a combination HIV prevention intervention including universal testing and treatment (UTT) on HIV stigma among people living with HIV, and among community members and health workers not living with HIV.

Design:

This HIV stigma study was nested in the HPTN 071 (PopART) trial, a three-arm cluster randomised trial conducted between 2013 and 2018 in 21 urban/peri-urban communities (12 in Zambia and nine in South Africa).

Methods:

Using an adjusted two-stage cluster-level analysis, controlling for baseline imbalances, we compared multiple domains of stigma between the trial arms at 36 months. Different domains of stigma were measured among three cohorts recruited across all study communities: 4178 randomly sampled adults aged 18–44 who were living with HIV, and 3487 randomly sampled adults and 1224 health workers who did not self-report living with HIV.

Results:

Prevalence of any stigma reported by people living with HIV at 36 months was 20.2% in arm A, 26.1% in arm B, and 19.1% in arm C (adjusted prevalence ratio, A vs. C 1.01 95% CI 0.49–2.08, B vs. C 1.34 95% CI 0.65–2.75). There were no significant differences between arms in any other measures of stigma across all three cohorts. All measures of stigma reduced over time (0.2--4.1% reduction between rounds) with most reductions statistically significant.

Conclusion:

We found little evidence that UTT either increased or decreased HIV stigma measured among people living with HIV, or among community members or health workers not living with HIV. Stigma reduced over time, but slowly.

ClinicalTrials.gov number:

NCT01900977.
Acquired Thoracic Fistulas
Authors: Layyous Nadera , Yen Andrew , Chaturvedi Abhishek , Okamoto Kanenori , Padwal Jennifer A. , Abraham Peter , Brouha Sharon S.
Published: August 2020

Fistulas are abnormal connections between 2 epithelial-lined structures. Thoracic fistulas may result from nonanatomic communications between spaces within the thorax, such as the lung, tracheobronchial tree, pleural space, and mediastinal structures, or between thoracic spaces and extrathoracic structures, such as the gastrointestinal tract. Furthermore, thoracic fistulas may result in communication between thoracic spaces and the spine or vascular structures. Potential causes include trauma, infection, neoplasm, surgical intervention, or medical syndromes. In this article, we discuss various acquired thoracic fistulas and their potential causes, key multimodality imaging manifestations, and clinical significance.
The Effects of Adipose Derived Stromal Vascular Fraction and Platelet-Rich Plasma on Bone Healing of a Rat Model With Chronic Kidney Disease
Authors: Eyuboglu Atilla Adnan , Arpaci Enver , Albayati Abbas , Uysal Ahmet Cagri , Terzi Aysen , Bozalioglu Sema , Turnaoglu Hale , Balcik Cenk , Ozkan Burak , Ertas Nilgun Markal
Published: August 2020

Background

Chronic kidney disease (CKD) impairs osteoblast/osteoclast balance and damages bone structure with diminished mineralization and results in bone restoration disorders. In this study, we investigate the effects of adipose-derived stromal vascular fraction and platelet-rich plasma (PRP) on bone healing model in rats with CKD.

Methods

Sprague-Dawley rats were separated into 4 groups. All groups except group I (healthy control) had CKD surgery using 5/6 nephrectomy model. All groups had intramedullary pin fixation after receiving bone fracture using drilling tools. Group II rats were used as control group for CKD. Group III rats received PRP treatment on fracture site. Group IV rats received PRP and stromal vascular fraction treatment on fracture site.

Weight loss and blood samples were followed at the time of kidney surgery, third, sixth, and 12th weeks. Bone healing and callus formations were compared, biomechanically, radiologically, histopathologically, and immunohistochemically. Osteoblastic transformation of stem cells was assessed with DiI staining.

Results

Negative effects of CKD on bone healing were reduced by increasing mechanical, histological, radiological, and biochemical properties of the bone with stromal vascular fraction and PRP treatments. Although thickness of callus tissue delayed bone healing process, it also enhanced biomechanical features and bone tissue organization.

Conclusions

Platelet-rich plasma and adipose-derived stromal vascular fraction treatments were effective for bone healing in animal model, which can be promising for clinical trials.
Outcomes of Robotic Living Donor Right Hepatectomy From 52 Consecutive Cases
Authors: Rho Seoung Yoon , Lee Jae Geun , Joo Dong Jin , Kim Myoung Soo , Kim Soon Il , Han Dai Hoon , Choi Jin Sub , Choi Gi Hong
Published: August 2020

Objective:

To investigate the feasibility and safety of RLDRH

Summary of Background Data:

Data for minimally invasive living-donor right hepatectomy, especially RLDRH, from a relatively large donor cohort that have not been reported yet.

Methods:

From March 2016 to March 2019, 52 liver donors underwent RLDRH. The clinical and perioperative outcomes of RLDRH were compared with those of CODRH (n = 62) and LADRH (n = 118). Donor satisfaction with cosmetic results was compared between RLDRH and LADRH using a body image questionnaire.

Results:

Although RLDRH was associated with longer operative time (minutes) (RLDRH, 493.6; CODRH, 404.4; LADRH, 355.9; P < 0.001), mean estimated blood loss (mL) was significantly lower (RLDRH, 109.8; CODRH, 287.1; LADRH, 265.5; P = 0.001). Postoperative complication rates were similar among the 3 groups (RLDRH, 23.1%; CODRH, 35.5%; LADRH, 28.0%; P = 0.420). Regarding donor satisfaction, body image and cosmetic appearance scores were significantly higher in RLDRH than in LADRH. After propensity score matching, RLDRH showed less estimated blood loss compared to those of CODRH (RLDRH, 114.7 mL; CODRH, 318.4 mL; P < 0.001), but complication rates were similar among the three groups (P = 0.748).

Conclusions:

RLDRH resulted in less blood loss compared with that of CODRH and similar postoperative complication rates to CODRH and LADRH. RLDRH provided better body image and cosmetic results compared with those of LADRH. RLDRH is feasible and safe when performed by surgeons experienced with both robotic and open hepatectomy.
Plasma resuscitation with adjunctive peritoneal resuscitation reduces ischemic intestinal injury following hemorrhagic shock
Authors: Schucht Jessica E. , Matheson Paul J. , Harbrecht Brian G. , Bond Logan , Jones Shawn , Alkhateeb Khaled J. M. , Ashkettle Graham R. , Smith Jason W.
Published: August 2020

INTRODUCTION

Impaired intestinal microvascular perfusion following resuscitated hemorrhagic shock (HS) leads to ischemia-reperfusion injury, microvascular dysfunction, and intestinal epithelial injury, which contribute to the development of multiple organ dysfunction syndrome in some trauma patients. Restoration of central hemodynamics with traditional methods alone often fails to fully restore microvascular perfusion and does not protect against ischemia-reperfusion injury. We hypothesized that resuscitation (RES) with fresh frozen plasma (FFP) alone or combined with direct peritoneal resuscitation (DPR) with 2.5% Delflex solution might improve blood flow and decrease intestinal injury compared with conventional RES or RES with DPR alone.

METHODS

Sprague-Dawley rats underwent HS (40% mean arterial pressure) for 60 minutes and were randomly assigned to a RES group (n = 8): sham, HS–crystalloid resuscitation (CR) (shed blood + two volumes CR), HS-CR-DPR (intraperitoneal 2.5% peritoneal dialysis fluid), HS-FFP (shed blood + two volumes FFP), and HS-DPR-FFP (intraperitoneal dialysis fluid + two volumes FFP). Laser Doppler flowmeter evaluation of the ileum, serum samples for fatty acid binding protein enzyme-linked immunosorbent assay, and hematoxylin and eosin (H&E) staining were used to assess intestinal injury and blood flow. p Values of <0.05 were considered significant.

RESULTS

Following HS, the addition of DPR to either RES modality improved intestinal blood flow. Four hours after resuscitated HS, FABP-2 (intestinal) and FABP-6 (ileal) were elevated in the CR group but reduced in the FFP and DPR groups. The H&E staining demonstrated disrupted intestinal villi in the FFP and CR groups, most significantly in the CR group. Combination therapy with FFP and DPR demonstrated negligible cellular injury in H&E graded samples and a significant reduction in fatty acid binding protein levels.

CONCLUSION

Hemorrhagic shock leads to ischemic-reperfusion injury of the intestine, and both FFP and DPR alone attenuated intestinal damage; combination FFP-DPR therapy alleviated most signs of organ injury. Resuscitation with FFP-DPR to restore intestinal blood flow following shock could be an essential method of reducing morbidity and mortality after trauma.
Stop flailing: The impact of bicortically displaced rib fractures on pulmonary outcomes in patients with chest trauma — an American Association for the Surgery of Trauma multi-institutional study
Authors: Senekjian Lara , Birkas Yekaterina , Buhavac Milos , Dayal Saraswati , Mukherjee Kaushik , Nygaard Rachel , Pierce Sean , Buaza Graciella , Sperry Jason , Eriksson Evert , Leon Stuart M. , Kopelman Tammy , Spadafore Philomene , Kopatsis Anthony , Moore Forrest , Taylor Annette , Colonna Alexander , Enniss Toby , McCrum Marta , Nunez Jade , Young Jason , Nirula Raminder
Published: August 2020

BACKGROUND

Current evaluation of rib fractures focuses almost exclusively on flail chest with little attention on bicortically displaced fractures. Chest trauma that is severe enough to cause fractures leads to worse outcomes. An association between bicortically displaced rib fractures and pulmonary outcomes would potentially change patient care in the setting of trauma. We tested the hypothesis that bicortically displaced fractures were an important clinical marker for pulmonary outcomes in patients with nonflail rib fractures.

METHODS

This nine-center American Association for the Surgery of Trauma multi-institutional study analyzed adults with two or more rib fractures. Admission computerized tomography scans were independently reviewed. The location, degree of rib fractures, and pulmonary contusions were categorized. Univariate and multivariate logistic regression analyses were performed to identify independent predictors of pneumonia, acute respiratory distress syndrome (ARDS), and tracheostomy. Analyses were performed in nonflail patients and also while controlling for flail chest to determine if bicortically displaced fractures were independently associated with outcomes.

RESULTS

Of the 1,110 patients, 103 (9.3%) developed pneumonia, 78 (7.0%) required tracheostomy, and 30 (2.7%) developed ARDS. Bicortically displaced fractures were present in 277 (25%) of patients and in 206 (20.3%) of patients without flail chest. After adjusting for patient demographics, injury, and admission physiology, negative pulmonary outcomes occurred over twice as frequently in those with bicortically displaced fractures without flail chest (n = 206) when compared with those without bicortically displaced fractures—pneumonia (odds ratio [OR], 2.0; 95% confidence interval [CI], 1.1–3.6), ARDS (OR, 2.6; 95% CI, 1.0–6.8), and tracheostomy (OR, 2.7; 95% CI, 1.4–5.2). When adjusting for the presence of flail chest, bicortically displaced fractures remained an independent predictor of pneumonia, tracheostomy, and ARDS.

CONCLUSION

Patients with bicortically displaced rib fractures are more likely to develop pneumonia, ARDS, and need for tracheostomy even when controlling for flail chest. Future studies should investigate the utility of flail chest management algorithms in patients with bicortically displaced fractures.

LEVEL OF EVIDENCE

Prognostic and epidemiological study, level III.
Molecular docking, dynamics and free energy analyses of Acinetobacter baumannii OXA class enzymes with carbapenems investigating their hydrolytic mechanisms
Authors: Ramachandran Balajee , Jeyakanthan Jeyaraman , Lopes Bruno S.
Published: August 2020

Introduction.

Acinetobacter baumannii

is a critical priority pathogen listed by the World Health Organization due to increasing levels of resistance to carbapenem classes of antibiotics. It causes wound and other nosocomial infections, which can be life-threatening. Hence, there is an urgent need for the development of new classes of antibiotics.

Aim. To study the interaction of carabapenems with class D beta-lactamases (oxacillinases) and analyse drug resistance by studying enzyme–substrate complexes using modelling approaches as a means of establishing correlations with the phenotypic data.

Methodology. The three-dimensional structures of carbapenems (doripenem, ertapenem, imipenem and meropenem) were obtained from DrugBank and screened against class D beta-lactamases. Further, the study was extended with their variants. The variants’ structure was homology-modelled using the Schrödinger Prime module (Schrödinger LLC, NY, USA).

Results. The first discovered intrinsic beta-lactamase of

Acinetobacter baumannii

, OXA-51, had a binding energy value of −40.984 kcal mol−1, whereas other OXA-51 variants, such as OXA-64, OXA-110 and OXA-111, have values of −60.638, –66.756 and −67.751 kcal mol−1, respectively. The free energy values of OXA-51 variants produced better results than those of other groups.

Conclusions. Imipenem and meropenem showed MIC values of 2 and 8 µg ml−1, respectively against OXA-51 in earlier studies, indicating that these are the most effective drugs for treatment of

A. baumannii

infection. According to our results, OXA-51 is an active enzyme that shows better interactions and is capable of hydrolyzing carbapenems. When correlating the hydrogen-bonding interaction with MIC values, the predicted results are in good agreement and might provide initial insights into performing similar studies related to OXA variants or other antibiotic–enzyme-based studies.
Diversification in immunogenicity genes caused by selective pressures in invasive meningococci
Authors: Kremer Philip H.C. , Lees John A. , Ferwerda Bart , Bijlsma Merijn W. , MacAlasdair Neil , van der Ende Arie , Brouwer Matthijs C. , Bentley Stephen D. , van de Beek Diederik
Published: August 2020

We studied population genomics of 486

Neisseria meningitidis

isolates causing meningitis in the Netherlands during the period 1979–2003 and 2006–2013 using whole-genome sequencing to evaluate the impact of a hyperendemic period of serogroup B invasive disease. The majority of serogroup B isolates belonged to ST-41/44 (41 %) and ST-32 complex (16 %). Comparing the time periods, before and after the decline of serogroup B invasive disease, there was a decrease of ST-41/44 complex sequences (P=0.002). We observed the expansion of a sub-lineage within ST-41/44 complex sequences being associated with isolation from the 1979–2003 time period (P=0.014). Isolates belonging to this sub-lineage expansion within ST-41/44 complex were marked by four antigen allele variants. Presence of these allele variants was associated with isolation from the 1979–2003 time period after correction for multiple testing (Wald test, P=0.0043 for FetA 1–5; P=0.0035 for FHbp 14; P=0.012 for PorA 7–2.4 and P=0.0031 for NHBA two peptide allele). These sequences were associated with 4CMenB vaccine coverage (Fisher’s exact test, P<0.001). Outside of the sub-lineage expansion, isolates with markedly lower levels of predicted vaccine coverage clustered in phylogenetic groups showing a trend towards isolation in the 2006–2013 time period (P=0.08). In conclusion, we show the emergence and decline of a sub-lineage expansion within ST-41/44 complex isolates concurrent with a hyperendemic period in meningococcal meningitis. The expansion was marked by specific antigen peptide allele combinations. We observed preliminary evidence for decreasing 4CMenB vaccine coverage in the post-hyperendemic period.
A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-based Multiple Sequence Alignment
Authors: Roe David , Vierra-Green Cynthia , Pyo Chul-Woo , Geraghty Daniel E. , Spellman Stephen R. , Maiers Martin , Kuang Rui
Published: August 2020

Human chromosome 19q13.4 contains genes encoding killer-cell immunoglobulin-like receptors (KIR). Reported haplotype lengths range from 67 to 269 kilobases and contain 4 to 18 genes. The region has certain properties such as single nucleotide variation, structural variation, homology, and repetitive elements that make it hard to align accurately beyond single gene alleles. To the best of our knowledge, a multiple sequence alignment of KIR haplotypes has never been published or presented. Such an alignment would be useful to precisely define KIR haplotypes and loci, provide context for assigning alleles (especially fusion alleles) to genes, infer evolutionary history, impute alleles, interpret and predict co-expression, and generate markers. In order to extend the framework of KIR haplotype sequences in the human genome reference, 27 new sequences were generated including 24 haplotypes from 12 individuals of African American ancestry that were selected for genotypic diversity and novelty to the reference, to bring the total to 68 full length genomic KIR haplotype sequences. We leveraged these data and tools from our long-read KIR haplotype assembly algorithm to define and align KIR haplotypes at <5 kb resolution on average. We then used a standard alignment algorithm to refine that alignment down to single base resolution. This processing demonstrated that the high-level alignment recapitulates human-curated annotation of the human haplotypes as well as a chimpanzee haplotype. Further, assignments and alignments of gene alleles were consistent with their human curation in haplotype and allele databases. These results define KIR haplotypes as 14 loci containing 9 genes. The multiple sequence alignments have been applied in two software packages as probes to capture and annotate KIR haplotypes and as markers to genotype KIR from WGS.
Ig-VAE: Generative Modeling of Protein Structure by Direct 3D Coordinate Generation
Authors: Eguchi Raphael R. , Choe Christian A. , Huang Po-Ssu
Published: August 2020

Abstract

While deep learning models have seen increasing applications in protein science, few have been implemented for protein backbone generation—an important task in structure-based problems such as active site and interface design. We present a new approach to building class-specific backbones, using a variational auto-encoder to directly generate the 3D coordinates of immunoglobulins. Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools. We show that the Ig-VAE can be used to create a computational model of a SARS-CoV2-RBD binder via latent space sampling. We further demonstrate that the model’s generative prior is a powerful tool for guiding computational protein design, motivating a new paradigm under which backbone design is solved as constrained optimization problem in the latent space of a generative model.
The inner membrane protein YhdP modulates the rate of anterograde phospholipid flow inEscherichia coli
Authors: Grimm Jacqueline , Shi Handuo , Wang Wei , Mitchell Angela M. , Wingreen Ned S. , Huang Kerwyn Casey , Silhavy Thomas J.
Published: August 2020

The outer membrane (OM) of Gram-negative bacteria is a selective permeability barrier that allows uptake of nutrients while simultaneously protecting the cell from harmful compounds. The basic pathways and molecular machinery responsible for transporting lipopolysaccharides (LPS), lipoproteins, and β-barrel proteins to the OM have been identified, but very little is known about phospholipid (PL) transport. To identify genes capable of affecting PL transport, we screened for genetic interactions withmlaA*, a mutant in which anterograde PL transport causes the inner membrane (IM) to shrink and eventually rupture; characterization ofmlaA*-mediated lysis suggested that PL transport can occur via a high-flux, diffusive flow mechanism. We found that YhdP, an IM protein involved in maintaining the OM permeability barrier, modulates the rate of PL transport duringmlaA*-mediated lysis. Deletion ofyhdPfrommlaA* reduced the rate of IM transport to the OM by 50%, slowing shrinkage of the IM and delaying lysis. As a result, the weakened OM of ΔydhPcells was further compromised and ruptured before the IM duringmlaA*-mediated death. These findings demonstrate the existence of a high-flux, diffusive pathway for PL flow inEscherichia colithat is modulated by YhdP.

Significance Statement

The outer membrane (OM) of Gram-negative bacteria serves as a barrier that protects cells from harmful chemical compounds, including many antibiotics. Understanding how bacteria build this barrier is an important step in engineering strategies to circumvent it. A long-standing mystery in the field is how phospholipids (PLs) are transported from the inner membrane (IM) to the OM. We previously discovered that a mutation in the genemlaAcauses rapid flow of PLs to the OM, eventually resulting in IM rupture. Here, we found that deletion of the geneyhdPdelayed cell death in themlaAmutant by slowing flow of PLs to the OM. These findings reveal a high-flux, diffusive pathway for PL transport in Gram-negative bacteria modulated by YhdP.
Evaluation of Alginate-Based Bioinks for 3D Bioprinting, Mesenchymal Stromal Cell Osteogenesis, and Application for Patient-Specific Bone Grafts
Authors: Gonzalez-Fernandez Tomas , Tenorio Alejandro J. , Campbell Kevin T. , Silva Eduardo A. , Leach J. Kent
Published: August 2020

To realize the promise of 3D bioprinting, it is imperative to develop bioinks that possess the biological and rheological characteristics needed for the printing of cell-laden tissue grafts. Alginate is widely used as a bioink because its rheological properties can be modified through pre-crosslinking or the addition of thickening agents to increase printing resolution. However, modification of alginate’s physicochemical characteristics using common crosslinking agents can affect its cytocompatibility. Therefore, we evaluated the printability, physicochemical properties, and osteogenic potential of four common alginate bioinks: alginate-CaCl2(alg-CaCl2), alginate-CaSO4(alg-CaSO4), alginate-gelatin (alg-gel) and alginate-nanocellulose (alg-ncel) for the 3D bioprinting of patient-specific osteogenic grafts. While all bioinks possessed similar viscosity, printing fidelity was lower in the pre-crosslinked bioinks. When used to print geometrically defined constructs, alg-CaSO4and alg-ncel exhibited higher mechanical properties and lower mesh size than those printed with alg-CaCl2or alg-gel. The physical properties of these constructs affected the biological performance of encapsulated bone marrow-derived mesenchymal stromal cells (MSCs). Cell-laden constructs printed using alg-CaSO4and alg-ncel exhibited greater cell apoptosis and contained fewer living cells 7 days post-printing. In addition, effective cell-matrix interactions were only observed in alg-CaCl2printed constructs. When cultured in osteogenic media, MSCs in alg-CaCl2constructs exhibited increased osteogenic differentiation compared to the other three bioinks. This bioink was then used to 3D print anatomically accurate cell-laden scaphoid bones that were capable of partial mineralization after 14 days ofin vitroculture. These results highlight the importance of bioink properties to modulate cell behavior and the biofabrication of clinically relevant bone tissues.
An AI-powered blood test to detect cancer using nanoDSF
Authors: Tsvetkov Philipp O. , Eyraud Rémi , Ayache Stéphane , Bougaev Anton A. , Malesinski Soazig , Benazha Hamed , Gorokhova Svetlana , Buffat Christophe , Dehais Caroline , Sanson Marc , Bielle Franck , Figarella-Branger Dominique , Chinot Olivier , Tabouret Emeline , Devred François
Published: August 2020

We describe a novel cancer diagnostic method based on plasma denaturation profiles obtained by a non-conventional use of Differential Scanning Fluorimetry. We show that 84 glioma patients and 63 healthy controls can be automatically classified using denaturation profiles with the help of machine learning algorithms with 92% accuracy. Proposed high throughput workflow can be applied to any type of cancer and could become a powerful pan-cancer diagnostic and monitoring tool from a simple blood test.
P2X receptors inAplysia californica: Chemosensory systems, bio-energetic and development
Authors: Györi János , Kohn Andrea B. , Moroz Leonid L.
Published: August 2020

ATP and its ionotropic P2X receptors are components of one of the most ancient signaling systems. However, little is known about the distribution and function of purinergic transmission in invertebrates. Here, we cloned, expressed, and pharmacologically characterized P2X receptors in the sea slugAplysia californica– a prominent model in cellular and system neuroscience. We showed that ATP and P2X receptors are essential signaling components within the unique bioenergetic center located in the CNS ofAplysia, also known as the cerebral F-cluster of insulin-containing neurons. Functional P2X receptors were successfully expressed inXenopusoocytes to characterize their ATP-dependence (EC50=306μM), two-phased kinetics, ion selectivity (Na+-dependence), sensitivity to the ATP analog Bz-ATP (~20% compare to ATP) and antagonists (with PPADS as a more potent inhibitor compared to suramin). Next, using RNA-seq, we characterized the expression of P2X receptors across more than a dozenAplysiaperipheral tissues and developmental stages. We showed that P2X receptors are predominantly expressed in chemosensory structures and during early cleavage stages. The localization and pharmacology of P2X receptors inAplysiahighlight the evolutionary conservation of bioenergetic sensors and chemosensory purinergic transmission across animals. This study also provides a foundation to decipher homeostatic mechanisms in development and neuroendocrine systems.

Graphical Abstract

We show that ATP and its ligand-gated P2X receptors are essential signaling components within both the chemosensory systems and the unique bioenergetic center, present in the CNS of the sea slugAplysia californica– a prominent model in neuroscience. Expression and pharmacology of P2X receptors inAplysiaconfirms the preservation of evolutionary conserved bioenergetic sensors across animals and provide new tools to decipher homeostatic mechanisms in neuro-endocrine systems in general.
Early birds, late owls, and the ecological role of intra-population chronotype variation
Authors: Royzrakh-Pasternak Ella , Dayan Tamar , Levy Ofir , Kronfeld-Schor Noga
Published: August 2020

While the molecular mechanisms underlying variation in chronotypes within populations have been studied extensively, the ultimate selective forces governing it are poorly understood. The proximate cause is variation in clock genes and protein expression, which produces variation in tau (period length of the circadian clock), with early individuals having shorter tau. We studied within-population variation in foraging activity times of twoAcomysspecies in the field. This variation manifested in a regular and consistent sequence of individual foraging activity that is positively and strongly correlated with variation in tau. Thus, variation in circadian clock period length (tau) appears to be the mechanism underlying the regular pattern of intraspecific temporal partitioning. Late chronotypes also spent more time torpid than earlier ones, suggesting an energetic cost to this strategy and possible tradeoffs. We suggest that variation in tau is an adaptive mechanism to reduce competition between individuals within a population.
Antagonistic crosstalk fine-tunes sensitivities of IRE1 and PERK signaling during unfolded protein response
Authors: Jiang Jun , Qu Yimiao , Liu Xiang , Tang Chao , Wei Ping
Published: August 2020

When endoplasmic reticulum (ER) stress occurs, a collection of phylogenetically conserved signaling pathways, termed unfolded protein response (UPR) pathways, monitors the stress level in the ER and is activated to restore homeostasis. If stress is overwhelming, activation of these signaling pathways also leads to apoptosis. The initial response in the ER is fluxed into several parallel branches, i.e., IRE1, PERK, and ATF6 branch. How they coordinate in response to different ER stress levels remains largely unknown. Here, we constructed a dual-reporter system to simultaneously monitor and quantify the response of both the IRE1 and PERK branches. We found that the IRE1 and PERK branches were highly coordinated via mutual inhibition. Furthermore, IRE1 branch was more sensitive to ER stress than the PERK branch under low ER stress and IRE1 activity was attenuated under high ER stress. The differential sensitivity between the two branches arises from the interbranch inhibitor p58IPK, rather than the intra-branch inhibitor GADD34. Our results suggested a model where cells use the antagonistic crosstalk between parallel UPR signaling pathways to fine-tune their activities in response to different ER stress levels.
Non-invasive brain-spine interface: continuous brain control of trans-spinal magnetic stimulation using EEG
Authors: Insausti-Delgado Ainhoa , López-Larraz Eduardo , Nishimura Yukio , Ziemann Ulf , Ramos-Murguialday Ander
Published: August 2020

Brain-controlled neuromodulation therapies have emerged as a promising tool to promote functional recovery in patients with motor disabilities. This neuromodulatory strategy is exploited by brain-machine interfaces and could be used for restoring lower limb muscle activity or alleviating gait deficits. Towards a non-invasive approach for leg neurorehabilitation, we present a set-up that combines acquisition of electroencephalographic (EEG) activity to volitionally control trans-spinal magnetic stimulation (ts-MS). We engineered, for the first time, a non-invasive brain-spine interface (BSI) to contingently connect motor cortical activation during leg motor imagery with the activation of leg muscles via ts-MS. This novel brain-controlled stimulation was validated with 10 healthy participants who underwent one session including different ts-MS conditions. After a short screening of their cortical activation during lower limb motor imagery, the participants used the closed-loop system at different stimulation intensities and scored system usability and comfort. We demonstrate the efficiency and robustness of the developed system to remove online stimulation artifacts from EEG regardless of ts-MS intensity used. All the participants reported absence of pain due to ts-MS and good usability. Our results also revealed that ts-MS controlled afferent and efferent intensity-dependent modulation of the nervous system. The here presented system represents a novel non-invasive means to neuromodulate peripheral nerve activity of lower limb using brain-controlled spinal stimulation.
A UropathogenicE. coliUTI89 model of prostatic inflammation and collagen accumulation for use in studying aberrant collagen production in the prostate
Authors: Ruetten Hannah , Sandhu Jaskiran , Mueller Brett , Wang Peiqing , Zhang Helen L. , Wegner Kyle A. , Cadena Mark , Sandhu Simran , Abler Lisa , Zhu Jonathan , O’Driscoll Chelsea A. , Chelgren Britta , Wang Zunyi , Shen Tian , Barasch Jonathan , Bjorling Dale E. , Vezina Chad M.
Published: August 2020

Bacterial infection is one known etiology of prostatic inflammation. Prostatic inflammation is associated with prostatic collagen accumulation and both are linked to progressive lower urinary tract symptoms in men. We characterized a model of prostatic inflammation utilizing transurethral instillations ofE. coliUTI89 in C57BL/6J male mice with the goal of determining the optimal instillation conditions, understanding the impact of instillation conditions on urinary physiology, and identifying ideal prostatic lobes and collagen 1a1 prostatic cell types for further analysis. The smallest instillation volume tested (50 µL) distributes exclusively to bladder, 100 and 200 µL volumes distributes to bladder and prostate, and a 500 µL volume distributes to bladder, prostate and ureter. A threshold optical density (OD) of 0.4E. coliUTI89 in the instillation fluid is necessary for significant (p < 0.05) prostate colonization.E. coliUTI89 infection results in a low frequency, high volume spontaneous voiding pattern. This phenotype is due to exposure toE. coliUTI89, not catheterization alone, and is minimally altered by a 50 µL increase in instillation volume and doubling ofE. coliconcentration. Prostate inflammation is isolated to the dorsal prostate and is accompanied by increased collagen density. This is partnered with increased density of PTPRC+, ProCOL1A1+ co-positive cells and decreased density of ACTA2+, ProCOL1A1+ co-positive cells. Overall, we determined that this model is effective in altering urinary phenotype and producing prostatic inflammation and collagen accumulation in mice.