bluuebunny/crossref_metadata_2025 huggingface dataset:
Subjective and Objective Effectiveness of Eustachian Tube Balloon Dilatation for Patients With Eustachian Tube Dysfunction—Evaluation in a Pressure Chamber
Authors: Jansen Stefanie , Peters Nele , Hinkelbein Jochen , Klußmann Jens Peter , Beutner Dirk , Meyer Moritz Friedo
Published: April 2020

Introduction:

The Eustachian tube plays a crucial role in pressure equalization between the middle ear and ambient pressure for fast and large pressure differences. In patients with chronic Eustachian tube dysfunction, Eustachian tube balloon dilatation is increasingly used as surgical therapy. Subjectively, many patients report an improvement of the symptoms postoperatively. Hence, there is a need to objectively measure this effect.

Methods:

The objectivity of Eustachian tube balloon dilatation was evaluated using a precise method of measuring Eustachian tube function. In a hypo/hyperbaric pressure chamber, 23 ears in 13 patients were exposed to a standardized profile of compression and decompression before Eustachian tube balloon dilatation and 4 weeks afterwards. Standardized parameters of Eustachian tube function were determined and statistically compared before and 4 weeks after intervention. In addition, an Eustachian Tube Dysfunction Questionnaire-7 (ETDQ7) questionnaire was completed beforehand and 4 weeks postoperatively to determine subjective surgical success.

Results:

The results from the ETDQ7 questionnaire showed a significant improvement in symptoms after Eustachian tube balloon dilatation (p = 0.0002). Objective measurements results showed a significant reduction of the Eustachian tube opening pressure during pressure decrease 4 weeks after intervention (p = 0.0012).

Conclusion:

Eustachian tube balloon dilatation significantly reduced Eustachian tube opening pressure, in addition to subjective improvement of symptoms determined by ETDQ7.
Association between effective hepatic blood flow and the severity and prognosis of hepatitis B virus-related acute on chronic liver failure
Authors: Chen Dabiao , Wen Shihua , Wu Zebin , Gu Yurong , Chen Youming , Chen Xiaotong , Zhang Yanyan , Lin Binliang , Peng Liang , Zheng Yubao , Gao Zhiliang
Published: April 2020

Background:

Hepatic inflammation resulted in hepatocyte necrosis and microcirculatory dysfunction in acute on chronic liver failure (ACLF) with cirrhosis or not. The influence of effective hepatic blood flow (EHBF) on the severity of liver failure has not been fully elucidated.

Aim:

The aim of this study was to assess the correlation between the EHBF and the severity and the prediction of 90-day mortality rate of hepatitis B virus-related ACLF (HBV-ACLF).

Methods:

In this retrospective study, patients hospitalized for HBV-ACLF or decompensated cirrhosis and who underwent an indocyanine green (ICG) clearance test between June 2016 and July 2018 were enrolled. EHBF was measured by the ICG clearance test and patients were categorized into the ACLF without cirrhosis (HBV-ACLF-no-Cir), ACLF with cirrhosis (HBV-ACLF-Cir) and decompensated cirrhosis (HBV-De-Cir).

Results:

A total of 522 patients (HBV-ACLF-no-Cir: 84, HBV-ACLF-Cir: 111 and HBV-De-Cir: 327) were enrolled. The mean EHBF in the HBV-De-Cir was significantly higher than that in the HBV-ACLF-no-Cir and HBV-ACLF-Cir (0.36 vs. 0.21 vs. 0.20 L/min, P < 0.001). EHBF was significantly correlated with the total bilirubin, prothrombin activity and model for end-stage liver disease (MELD) in the HBV-ACLF-no-Cir. The predicted 90-day mortality rate using the MELD, EHBF, ICG-retention rate at 15 min (R15%) and EHBF-R15% scores were similar. The sensitivity and specificity of the EHBF varied between 68.5–80.2% and 45.8–73.7%, respectively. The EHBF-MELD score had the highest specificity.

Conclusion:

EHBF was significantly lower in the patients with ACLF compared to decompensated cirrhosis. The EHBF were closely related to the severity of HBV-ACLF and can be used for predicting the 90-day mortality rate of HBV-ACLF.
Clinical outcomes of 177lutetium-prostate-specific membrane antigen therapy in advanced prostate cancer—a prospective pilot study in an Asian population
Authors: Thang Sue Ping , Lam Winnie Wing Chuen , Tong Aaron Kian Ti , Allen John Carson , Ler Anna Siah Lee , Tay Young Soon , Somanesan Soma , Kanesvaran Ravindran , Wong Alvin Seng Cheong , Ng David Chee Eng
Published: April 2020

Objective

Metastatic castration-resistant prostate cancers are aggressive tumors with poor prognosis. Prostate-specific membrane antigen-targeted radionuclide therapy is a potential treatment for these patients. Here, we report our initial experience in Singapore.

Methods

Twenty men (median age 70) with progressive disease were prospectively recruited. Prostate-specific membrane antigen and fluorodeoxyglucose-PET/computed tomography were performed to confirm high prostate-specific membrane antigen-expression. Up to four cycles of 177lutetium-prostate-specific membrane antigen-I&T at 6–8 weekly intervals were administered. Patients were restaged 3 months following treatment. Primary endpoints were prostate-specific antigen decline ≥50% and treatment-related toxicity. Additional endpoints included radiological and clinical response as well as progression-free survival and overall survival from first cycle.

Results

Sixty-seven cycles were administered (median 4 cycles per patient, mean 6.5 GBq per cycle). Sixty five percent had ≥1 line of prior chemotherapy, 90% abiraterone, enzalutamide or both, and 30% radium-223 radionuclide therapy. All had bone metastases and 35% had visceral metastases. Prostate-specific antigen decline ≥50% was achieved in 50%. Grade 3–4 hematotoxicity was seen in up to 15%. Grade 3–4 non-hematotoxicity was not observed. Eleven patients had restaging scans 3 months post-treatment (5 = partial response, 6 = progressive disease). Fifty-seven percent (4/7) with bone pain had pain improvement. Median progression-free survival was 5.9 months and median overall survival 13.1 months. Patients with prostate-specific antigen decline ≥50% had longer progression-free survival and overall survival.

Conclusion

177Lutetium-prostate-specific membrane antigen-I&T therapy is effective with tolerable side effects in our local setting. Prostate-specific antigen decline ≥50% is associated with longer progression-free survival and overall survival.
The use of multiparametric 18F-fluoro-l-3,4-dihydroxy-phenylalanine PET/MRI in post-therapy assessment of patients with gliomas
Authors: Fraioli Francesco , Shankar Ananth , Hyare Harpreet , Ferrazzoli Valentina , Militano Vincenzo , Samandouras George , Mankad Khsitij , Solda Francesca , Zaccagna Fulvio , Mehdi Elnur , Lyasheva Maria , Bomanji Jamshed , Novruzov Fuad
Published: April 2020

Purpose

To determine the utility of 18F-fluoro-l-3,4-dihydroxy-phenylalanine (18F-DOPA) PET/MRI versus cross-sectional MRI alone in glioma response assessment and identify whether the two techniques demonstrate different tumour features.

Methods

18F-DOPA PET/MRI studies from 40 patients were analysed. Quantitative PET parameters and conventional MRI features were recorded. Tumour volume was assessed on both PET and MRI. Using dynamic susceptibility contrast perfusion-weighted imaging, maps of cerebral blood flow (CBF) and cerebral blood volume (CBV) were obtained. Within volume of tumours of tumour features and normal-appearing white matter (NAWM) drawn on MRI, standardised uptake value (SUV)max, CBF and CBV were recorded. Presence of residual active tumour was assessed by qualitative visual assessment. Receiver operating characteristic analysis was performed univariately and on parameter combination to analyse ability to determine presence/absence of disease. Reference standard for presence of viable tissue was biopsy or clinical follow-up.

Results

Median SUVmax was 3.4 for low-grade glioma (LGG) and 3.3 for high-grade glioma (HGG). There was a significant correlation between PWI parameters and WHO grade (P < 0.001), but no correlation with SUVmax. Median 18F-DOPA volume was 8216.88 mm3 for HGG and 6284.94 mm3 for LGG; MRI volume was 6316.57 mm3 and 5931.55 mm3, respectively. SUVmax analysis distinguished enhancing and nonenhancing components from necrosis and NAWM and demonstrated active disease in nonenhancing regions. Visually, the modalities were concordant in 37 patients. Combining the multiparametric PET/MRI approach with all available data-enhanced detection of the presence of tumour (area under the curve 0.99, P < 0.01).

Conclusion

MRI and 18F-DOPA are complementary modalities for assessment of tumour burden. Matching 18F-DOPA and MRI in assessing residual tumour volume may better delineate the radiotherapy target volume.
Radionuclide esophageal transit scintigraphy in chronic indeterminate and cardiac forms of Chagas disease
Authors: Dumont Sandra Monetti , Costa Henrique Silveira , Chaves Ana Thereza , Nunes Maria do Carmo Pereira , Marino Viviane Parisotto , Rocha Manoel Otávio da Costa
Published: April 2020

Objectives

This study was designed to investigate digestive and heart associations, using esophageal transit scintigraphy in three different groups: patients exclusively with the dilated cardiac form of Chagas disease (DCCh), an indeterminate form of Chagas disease, and healthy controls. As a hypothesis, we assumed that autonomic chagasic denervation is a global process.

Materials and methods

Twenty healthy controls and 75 outpatients with Chagas disease, divided into indeterminate form (n = 33) and (DCCh, n = 42), underwent esophageal scitigraphy. The esophageal transit time (ETT) and percentage of esophageal emptying (%EE) were analyzed by group and correlated with left ventricular ejection fraction (LVEF).

Results

ETT alterations were found in 57% of indeterminate form and 80% of DCCh. The observed values of ETT and %EE in Chagas disease groups were significantly different from the controls (P-value <0.001). The lowest median ETT was observed for the controls (median = 8.0), followed by indeterminate form (median = 16.5) and DCCh (median = 60.0). Regarding %EE, a higher median value was observed for the controls (median = 92.3), followed by indeterminate form (median = 86.7) and DCCh (median = 56.9). In the DCCh group, ETT and %EE were significantly correlated with LVEF values (r = 0.398; P = 0.015) and (r = 0.475; P = 0.003), respectively.

Conclusion

An association between left ventricular systolic dysfunction and functional esophageal alterations was observed which was interpreted as indirect evidence of concomitance of gastrointestinal and cardiac disorders. We also found that the greater the impairment of the esophagus’s autonomic function, the worse the cardiac dysfunction.
In the evaluation of patients with skull base osteomyelitis, does 18F-FDG PET CT have a role?
Authors: Kulkarni Smita Chinmay , Padma Subramanyam , Shanmuga Sundaram Palaniswamy
Published: April 2020

Purpose

To evaluate the diagnostic performance of regional fluorine-18 fluorodeoxyglucose (18F-FDG) positron emission tomography-computed tomography (PET-CT) in patients with skull base osteomyelitis (SBO) and to compare with magnetic resonance imaging (MRI) whenever available.

Materials and methods

A total of 77 patients (male:female = 56:21; mean age 66.4 ± 9.4 years) with clinically suspected SBO, who underwent regional 18F-FDG PET-CT were included in this retrospective study. 18F-FDG PET-CT images were analyzed for presence, localization and intensity of FDG uptake. Diagnostic performance of 18F-FDG PET-CT was analyzed based on histopathology, culture, and clinical/imaging follow-up. The agreement analysis between 18F-FDG PET-CT and MRI findings was performed in 56 patients.

Results

The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of 18F-FDG PET-CT for diagnosing SBO were 96.7, 93.3, 98.3, 87.5, and 96.1%, respectively. The average SUVmax of the lesions was 5.9 ± 3.5. The SUVmax of the fungal lesions was lower than that of bacterial lesions with P-value of <0.001. On comparing variables like C-reactive protein, erythrocyte sedimentation rate, and SUVmax for prediction of recurrence/progression, by plotting an ROC curve, the SUVmax was found to be an independent prognostic marker. 56 out of 77 patients had undergone both 18F-FDG PET-CT and MRI. The agreement analysis between the modalities showed almost perfect agreement for delineation of soft tissue and bony involvement with κ values of 0.82 and 0.81, respectively.

Conclusion

18F-FDG PET-CT is a sensitive tool in evaluation of patients with SBO. It shows a very good agreement with the MRI. It plays a critical role in treatment response evaluation.
Gender differences in brown adipose tissue-related brain functional networks: an 18F-FDG-PET study
Authors: Shao Xiaoliang , Chen Yuqi , Shao Xiaonan , Wang Suhong , Wang Suwen , Wang Yuetao
Published: April 2020

Purpose

Thermogenesis of brown adipose tissue (BAT) is controlled by central modulating mechanisms, although changes in brain metabolism of BAT-positive subjects with different genders are still unclear. We hypothesized that changes in regional cerebral glucose metabolic activity were associated with BAT activities, and this association differed in different genders.

Methods

Brain glucose metabolism of 26 BAT-positive and 26 BAT-negative healthy subjects was compared using a brain fluorodeoxyglucose (FDG)-PET scan, and gender differences in BAT-related brain functional networks and effect of sex hormones were assessed by comparing the brain PET images of BAT-positive and BAT-negative subjects of different genders and postmenopausal female subjects.

Results

Compared with controls, BAT-positive male subjects had a significant hypermetabolic area in the right extranuclear and significant hypometabolic areas in the right inferior parietal lobule and right inferior frontal gyrus; while at the same threshold, BAT-positive female subjects had richer hypermetabolic regions, including bilateral limbic lobes, bilateral frontal lobes, right cerebellum, left sublobar, and right parietal lobe. However, BAT-positive postmenopause female subjects only showed significant hypometabolic regions in left lingual gyrus.

Conclusions

BAT-related brain functional networks are different between male and female subjects. Female networks are more significant and more concentrated while male networks are smaller and more dispersed, and these gender differences may be related to sex hormones.
Diagnostic performances of F-18 FDG PET or PET/CT for detection of post-transplant lymphoproliferative disorder: a systematic review and meta-analysis
Authors: Kim Dae-Hwan , Kim Seong-Jang
Published: April 2020

Objective

The purpose of the current study was to investigate the diagnostic performance of F-18 fluorodeoxyglucose (FDG) PET or PET/computed tomography (PET/CT) for detection of post-transplant lymphoproliferative disorder (PTLD) through a systematic review and meta-analysis.

Methods

The PubMed and EMBASE database, from the earliest available date of indexing through 30 November 2019, were searched for studies evaluating the diagnostic performance of F-18 FDG PET or PET/CT for the diagnosis of PTLD.

Results

Across seven results of five studies (1276 patients), the pooled sensitivity for F-18 FDG PET or PET/CT was 0.90 [95% confidence interval (CI) 0.85–0.93] without heterogeneity (I2 = 23.3, 95% CI 0.0–85.7, P = 0.25) and a pooled specificity of 0.90 (95% CI 0.86–0.93) without heterogeneity (I2 = 0.0, 95% CI 0.0–100.0, P = 0.82). Likelihood ratio (LR) syntheses gave an overall positive likelihood ratio (LR+) of 9.4 (95% CI 6.5–13.7) and negative likelihood ratio (LR−) of 0.11 (95% CI 0.08–0.17). The pooled diagnostic odds ratio was 83 (95% CI 46–149). The hierarchical summary receiver operating characteristic shows the areas under the curve was 0.96 (95% CI 0.94–0.97).

Conclusion

The current meta-analysis showed the high sensitivity and specificity of F-18 FDG PET or PET/CT for the detection of PTLD. At present, the literature regarding the use of F-18 FDG PET or PET/CT for the detection of PTLD remains limited; thus, further large multicenter studies would be necessary to substantiate the diagnostic accuracy of F-18 FDG PET or PET/CT for the diagnosis of PTLD.
Optimizing Analgesic Use During Infant Lumbar Puncture in the Emergency Department
Authors: Balay Erin E. , Hendrickson Marissa A. , Harvey Brian , Dewald Jennifer , Johnson Brittany , Louie Jeffrey
Published: April 2020

Introduction:

Lumbar puncture (LP) for the collection of cerebrospinal fluid is an important diagnostic tool for the evaluation of febrile or ill-appearing infants. This invasive procedure is painful for patients; inadequate analgesia may have lasting effects. The American Academy of Pediatrics recommends analgesia during all LP procedures, and oral sucrose alone does not offer sufficient analgesia. Our objective was to identify analgesic use trends during infant LP in our emergency department and create a system of analgesic administration. We aimed for complete compliance with one method of analgesia and an increase in our use of 2 or more methods to 85% over 12 months.

Methods:

We utilized Plan-Do-Study-Act cycle methodology and retrospective chart review. Five interventions focused on staff communication, collaboration, and education. Inclusion criteria: infants <60 days who underwent LP procedure due to fever >38°C, hypothermia <36.5°C of unknown origin, or ill-appearance.

Results:

One hundred infant LPs analyzed: 52 preintervention and 48 intervention. The use of one analgesic increased from 98% preintervention to 100%. The use of 2 or more analgesics increased from 58% preintervention to 87%. Topical lidocaine use increased from 56% preintervention to 73%. LP success rates were high in both groups, with no statistically significant change in the success rate.

Conclusion:

We created a streamlined process to ensure all infants undergoing lumbar puncture received at least 1 analgesic and increased the proportion of infants treated with 2 or more analgesics. This work could be expanded to improve analgesia during other invasive procedures in the emergency department.
Applied Online Crowdsourcing in Plastic and Reconstructive Surgery
Authors: Suchyta Marissa , Azad Amee , Patel Ashraf A. , Khosla Rohit K. , Lorenz H. Peter , Nazerali Rahim S.
Published: April 2020

Background

Aesthetic outcomes of unilateral cleft lip repairs have important psychosocial implications for patients who are heavily influenced by social perceptions. Online crowdsourcing offers the unique potential to efficiently recruit large numbers of laypeople to assess public perception. The aim of this study was to use the online crowdsourcing platform Mechanical Turk to compare the postoperative outcomes of Fisher, Millard, and Mohler cleft lip repair techniques.

Methods

Two hundred fifty-four participants were recruited through Mechanical Turk to evaluate 29 cropped and deidentified photographs of children, 8 photographs were controls without cleft lips and 21 were children with unilateral cleft lips who had undergone Fisher, Millard, or Mohler repairs (7 in each group). Respondents were asked whether a scar was present, whether they would be personally satisfied with the surgical result and used a Likert scale from 1 to 5 to rate overall appearance, scar severity, and nasal symmetry.

Results

Fewer respondents reported that a scar was present when assessing postoperative photographs of Fisher repairs (70.3 ± 8.6%) compared with Millard (92.0 ± 1.5%) or Mohler (88.8 ± 3.1%) repairs. Average rating of scar severity was also lower for Fisher (1.9) compared with Millard (2.6) or Mohler (2.6) repairs. Average ratings of nose symmetry, general appearance, and satisfaction with operative result were not statistically significantly different between the repair groups.

Conclusions

This study demonstrates the potential of online crowdsourcing to assess public perception of plastic surgery outcomes. The Mechanical Turk platform offers a reduction in selection bias, ease of study design, and enhanced efficiency of large-scale participant recruitment. Results indicate that the Fisher repair led to the most favored aesthetic outcomes compared with the Millard and Mohler techniques, particularly with regard to scar severity. Crowdsourcing is a powerful tool to assess layperson perception of plastic surgery outcomes and can be used to better guide surgical decision-making.
Risk Factors for Urinary Incontinence in Chinese Women: A Cross-sectional Survey
Authors: Xie Xiaoqian , Chen Yaxiao , Khan Aisha , Long Tengfei , Li Siying , Xie Meiqing
Published: April 2020

Objective

Urinary incontinence is highly prevalent among women, with a substantial effect on health-related quality of life. This article aimed to investigate the independent factors for urinary incontinence (UI) and the relative importance of each factor.

Methods

This study was a cross-sectional survey of Chinese women in Guangzhou. Female 20 years and older were invited to participate. The International Consultation on Incontinence Questionnaire-Urinary Incontinence Short Form was used to determine whether respondents are experiencing UI. Univariate and multivariate unconditional logistic regression analyses were performed to determine the significant risk factors associated with UI.

Results

A total of 2626 women were invited to participate in the survey. The response rate was 80.5% (2114/2626). The prevalence of UI among the study population was 31.2%. Old age, increased body mass index, childbirth, family history of any female pelvic floor disorders, symptoms of chronic cough or rhinitis, wearing a corset, and often drinking were independent risk factors for UI.

Conclusions

Urinary incontinence is common among Chinese women in Guangzhou. Among the factors that we are concerned with, old age and vaginal delivery are the two with greatest impact. Moreover, wearing a corset and drinking are the 2 lifestyle factors associated with UI.
Predictors for Pelvic Organ Prolapse Recurrence After Sacrocolpopexy: A Matched Case-Control Study
Authors: Chang Olivia H. , Davidson Emily R.W. , Thomas Tonya N. , Paraiso Marie Fidela R. , Ferrando Cecile A.
Published: April 2020

Objective

This study aimed to identify risk factors for prolapse recurrence after sacrocolpopexy.

Methods

This was a retrospective chart review with cross-sectional follow-up survey of 709 patients who underwent sacrocolpopexy of any modality from 2004 to 2014. Cases were defined as those with a composite failure, defined as having subjective bulge symptoms, retreatment, or anatomic prolapse (≥stage 2 prolapse on the Pelvic Organ Prolapse Quantification system). Controls were patients without composite failure. The cases and controls were matched by surgeon and by date of surgery in a 1:4 ratio.

Results

We identified 153 cases and matched them to 487 controls. The overall incidence of prolapse recurrence was 21.6% (95% confidence interval [CI], 18.2%–24.1%). Of the recurrence cases, 34 (22.2%) underwent surgical retreatment; the most common surgical retreatment was a posterior colporrhaphy (n = 16 [47.1%]). On multivariable logistic regression, a preoperative genital hiatus size ≥4 cm (adjusted odds ratio [adjOR], 1.95; 95% CI, 1.18–3.25) and concurrent anterior colporrhaphy (adjOR, 2.11; 95% CI, 1.06–4.18) were associated with increased odds of having a composite failure. Patients who had a concurrent posterior colporrhaphy had lower odds of experiencing a failure (adjOR, 0.62; 95% CI, 0.42–0.94).

Conclusions

In this large retrospective chart review of women who underwent sacrocolpopexy with a cross-sectional survey follow-up time frame of nearly 7 years, patients with a preoperative genital hiatus of 4 cm or greater and need for concurrent anterior colporrhaphy at the time of their index surgery had higher odds of prolapse recurrence. Conversely, women who underwent a concurrent posterior colporrhaphy had lower odds of a recurrence.
Epigenetic transgenerational effects on RNAi in Arabidopsis
Authors: Hu Qüan’an , Ailhas Jérôme , Blevins Todd , Klahre Ulrich , Vazquez Franck , Mette Michael Florian , Meins Frederick
Published: April 2020

Epigenetic states and even certain environmental responses in nematodes, mammals and seed plants can be inherited over successive generations. RNAi in plants is an epigenetic form of RNA degradation that is normally reset early in development. In contrast, competence, i.e., the susceptibility of a transgene for RNAi, is believed to be genetically determined and faithfully transmitted over many generations. Unexpectedly, we found that the same yellow fluorescent protein (YFP) transgene in a monogenic, homozygous line ofArabidopsisexhibited two epigenetic states of RNAi: type I, which is initiated in rosette leaves and is stable in later developmental stages, and, type II, which is initiated after floral induction and is unstable. The incidence of type I plants descended from type I parents decreased over three successive generations of self-fertilized plants. By the third generation, a substantial fraction of plants from type I parents exhibited either the type II phenotype or remained high-YFP expressing throughout sporophytic development, indicating that silencing had been completely lost. Similarly, plants descended from type II parents showed a progressive shift from the type II phenotype and a complete loss of silencing. These results show that the silencing types (or states) of parental plants have significant influence on both silencing determination and silencing types (or states) of their offspring, however, this influence fades through several generations of self; as regardless of the types of the parental lines, competence for RNA silencing tends to loss after generations. Thus, we propose that RNA silencing in plants can be the target of transgenerational effects.

While the underlying mechanisms are still unknown, our findings in theArabidopsisRNA silencing system complement the current understanding of heritable RNAi inC. elegans,that this phenomenon is likely a common mechanism in Eukaryote systems.
Investigation on the requirements for YbbN/CnoX displaying thiol-disulfide oxidoreductase and chaperone activities
Authors: de Abreu Meireles Diogo , Yokomizo César Henrique , Netto Luís Eduardo Soares
Published: April 2020

YbbN/CnoX are proteins that display a Trx domain linked to a tetratricopeptide (TPR) domain, which are involved in protein-protein interactions and protein folding processes. YbbN fromEscherichia coli(EcYbbN) displays a co-chaperone (holdase) activity that is induced by HOCl (bleach).EcYbbN contains a SQHC motif within the Trx domain and displays no thiol-disulfide oxidoreductase activity.EcYbbN also presents a second Cys residue at Trx domain (Cys63) 24 residues away from SQHF motif that can form mixed disulfides with substrates. Here, we comparedEcYbbN with two other YbbN proteins: fromXylella fastidiosa(XfYbbN) and fromPseudomonas aeruginosa(PaYbbN). WhileEcYbbN displays two Cys residues along a SQHC[N24]C motif;XfYbbN andPaYbbN present two and three Cys residues in the CAPC[N24]V and CAPC[N24]C motifs, respectively. These three proteins are representatives of evolutionary conserved YbbN subfamilies. In contrast toEcYbbN, bothXfYbbN andPaYbbN: (1) reduced an artificial disulfide (5,5′-dithiobis-(2-nitrobenzoic acid) = DTNB); and (2) supported the peroxidase activity of Peroxiredoxin Q fromX. fastidiosa, suggesting thatin vivothese proteins might function similarly to the canonical Trx enzymes. Indeed,XfYbbN was reduced byXfTrx reductase with a high catalytic efficiency (kcat/Km=1.27 × 107M−1.s−1), like the canonicalXfTrx (XfTsnC). Furthermore,EcYbbN (as described before) andXfYbbN, but notPaYbbN displayed HOCl-induced holdase activity. Remarkably,EcYbbN gained disulfide reductase activity while lost the HOCl-activated chaperone function when the SQHC was replaced by CQHC. In contrast, theXfYbbN C40A mutant lost the disulfide reductase activity, while kept its HOCl-induced chaperone function. Finally, we generated aP. aeruginosastrain with theybbNgene deleted, which did not present increased sensitivity to heat shock or to oxidants or to reductants. Altogether, our results suggest that different YbbN/CnoX proteins display distinct properties and activities, depending on the presence of the three conserved Cys residues.

Graphical Abstract

Highlights

- CXXC motif is required for the thiol-disulfide reductase activity of YbbN proteins.

-XfYbbN andPaYbbN display thiol-disulfide oxidoreductase activity

- The affinities ofXfTrxR forXfYbbN andXfTsnC (canonical Trx) are comparable

-XfYbbN andEcYbbN, but notPaYbbN, display holdase activity induced by hypochlorous acid

- EngineeringEcYbbN/CnoX by inserting a Cys residue in the SQHC motif resulted in a gain of function (thiol-disulfide oxidoreductase activity) and abolished the HOCl-induced holdase activity.
Cardiomyocyte Contractile Impairment in Heart Failure Results from Reduced BAG3-mediated Sarcomeric Protein Turnover
Authors: Martin Thomas G. , Myers Valerie D. , Dubey Praveen , Dubey Shubham , Perez Edith , Moravec Christine S. , Willis Monte S. , Feldman Arthur M. , Kirk Jonathan A.
Published: April 2020

The association between reduced myofilament force-generating capacity (Fmax) and heart failure (HF) is clear, however the underlying molecular mechanisms are poorly understood. Here, we show the Fmaxdecrease arises from impaired BAG3-mediated sarcomere turnover. Myofilament BAG3 decreased in human HF and predicted the extent of Fmaxdecrease. This relationship was confirmed using BAG3+/-mice, which had reduced Fmaxand increased myofilament ubiquitination, suggesting impaired protein turnover. We show cardiac BAG3 operates via the chaperone-assisted selective autophagy complex (CASA), conserved from skeletal muscle, and confirm sarcomeric CASA localization is BAG3/proteotoxic stress-dependent. To determine if increasing BAG3 expression in HF would restore sarcomere proteostasis/Fmax, HF mice were treated with AAV9/BAG3. Gene therapy fully restored Fmaxafter four weeks and decreased ubiquitination. Using mass spectrometry, we identified several sarcomere proteins with increased ubiquitination in HF and four that decreased with AAV9/BAG3. Our findings indicate BAG3-mediated sarcomere turnover is required for myofilament functional maintenance.
Isoform-specific regulation of HCN4 channels by a family of endoplasmic reticulum proteins
Authors: Peters Colin H. , Myers Mallory E. , Juchno Julie , Haimbaugh Charlie , Bichraoui Hicham , Du Yanmei , Bankston John R. , Walker Lori A , Proenza Catherine
Published: April 2020

Ion channels in excitable cells function in macromolecular complexes in which auxiliary proteins modulate the biophysical properties of the pore-forming subunits. Hyperpolarization-activated, cyclic nucleotide-sensitive HCN4 channels are critical determinants of membrane excitability in cells throughout the body, including thalamocortical neurons and cardiac pacemaker cells. We previously showed that the properties of HCN4 channels differ dramatically in different cell types, possibly due to the endogenous expression of auxiliary proteins. Here, we report the discovery of a family of endoplasmic reticulum transmembrane proteins that interact with and modulate HCN4. Lymphoid-restricted membrane protein (LRMP, Jaw1) and inositol trisphosphate receptor-associated guanylate kinase substrate (IRAG, Mrvi1, Jaw1L) are homologous proteins with small ER luminal domains and large cytoplasmic domains. Despite their homology, LRMP and IRAG have distinct effects on HCN4. LRMP is a loss-of-function modulator that inhibits the canonical depolarizing shift in the voltage-dependence of HCN4 activation in response to binding of cAMP. In contrast, IRAG causes a gain of HCN4 function by depolarizing the basal voltage-dependence of activation in the absence of cAMP. The mechanisms of action of LRMP and IRAG are novel; they are independent of trafficking and cAMP binding, and they are specific to the HCN4 isoform. We also found that IRAG is highly expressed in the mouse sinoatrial node where computer modeling predicts that its presence increases HCN4 availability. Our results suggest important roles for LRMP and IRAG in regulation of cellular excitability and as tools for advancing mechanistic understanding of HCN4 channel function.

Significance statement

The pore-forming subunits of ion channels are regulated by auxiliary interacting proteins. Hyperpolarization-activated cyclic nucleotide-sensitive isoform 4 (HCN4) channels are critical determinants of electrical excitability in many types of cells including neurons and cardiac pacemaker cells. Here we report the discovery of two novel HCN4 regulatory proteins. Despite their homology, the two proteins — lymphoid-restricted membrane protein (LRMP) and inositol trisphosphate receptor-associated guanylate kinase substrate (IRAG) — have opposing effects on HCN4, causing loss- and gain-of-function, respectively. LRMP and IRAG are expected to play critical roles in regulation of physiological processes ranging from wakefulness to heart rate through their modulation of HCN4 channel function.
Fluctuation relations and fitness landscapes of growing cell populations
Authors: Genthon Arthur , Lacoste David
Published: April 2020

We construct a pathwise formulation of a growing population of cells, based on two different samplings of lineages within the population, namely the forward and backward samplings. We show that a general symmetry relation, called fluctuation relation relates these two samplings, independently of the model used to generate divisions and growth in the cell population. Known models of cell size control are studied with a formalism based on path integrals or on operators. We investigate some consequences of this fluctuation relation, which constrains the distributions of the number of cell divisions and leads to inequalities between the mean number of divisions and the doubling time of the population. We finally study the concept of fitness landscape, which quantifies the correlations between a phenotypic trait of interest and the number of divisions. We obtain explicit results when the trait is the age or the size, for age and size-controlled models.
Integrating XMALab and DeepLabCut for high-throughput XROMM
Authors: Laurence-Chasen JD , Manafzadeh AR , Hatsopoulos NG , Ross CF , Arce-McShane FI
Published: April 2020

Marker tracking is a major bottleneck in studies involving X-ray Reconstruction of Moving Morphology (XROMM). Here, we tested whether DeepLabCut, a new deep learning package built for markerless tracking, could be applied to videoradiographic data to improve data processing throughput. Our novel workflow integrates XMALab, the existing XROMM marker tracking software, and DeepLabCut while retaining each program’s utility. XMALab is used for generating training datasets, error correction, and 3D reconstruction, whereas the majority of marker tracking is transferred to DeepLabCut for automatic batch processing. In the two case studies that involved anin vivobehavior, our workflow achieved a 6 to 13-fold increase in data throughput. In the third case study, which involved an acyclic,post mortemmanipulation, DeepLabCut struggled to generalize to the range of novel poses and did not surpass the throughput of XMALab alone. Deployed in the proper context, this new workflow facilitates large scale XROMM studies that were previously precluded by software constraints.
A Variable Clock Underlies Internally Generated Hippocampal Sequences
Authors: Deng Xinyi , Chen Shizhe , Sosa Marielena , Karlsson Mattias P. , Wei Xue-Xin , Frank Loren M.
Published: April 2020

Humans have the ability to store and retrieve memories with various degrees of specificity, and recent advances in reinforcement learning have identified benefits to learning when past experience is represented at different levels of temporal abstraction. How this flexibility might be implemented in the brain remains unclear. We analyzed the temporal organization of rat hippocampal population spiking to identify potential substrates for temporally flexible representations. We examined activity both during locomotion and during memory-associated population events known as sharp wave-ripples (SWRs). We found that spiking during SWRs is rhythmically organized with higher event-to-event variability than spiking during locomotion-associated population events. Decoding analyses using clusterless methods further indicate that similar spatial experience can be replayed in multiple SWRs, each time with a different rhythmic structure whose periodicity is sampled from a lognormal distribution. This variability increases with experience despite the decline in SWR rates that occurs as environments become more familiar. We hypothesize that the variability in temporal organization of hippocampal spiking provides a mechanism for storing experiences with various degrees of specificity.
MEK reduces cancer-specific PpIX accumulation through the RSK-ABCB1 and HIF-1α-FECH axes
Authors: Chelakkot Vipin Shankar , Liu Kaiwen , Yoshioka Ema , Saha Shaykat , Xu Danyang , Licursi Maria , Dorward Ann , Hirasawa Kensuke
Published: April 2020

The efficacy of aminolevulinic acid (5-ALA)-based photodynamic diagnosis (5-ALA-PDD) and photodynamic therapy (5-ALA-PDT) is dependent on the 5-ALA-induced cancer-specific accumulation of protoporphyrin IX (PpIX). We previously reported that inhibition of oncogenic Ras/MEK increases PpIX accumulation in cancer cells by reducing PpIX efflux through ATP-binding cassette sub-family B member 1 (ABCB1) as well as PpIX conversion to heme by ferrochelatase (FECH). Here, we sought to identify the downstream pathways of Ras/MEK involved in the regulation of PpIX accumulation via ABCB1 and FECH. First, we demonstrated that Ras/MEK activation reduced PpIX accumulation in RasV12-transformed NIH3T3 cells and HRAS transgenic mice. Knockdown of p90 ribosomal S6 kinases (RSK) 2, 3, or 4 increased PpIX accumulation in the RasV12-transformed NIH3T3 cells. Further, treatment with an RSK inhibitor reduced ABCB1 expression and increased PpIX accumulation. Moreover, HIF-1α expression was reduced when the RasV12-transformed NIH3T3 cells were treated with a MEK inhibitor, demonstrating that HIF-1α is a downstream element of MEK. HIF-1α inhibition decreased the activity of FECH and increased PpIX accumulation. Finally, we demonstrated the involvement of RSKs and HIF-1α in the regulation of PpIX accumulation in human cancer cell lines (DLD-1, SNB-75, Hs 578T, and MDA MB 231). These results demonstrate that the RSK-ABCB1 and HIF-1α-FECH axes are the downstream pathways of Ras/MEK involved in the regulation of PpIX accumulation.
Establishment of a Human Induced Pluripotent Stem Cell-Derived Neuromuscular Co-Culture Under Optogenetic Control
Authors: Swartz Elliot W. , Shintani Greg , Wan Jijun , Maffei Joseph S. , Wang Sarah H. , Miller Bruce L. , Havton Leif A. , Coppola Giovanni
Published: April 2020

The failure of the neuromuscular junction (NMJ) is a key component of degenerative neuromuscular disease, yet how NMJs degenerate in disease is unclear. Human induced pluripotent stem cells (hiPSCs) offer the ability to model disease via differentiation toward affected cell types, however, the re-creation of anin vitroneuromuscular system has proven challenging. Here we present a scalable, all-hiPSC-derived co-culture system composed of independently derived spinal motor neurons (MNs) and skeletal myotubes (sKM). In a model ofC9orf72-associated disease, co-cultures form functional NMJs that can be manipulated through optical stimulation, eliciting muscle contraction and measurable calcium flux in innervated sKM. Furthermore, co-cultures grown on multi-electrode arrays (MEAs) permit the pharmacological interrogation of neuromuscular physiology. Utilization of this co-culture model as a tunable, patient-derived system may offer significant insights into NMJ formation, maturation, repair, or pathogenic mechanisms that underlie NMJ dysfunction in disease.
Using seedling phenotypic traits to select local seed sources for large-scale restoration: methods and outcomes in a Great Basin case study
Authors: Leger Elizabeth A. , Barga Sarah , Agneray Alison C. , Baughman Owen , Burton Robert , Williams Mark
Published: April 2020

Establishing plants from seed is often a limitation to restoration success in semi-arid systems. For restoration purposes, managers can either use widely-available commercial seeds, which are often sourced from far outside the seeding area, or take extra steps to use locally collected seeds. If local seeds have traits more conducive to seedling establishment in degraded sites, they could increase restoration success. Here, we asked whether wild-collected seeds of two native perennial grasses,Elymus elymoidesandPoa secunda, had more favorable characteristics than commercial sources. Seeds were collected from four populations within the Winnemucca District of the Nevada Bureau of Land Management, which manages lands within the Great Basin, US. Collections were screened for seed and seedling characteristics associated with increased plant performance in invaded Great Basin systems, and we provide a detailed methodology for these measurements. Relative to commercial seeds, wild-collected seeds had more characteristics identified as beneficial for seedling establishment including earlier emergence, higher specific root length, more root tips, and smaller overall size (E. elymoides), and earlier emergence, longer roots, higher root mass ratio, and more root tips (P. secunda). Commercial sources had significantly larger seeds than wild populations, a trait that had mixed effects on performance in previous research, and one that may change as wild collections are increased in agronomic conditions. These results suggest that locally-sourced populations are more likely to perform well in invaded areas, providing support for efforts to collect, screen, and increase local sources of seeds to improve restoration success.

Implications for Practice

Collecting and increasing local seeds requires more time and effort than purchasing commercially-available seeds, but if these sources have a greater chance at surviving in restoration sites, this effort is warranted

In our study, remnant local populations possessed more potentially adaptive traits than commercially-available alternatives, indicating they may be superior sources for the restoration of disturbed sites in their local regions

Screening multiple seed sources for potentially adaptive seed and seedling traits can be a relatively quick and effective way to select the most promising seeds for increase
Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model
Authors: Zhang Heming , Feng Jiarui , Zeng Amanda , Payne Philip , Li Fuhai
Published: April 2020

Drug combinations targeting multiple targets/pathways are believed to be able to reduce drug resistance. Computational models are essential for novel drug combination discovery. In this study, we proposed a new simplified deep learning model,DeepSignalingSynergy, for drug combination prediction. Compared with existing models that use a large number of chemical-structure and genomics features in densely connected layers, we built the model on a small set of cancer signaling pathways, which can mimic the integration of multi-omics data and drug target/mechanism in a more biological meaningful and explainable manner. The evaluation results of the model using the NCI ALMANAC drug combination screening data indicated the feasibility of drug combination prediction using a small set of signaling pathways. Interestingly, the model analysis suggested the importance of heterogeneity of the 46 signaling pathways, which indicates that some new signaling pathways should be targeted to discover novel synergistic drug combinations.
Interpretable Deep Learning for De Novo Design of Cell-Penetrating Abiotic Polymers
Authors: Schissel Carly K. , Mohapatra Somesh , Wolfe Justin M. , Fadzen Colin M. , Bellovoda Kamela , Wu Chia-Ling , Wood Jenna A. , Malmberg Annika B. , Loas Andrei , Gómez-Bombarelli Rafael , Pentelute Bradley L.
Published: April 2020

There are more amino acid permutations within a 40-residue sequence than atoms on Earth. This vast chemical search space hinders the use of human learning to design functional polymers. Here we couple supervised and unsupervised deep learning with high-throughput experimentation to drive the design of high-activity, novel sequences reaching 10 kDa that deliver antisense oligonucleotides to the nucleus of cells. The models, in which natural and unnatural residues are represented as topological fingerprints, decipher and visualize sequence-activity predictions. The new variants boost antisense activity by 50-fold, are effective in animals, are nontoxic, and can also deliver proteins into the cytosol. Machine learning can discover functional polymers that enhance cellular uptake of biotherapeutics, with significant implications toward developing therapies for currently untreatable diseases.

One sentence summary

Deep learning generates de novo large functional abiotic polymers that deliver antisense oligonucleotides to the nucleus.
Large hydrogen isotope fractionations distinguish nitrogenase-derived methane from other sources
Authors: Luxem Katja E. , Leavitt William D. , Zhang Xinning
Published: April 2020

Nitrogenase is the main source of natural fixed nitrogen for the biosphere. Two forms of this metalloenzyme, the vanadium (V) and iron (Fe)-only nitrogenases, were recently found to reduce small amounts of carbon dioxide into the potent greenhouse gas methane. Here we report carbon and hydrogen stable isotopic compositions and fractionations of methane generated by V- and Fe-only nitrogenases in the metabolically versatile nitrogen fixerRhodopseudomonas palustris. The stable carbon isotope fractionation imparted by both forms of alternative nitrogenase are within the range observed for hydrogenotrophic methanogenesis (13αCO2/CH4= 1.051 ± 0.002 for V-nitrogenase and 1.055 ± 0.001 for Fe-only nitrogenase, mean ± SE). In contrast, the hydrogen isotope fractionations (2αH2O/CH4= 2.071 ± 0.014 for V-nitrogenase and 2.078 ± 0.018 for Fe-only nitrogenase) are the largest of any known biogenic or geogenic pathway. The large2αH2O/CH4shows that the reaction pathway nitrogenases use to form methane strongly discriminates against2H, and that2αH2O/CH4distinguishes nitrogenase-derived methane from all other known biotic and abiotic sources. These findings on nitrogenase-derived methane will help constrain carbon and nitrogen flows in microbial communities and the role of the alternative nitrogenases in global biogeochemical cycles.

Importance

All forms of life require nitrogen for growth. Many different kinds of microbes living in diverse environments make inert nitrogen gas from the atmosphere bioavailable using a special protein,nitrogenase. Nitrogenase has a wide substrate range, and in addition to producing bioavailable nitrogen, some forms of nitrogenase also produce small amounts of the greenhouse gas methane. This is different from other microbes that produce methane to generate energy. Until now, there was no good way to determine when microbes with nitrogenases are making methane in nature. Here, we developed an isotopic fingerprint that allows scientists to distinguish methane from microbes making it for energy versus those making it as a byproduct of nitrogen acquisition. With this new fingerprint, it will be possible to improve our understanding of the relationship between methane production and nitrogen acquisition in nature.