bluuebunny/crossref_metadata_2025 huggingface dataset:
A Preliminary Report of the Biochemical and Clinical Effects of 1,4-Diaminobutane on Prevention of Human Hypertrophic Scars
Authors: Dolynchuk Kenneth N. , Tredget Edward E.
Published: December 2019

Objective evidence for the role of inhibition of collagen cross-linking in human scar using a nontoxic topical inhibitor, 1,4-diaminobutane (1,4 DAB), in patients with scars at risk for hypertrophic scar formation is presented. The authors used a concentration of 1,4 DAB of 0.8% (weight/volume) in a cream base similar to Glaxal Base. Application was once per day at night. The control was treated with cream base alone. In treatment phase studies at 2 months, tissue biopsies were performed and used to determine a therapeutic effect biochemically in paired scars harvested chosen with typical hypertrophic scars at two major treatment centers. Tissue transglutaminase activity revealed a significant reduction of the ε-(γ-glutamyl)lysine cross-links in the treated scars: 7.96 ± 1.51 pmol/µmol amino acid versus 14.78 ± 3.52 pmol/µmol amino acid. A subset of paired scars (n = 15) was also analyzed for soluble procollagen type III amino propeptide. The effect was a significant increase in procollagen type III amino propeptide in the scars treated with 1,4 DAB compared with sham-treated scars: 47.75 ± 4.6 µg/mg wet weight versus 39.08 ± 6.02 µg/mg wet weight, respectively. Levels of tissue 1,4 DAB was found to be twice as high in the presence of the active cream versus in the tissue of the control group. In subsequent prophylaxis studies, the authors treated 44 breast reduction patients prospectively with active cream to one or the other side in a double-blind randomized fashion. Hardness (in grams) measured using a Rex Durometer at 6 and 12 weeks postoperatively along with photographs were analyzed. The mean value ± SD of 24.98 ± 1.2 g on the active side versus 31.76 ± 1.1 g on the sham side was significantly different (p < 0.05). The patient scale scores of the Patient and Observer Scar Assessment Scale were also requested by survey in a responding 27-patient subgroup at a minimum 1 year postoperatively, and the differences between the two sides were found to be statistically significant, where the mean on the active side was 14.07 ± 1.34 and the mean on the sham side was 21.41 ± 1 (p < 0.05). The results are evidence to support the use of this agent in prevention of hypertrophic scars.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, II.
Quality and Safety in Healthcare, Part LIX
Authors: Harolds Jay A.
Published: December 2019

Decreasing the physician workload by promoting processes that produce greater efficiency, including the use of teams and delegating certain jobs to nurses, advanced practice providers, and scribes, is very helpful to reduce burnout and promote wellness. The team approach and enlightened leadership at all levels are important to maximize productivity, have common goals doing meaningful work, and have more control over the environment at work, all of which also results in less burnout and greater wellness.
Incidence of Radioembolization-Induced Liver Disease and Liver Toxicity Following Repeat 90Y-Radioembolization
Authors: Elsayed Mohammad , Ermentrout Robert M. , Sethi Ila , Bercu Zachary L. , Galt James R. , Whitmore Morgan , Brandon David C. , Schuster David M. , Kokabi Nima
Published: December 2019

Purpose

The complication profile following repeat 90Y-radioembolization (RE) is not well understood, and repeat RE is sometimes avoided because of concerns for RE-induced liver disease (REILD) and liver toxicity. The purpose of this study was to examine the incidence of REILD and liver toxicity following repeat 90Y-RE and to identify potential risk factors.

Methods

A retrospective analysis of patients undergoing repeat RE to the same hepatic lobe between 2013 and 2018 was performed. Baseline factors were evaluated as predictors of liver toxicity, mortality, and REILD, which was defined as the presence symptomatic ascites or jaundice in the absence of biliary obstruction within 8 weeks following RE. Post-RE complications were graded according to the Common Terminology Criteria for Adverse Events version 5.

Results

A total of 39 patients underwent repeat RE with 14 (35.9%) experiencing Common Terminology Criteria for Adverse Events toxicity of grade 2 or greater, 3 (10.3%) grade 3, and no grade 4 or greater. A Model for End Stage Liver Disease score of 8 or greater was associated with grade 2 toxicity or greater (26.7% vs 75%; P = 0.013). Only 3 patients (7.7%) experienced REILD due to symptomatic ascites without jaundice. Greater than 2 REs were associated with a greater rate of 6-month mortality (12% vs 58.3%, P = 0.003), 12-month mortality (28% vs 75%, P = 0.007), and REILD (0% vs 21.4%, P = 0.016). Age, sex, microsphere type, cirrhosis, Child-Pugh, and Eastern Cooperative Oncology Group status were not significantly associated with complications, REILD, or survival.

Conclusions

Repeat 90Y-RE appears to be well tolerated with a low rate of high-grade adverse events and REILD.
Primary Ewing Sarcoma/Primitive Neuroectodermal Tumor of Kidney With Inferior Vena Cava Thrombus
Authors: Tripathy Sarthak , Shamim Shamim Ahmed , Chellapuram Santosh , Barwad Adarsh , Rastogi Sameer
Published: December 2019

Primary Ewing sarcoma/primitive neuroectodermal tumor is a group of rare aggressive tumors in adults derived from neuroectoderm, and primary renal involvement is extremely rare. We describe an 18F-FDG PET/CT findings of a 28-year-old man who presented with left renal mass with inferior vena cava thrombus, which turned out to be primary Ewing sarcoma on histopathology specimen post left nephrectomy.
Nigrostriatal Degeneration in the Cognitive Part of the Striatum in Parkinson Disease Is Associated With Frontomedial Hypometabolism
Authors: Apostolova Ivayla , Lange Catharina , Frings Lars , Klutmann Susanne , Meyer Philipp T. , Buchert Ralph
Published: December 2019

Purpose

The present study investigated possible associations between cortical dysfunction/degeneration as measured by 18F-FDG PET and nigrostriatal degeneration according to the specific 123I-FP-CIT binding ratio (SBR) in striatal subregions defined by striato-cortical anatomical connectivity in Parkinson disease (PD) patients.

Materials and Methods

The study included 41 patients (61.4 ± 12.8 years) with PD-typical reduction of striatal FP-CIT SBR and no sign of atypical parkinsonian syndrome on FDG PET. FP-CIT SBR was determined separately in the cognitive (composite of executive and limbic) and sensorimotor part of the striatum according to the Oxford-GSK-Imanova Striatal Connectivity Atlas. Scaled FDG uptake was tested voxelwise for correlation with FP-CIT SBR (familywise error corrected P < 0.05).

Results

A large cluster (17.6 mL) of significant correlation of scaled FDG uptake with FP-CIT SBR in the cognitive part of the striatum, corrected for SBR in the sensorimotor part, was detected in the bilateral medial frontal cortex and the anterior cingulate cortex (partial correlation coefficient R = 0.767); small clusters were detected in ipsilateral caudate and ipsilateral thalamus. There was a small contralateral occipital cluster (3.0 mL) of significant correlation between FDG uptake and sensorimotor SBR corrected for cognitive SBR (R = 0.709).

Conclusions

The correlation between nigrostriatal degeneration in the cognitive striatum and reduced cerebral glucose metabolism in the medial parts of the frontal cortex including the anterior cingulate suggests that nigrostriatal degeneration is specifically involved in the pathogenesis of cognitive deficits associated with medial frontal dysfunction such as impaired inhibitory control.
68Ga-PMSA Uptake in the Lung
Authors: Usmani Sharjeel , Sadeq Alya'a , Marafi Fahad , Esmail Abdulredha , al Kandari Fareeda , Ahmed Najeeb
Published: December 2019

68Ga-PSMA is a promising tracer for both primary staging and detection of biochemical recurrence in prostate cancer. PSMA is also expressed in the neovascular endothelium of various solid malignancies possibly due to tumor-associated angiogenic factors and endothelial cell sprouting. We report a case of a 73-year-old man of prostate cancer with rising prostate-specific antigen levels. 68Ga-PSMA PET/CT was performed, which showed a focal lung lesion, with subsequent histological confirmation of adenocarcinoma of the lung. Incidental lung lesions on 68Ga-PSMA in prostate cancer patients should elicit a differential of primary lung malignancy, especially if clinical and morphological suspicion is high.
Hürthle Cell Thyroid Adenoma Showing Avid Uptake on 18F-PSMA-1007 PET/CT
Authors: Tang Kun , Wang Zhiqiang , Lin Jie , Zheng Xiangwu
Published: December 2019

We report the case of a 74-year-old man with suspected recurrent prostate carcinoma who underwent 18F-PSMA-1007 PET/CT for restaging the disease. PET/CT imaging presented an incidentaloma with intense 18F-PSMA-1007 uptake in the right thyroid lobe. Biopsy and genomic sequencing test confirmed the diagnosis of Hürthle cell thyroid adenoma. Therefore, it is important to raise awareness of this benign lesion in the differential diagnosis of incidental thyroid nodules with high 18F-PSMA-1007 activity.
Twelve-Year Survival of a Patient With Lymph Node, Pulmonary, Bone, Cardiac and Intraspinal Metastases of a Rectal Neuroendocrine Neoplasm Treated With Peptide Receptor Radionuclide Therapy—The Value of Salvage Peptide Receptor Radionuclide Therapy
Authors: Zhang Jingjing , Kulkarni Harshad R. , Singh Aviral , Baum Richard P.
Published: December 2019

We report here the 12-year survival after the first peptide receptor radionuclide therapy (PRRT) of a patient with metastatic rectal neuroendocrine neoplasms, who received 7 cycles of PRRT with 177Lu/90Y-DOTATATE/DOTATOC in 4 treatment phases. The patient demonstrated excellent response to each cycle of treatment, without any adverse effect even after repeated PRRT cycles. Most recently, immunohistochemistry revealed a G3 neuroendocrine neoplasm and intraspinal metastasis were successfully resected by neurosurgical intervention. This case nicely demonstrates that several “salvage” PRRTs can be given over many years leading to repetitive benefit for the patient and saving patients of possible toxicity of alternative treatments.
Patient-centered Radiology
Authors: Cook Tessa S.
Published: December 2019

Radiology is unique compared with most other medical specialties in that care can sometimes be delivered without speaking to or touching the patient. Although radiologists have increasingly become involved in patient safety, quality improvement, informatics, and advocacy, they must still work harder than other medical specialties to be considered “patient-facing.” While cardiothoracic radiologists have likely experienced fewer opportunities to directly interface with patients, shared decision-making with patients around lung cancer screening and radiation dose optimization are both excellent examples of patient-centered and family-centered care in cardiothoracic imaging. Many cardiothoracic examinations necessitate medication administration or customized breath-holds not required of other examinations and create an opportunity for discussion between cardiothoracic radiologists and patients. Opportunities to increase the patient-centered focus in radiology exist at every interface between the radiology practice and the patient. Implementing the principles of patient-centered and family-centered care in a radiology department or practice requires the participation and engagement of all stakeholders, including patients.
Readmission for infection after blunt splenic injury: A national comparison of management techniques
Authors: Cioci Alessia C. , Parreco Joshua P. , Lindenmaier Laurence B. , Olufajo Olubode A. , Namias Nicholas , Askari Reza , DeRosa Luis , Rattan Rishi
Published: December 2019

BACKGROUND

As nonoperative management (NOM) of blunt splenic injury (BSI) increases, understanding risks, especially infectious complications, becomes more important. There are no national studies on BSI outcomes that track readmissions across hospitals. Prior studies demonstrate that infection is a major cause of readmission after trauma and that a significant proportion is readmitted to different hospitals. The purpose of this study was to compare nationwide outcomes of different treatment modalities for BSI including readmissions to different hospitals.

METHODS

The Nationwide Readmissions Database for 2010 to 2014 was queried for patients 18 years to 64 years old admitted nonelectively with a primary diagnosis of BSI. Organ space infection; a composite infectious incidence of surgical site infection (SSI), urinary tract infection, and pneumonia; and sepsis were identified in three groups: NOM, splenic artery embolization (SAE), and operative management (OM). Rates of infection were quantified during index admission and 30-day and 1-year readmission. Multivariable logistic regression was performed. Results were weighted for national estimates.

RESULTS

Of the 37,986 patients admitted for BSI, 54.1% underwent NOM, 12.2% SAE, and 33.7% OM. Compared with OM and NOM, SAE had the highest rates of organ space SSI at 1 year (3.9% vs. 2.2% vs. 1.7%, p < 0.001). Compared with NOM, at 1 year, SAE had higher rates of infection (17.2% vs. 8.1%, p < 0.001) and sepsis (3.2% vs. 1.1%, p < 0.001). Compared with NOM, SAE had an increased risk of infection (odds ratio [OR], 1.24; 95 confidence interval [95% CI], 1.10–1.39; p < 0.001) and sepsis (OR, 1.37; 95% CI, 1.06–1.76; p < 0.001) at 1 year. At 1 year, SAE had increased risk of organ space SSI (OR, 1.99; 1.60–2.47; p < 0.001) but OM did not.

CONCLUSION

Blunt splenic injury treated with SAE is at increased risk of both immediate and long-term infectious complications. Despite being considered splenic preservation, surgeons should be aware of these risks and incorporate such knowledge into their practice accordingly.

LEVEL OF EVIDENCE

Epidemiological study, level IV.
Preoperative computed tomography is poor in detecting tumors of the appendix among patients with acute appendicitis: A cohort study of 5,224 appendectomies
Authors: Kangaspunta Helmi , Tahkola Kyösti , Wirta Erkki-Ville , Kotaluoto Sannamari , Laukkarinen Johanna , Ukkonen Mika
Published: December 2019

BACKGROUND

Neoplastic processes are among the known etiologies for acute appendicitis. While conservative treatment with antibiotics alone has been proposed as a treatment for uncomplicated appendicitis, the presence of tumors should be excluded when offering patients this option. The aim of this study was to assess the accuracy of computed tomography (CT) in detecting appendiceal tumors.

METHOD

Consecutive patients operated on for acute appendicitis between January 2007 and October 3, 2018, in our university hospital were included. Whenever appendiceal tumor was histopathologically confirmed, CT interpretations and surgical reports were carefully reviewed. All CT scans were reanalyzed by consultant body radiologists. Discrepancies between the preliminary and final radiological interpretations were noted.

RESULTS

A total of 5,224 patients underwent appendectomy, of whom 4,766 had histopathologically confirmed acute appendicitis. Eighty-four patients (median, 61 (13–89) years; 54% female) were diagnosed with appendiceal tumor. Fifty-two patients (62%) had uncomplicated appendicitis. Although incidence of tumors was associated with older age, tumors were found in all ages. The share of tumors increased from 1.7% to 3.0%/year during the study. The most common tumors were neuroendocrine tumors (n = 33), low-grade appendiceal mucinous neoplasms (n = 14), and adenocarcinomas (n = 11). Sixty-one patients (73%) underwent preoperative CT. Computed tomography interpretation during on-call hours suspected tumor in only one case (3.4%) with invasive tumor, and in five cases (16%) with noninvasive tumor.

CONCLUSION

Appendiceal tumors are possible findings in appendix specimens, and most patients had uncomplicated acute appendicitis. In light of findings we conclude that CT cannot be used to exclude neoplastic etiology underlying acute appendicitis.

LEVEL OF EVIDENCE

Diagnostic, level IV.
The American Association for the Surgery of Trauma renal injury grading scale: Implications of the 2018 revisions for injury reclassification and predicting bleeding interventions
Authors: Keihani Sorena , Rogers Douglas M. , Putbrese Bryn E. , Anderson Ross E. , Stoddard Gregory J. , Nirula Raminder , Luo-Owen Xian , Mukherjee Kaushik , Morris Bradley J. , Majercik Sarah , Piotrowski Joshua , Dodgion Christopher M. , Schwartz Ian , Elliott Sean P. , DeSoucy Erik S. , Zakaluzny Scott , Sherwood Brenton G. , Erickson Bradley A. , Baradaran Nima , Breyer Benjamin N. , Fick Cameron N. , Smith Brian P. , Okafor Barbara U. , Askari Reza , Miller Brandi D. , Santucci Richard A. , Carrick Matthew M. , Allen LaDonna , Norwood Scott , Hewitt Timothy , Burks Frank N. , Heilbrun Marta E. , Gross Joel A. , Myers Jeremy B.
Published: December 2019

BACKGROUND

In 2018, the American Association for the Surgery of Trauma (AAST) published revisions to the renal injury grading system to reflect the increased reliance on computed tomography scans and non-operative management of high-grade renal trauma (HGRT). We aimed to evaluate how these revisions will change the grading of HGRT and if it outperforms the original 1989 grading in predicting bleeding control interventions.

METHODS

Data on HGRT were collected from 14 Level-1 trauma centers from 2014 to 2017. Patients with initial computed tomography scans were included. Two radiologists reviewed the scans to regrade the injuries according to the 1989 and 2018 AAST grading systems. Descriptive statistics were used to assess grade reclassifications. Mixed-effect multivariable logistic regression was used to measure the predictive ability of each grading system. The areas under the curves were compared.

RESULTS

Of the 322 injuries included, 27.0% were upgraded, 3.4% were downgraded, and 69.5% remained unchanged. Of the injuries graded as III or lower using the 1989 AAST, 33.5% were upgraded to grade IV using the 2018 AAST. Of the grade V injuries, 58.8% were downgraded using the 2018 AAST. There was no statistically significant difference in the overall areas under the curves between the 2018 and 1989 AAST grading system for predicting bleeding interventions (0.72 vs. 0.68, p = 0.34).

CONCLUSION

About one third of the injuries previously classified as grade III will be upgraded to grade IV using the 2018 AAST, which adds to the heterogeneity of grade IV injuries. Although the 2018 AAST grading provides more anatomic details on injury patterns and includes important radiologic findings, it did not outperform the 1989 AAST grading in predicting bleeding interventions.

LEVEL OF EVIDENCE

Prognostic and Epidemiological Study, level III.
Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations
Authors: Ramaker Ryne C. , Hardigan Andrew A. , Goh Say-Tar , Partridge E. Christopher , Wold Barbara , Cooper Sara J. , Myers Richard M.
Published: December 2019

DNA associated proteins (DAPs) classically regulate gene expression by binding to regulatory loci such as enhancers or promoters. As expanding catalogs of genome-wide DAP binding maps reveal thousands of loci that, unlike the majority of conventional enhancers and promoters, associate with dozens of different DAPs with apparently little regard for motif preference, an understanding of DAP association and coordination at such regulatory loci is essential to deciphering how these regions contribute to normal development and disease. In this study, we aggregated publicly available ChIP-seq data from 469 human DAPs assayed in three cell lines and integrated these data with an orthogonal dataset of 352 non-redundant,in vitro-derived motifs mapped to the genome within DNase hypersensitivity footprints in an effort to characterize regions of the genome that have exceptionally high numbers of DAP associations. We subsequently performed a massively parallel mutagenesis assay to search for sequence elements driving transcriptional activity at such loci and explored plausible biological mechanisms underlying their formation. We establish a generalizable definition for High Occupancy Target (HOT) loci and identify putative driver DAP motifs in HEPG2 cells, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and exhibit sequence conservation at HOT loci. The number of different DAPs associated with an element is positively associated with evidence of regulatory activity and, by systematically mutating 245 HOT loci, we localized regulatory activity to a central core region that depends on the motif sequences of our previously nominated driver DAPs. In sum, this work leverages the increasingly large number of DAP motif and ChIP-seq data publicly available to explore how DAP associations contribute to genome-wide transcriptional regulation.
Kinetic improvement of an algal diacylglycerol acyltransferase 1 via fusion with an acyl-CoA binding protein
Authors: Xu Yang , Caldo Kristian Mark P. , Falarz Lucas , Jayawardhane Kethmi , Chen Guanqun
Published: December 2019

Microalgal oils in the form of triacylglycerols (TAGs) are broadly used as nutritional supplements and biofuels. Diacylglycerol acyltransferase (DGAT) catalyzes the final step of acyl-CoA-dependent biosynthesis of TAG and is considered a key target for manipulating oil production. Although a growing number ofDGAT1s have been identified and over-expressed in some algal species, the detailed structure-function relationship, as well as the improvement of DGAT1 performance via protein engineering, remain largely untapped. Here, we explored the structure-function features of the hydrophilic N-terminal domain of DGAT1 from the green microalgaChromochloris zofingiensis(CzDGAT1). The results indicated that the N-terminal domain of CzDGAT1 was less disordered than those of the higher eukaryotic enzymes and its partial truncation or complete removal could substantially decrease enzyme activity, suggesting its possible role in maintaining enzyme performance. Although the N-terminal domains of animal and plant DGAT1s were previously found to bind acyl-CoAs, replacement of CzDGAT1 N-terminus by an acyl-CoA binding protein (ACBP) could not restore enzyme activity. Interestingly, the fusion of ACBP to the N-terminus of the full-length CzDGAT1 could enhance the enzyme affinity for acyl-CoAs and augment protein accumulation levels, which ultimately drove oil accumulation in yeast cells and tobacco leaves to higher levels than the full-length CzDGAT1. Overall, our findings unravel the distinct features of the N-terminus of algal DGAT1 and provide a strategy to engineer enhanced performance in DGAT1 via protein fusion, which may open a vista in generating improved membrane-bound acyl-CoA-dependent enzymes and boosting oil biosynthesis in plants and oleaginous microorganisms.

SIGNIFICANCE STATEMENT

Here, we explored the N-terminus of a microalgal DGAT1, a membrane-bound enzyme determining oil biosynthesis, usingin silicoanalysis, truncation mutagenesis, protein fusion andin vitroandin vivocharacterization, and demonstrated its distinct structure-function features from the higher eukaryotic enzymes. We further engineered enhanced performance in DGAT1 via N-terminal fusion of ACBP, and obtained a kinetically improved enzyme with augmented protein production levels, which could boost oil accumulation in yeast and plant vegetative tissues.
Ecological and evolutionary drivers of hemoplasma infection and bacterial genotype sharing in a Neotropical bat community
Authors: Becker Daniel J. , Speer Kelly A. , Brown Alexis M. , Fenton M. Brock , Washburne Alex D. , Altizer Sonia , Streicker Daniel G. , Plowright Raina K. , Chizhikov Vladimir E. , Simmons Nancy B. , Volokhov Dmitriy V.
Published: December 2019

Most emerging pathogens can infect multiple species, underscoring the importance of understanding the ecological and evolutionary factors that allow some hosts to harbor greater infection prevalence and share pathogens with other species. However, our understanding of pathogen jumps is primarily based around viruses, despite bacteria accounting for the greatest proportion of zoonoses. Because bacterial pathogens in bats (Order: Chiroptera) can have conservation and human health consequences, studies that examine the ecological and evolutionary drivers of bacterial prevalence and barriers to pathogen sharing are crucially needed. We here studied hemotropicMycoplasmaspp. (i.e., hemoplasmas) across a species-rich bat community in Belize over two years. Across 469 bats spanning 33 species, half of individuals and two-thirds of species were hemoplasma positive. Infection prevalence was higher for males and for species with larger body mass and colony sizes. Hemoplasmas displayed high genetic diversity (21 novel genotypes) and strong host specificity. Evolutionary patterns supported co-divergence of bats and bacterial genotypes alongside phylogenetically constrained host shifts. Bat species centrality to the network of shared hemoplasma genotypes was phylogenetically clustered and unrelated to prevalence, further suggesting rare—but detectable—bacterial sharing between species. Our study highlights the importance of using fine phylogenetic scales when assessing host specificity and suggests phylogenetic similarity may play a key role in host shifts for not only viruses but also bacteria. Such work more broadly contributes to increasing efforts to understand cross-species transmission and epidemiological consequences of bacterial pathogens.
Seq2DFunc: 2-dimensional convolutional neural network on graph representation of synthetic sequences from massive-throughput assay
Authors: Guo Haotian , Song Xiaohu , Lindner Ariel B.
Published: December 2019

In recent years, a pipeline of massively parallel reporter assay (MPRA), and next-generation sequencing (NGS) provided large-scale datasets to investigate biological mechanisms in detail. However, bigger data often leads to larger complexity. As a result, theories derived from low-throughput experiments lose explanatory power, requiring new methods to create predictive models. Here we focus on modeling functions of nucleic acid sequences, as a study case of massive-throughput assays. We report a deep learning approach, training a two-dimensional convolutional neural network (CNN) on an ordered graph representation of nucleic acid sequences to predict their functions (Seq2DFunc). To compare the performance of Seq2DFunc with conventional methods, we obtained customized database on a CRISPR RNA processing assay. For this specific assay, analyses of sequence and RNA structure determinants failed to explain the results regardless of dataset size. 1-dimensional CNN of raw sequences generate generally failed to converge at < 10,000 or fewer sequences. By contrast, Seq2DFunc trained on ∼ 7,000 sequences still provided 86% accuracy. Given a sufficient dataset (∼ 120,000 sequences) for training, Seq2DFunc (96% accuracy, 0.93 f1-score) still outperformed the best 1D CNN (92% accuracy, 0.83 f1-score). We anticipate Seq2DFunc can be a versatile downstream tool for deciphering massive-throughput assays for many fundamental studies. In addition, the use of smaller dataset is especially beneficial to reduce the experiment budget or required sequencing depth.
A genome-wide Approximate Bayesian Computation approach suggests only limited numbers of soft sweeps in humans over the last 100,000 years
Authors: Laval Guillaume , Patin Etienne , Boutillier Pierre , Quintana-Murci Lluis
Published: December 2019

Over the last 100,000 years, humans have spread across the globe and encountered a highly diverse set of environments to which they have had to adapt. Genome-wide scans of selection are powerful to detect selective sweeps. However, because of unknown fractions of undetected sweeps and false discoveries, the numbers of detected sweeps often poorly reflect actual numbers of selective sweeps in populations. The thousands of soft sweeps on standing variation recently evidenced in humans have also been interpreted as a majority of mis-classified neutral regions. In such a context, the extent of human adaptation remains little understood. We present a new rationale to estimate these actual numbers of sweeps expected over the last 100,000 years (denoted byX) from genome-wide population data, both considering hard sweeps and selective sweeps on standing variation. We implemented an approximate Bayesian computation framework and showed, based on computer simulations, that such a method can properly estimateX. We then jointly estimated the number of selective sweeps, their mean intensity and age in several 1000G African, European and Asian populations. Our estimations ofX, found weakly sensitive to demographic misspecifications, revealed very limited numbers of sweeps regardless the frequency of the selected alleles at the onset of selection and the completion of sweeps. We estimated ∼80 sweeps in average across fifteen 1000G populations when assuming incomplete sweeps only and ∼140 selective sweeps in non-African populations when incorporating complete sweeps in our simulations. The method proposed may help to address controversies on the number of selective sweeps in populations, guiding further genome-wide investigations of recent positive selection.
Influence of native endophytic bacteria on the growth and bacterial crown rot tolerance of papaya (Carica papaya)
Authors: Rivarez Mark Paul Selda , Parac Elizabeth P. , Dimasingkil Shajara Fatima M. , Mirnia Eka , Magdalita Pablito M.
Published: December 2019

The native plant microbiome is composed of diverse communities that influence its overall health, with some species known to promote plant growth and pathogen resistance. Here, we show the antimicrobial and growth promoting activities of autoclaved culture metabolites (ACMs) from native endophytic bacteria (NEB) in a papaya cultivar that is tolerant to bacterial crown rot (BCR) caused byErwinia mallotivora. Initially, bacterial colonization in recovering tissues of this cultivar was observed before onset of tissue regeneration or ‘regrowth’. We further isolated and characterized these bacteria and were able to identify two culturable stem NEB under generaKosakonia(EBW), related to Enterobacter, andSphingomonas(EBY). We also identified root NEB (BN, BS and BT) under genusBacillus. Inhibition assays indicated that ACMs from these NEB promptly (18-30h) and efficiently inhibited (60-65%)E. mallotivoraproliferationin vitro. Interestingly, when ACMs from BN and EBW were inoculated in surface-sterilized papaya seeds, germination was variably retarded (20-60% reduction) depending on plant genotype, but plant biomass accumulation was significantly stimulated, at around two-fold increase. Moreover, greenhouse experiments show that ACMs from all isolates, especially EBW, significantly reduced BCR incidence and severity in susceptible genotype, at around two-fold. In general, our observations of pathogen antagonism, plant growth promotion leading to disease reduction by ACMs of native endophytic bacteria suggested its contribution to increased fitness of papaya and tolerance against the (re)emerging BCR disease.
Heterogeneous habenular neuronal ensembles during selection of defensive behaviors
Authors: Lecca Salvatore , Namboodiri Vijay MK , Restivo Leonardo , Gervasi Nicolas , Pillolla Giuliano , Stuber Garret D. , Mameli Manuel
Published: December 2019

Optimal selection of threat-driven defensive behaviors is paramount to an animal’s survival. The lateral habenula (LHb) is a key neuronal hub coordinating behavioral responses to aversive stimuli. Yet, how individual LHb neurons represent defensive behaviors in response to threats remains unknown. Here we show that, in mice, a visual threat promotes distinct defensive behaviors, namely runaway (escape) and action-locking (immobile-like). Fiber photometry of bulk LHb neuronal activity in behaving animals revealed an increase and decrease of calcium signal time-locked with runaway and action-locking, respectively. Imaging single-cell calcium dynamics across distinct threat-driven behaviors identified independently active LHb neuronal clusters. These clusters participate during specific time epochs of defensive behaviors. Decoding analysis of this neuronal activity unveiled that some LHb clusters either predict the upcoming selection of the defensive action or represent the selected action. Thus, heterogeneous neuronal clusters in LHb predict or reflect the selection of distinct threat-driven defensive behaviors.
A High-Throughput Extraction and Analysis Method for Steroidal Glycoalkaloids in Tomato
Authors: Dzakovich Michael P. , Hartman Jordan L. , Cooperstone Jessica L.
Published: December 2019

Tomato steroidal glycoalkaloids (tSGAs) are a class of cholesterol-derived metabolites uniquely produced by the tomato clade. These compounds provide protection against biotic stress due to their fungicidal and insecticidal properties. Although commonly reported as being anti-nutritional, bothin vitroas well as pre-clinical animal studies have indicated that some tSGAs may have a beneficial impact on human health. However, the paucity of quantitative extraction and analysis methods presents a major obstacle for determining the biological and nutritional functions of tSGAs. To address this problem, we developed and validated the first comprehensive extraction and UHPLC-MS/MS quantification method for tSGAs. Our extraction method allows for up to 16 samples to be extracted simultaneously in 20 minutes with 93.0 ± 6.8% and 100.8 ± 13.1% recovery rates for tomatidine and alpha-tomatine, respectively. Our ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method was able to chromatographically separate analytes derived from 16 tSGAs representing 9 different tSGA masses, as well as two internal standards, in 13 minutes. Tomato steroidal glycoalkaloids that did not have available standards were annotated using high resolution mass spectrometry as well as product ion scans that provided fragmentation data. Lastly, we utilized our method to survey a variety of commonly consumed tomato-based products. Total tSGA concentrations ranged from 0.7 to 3.4 mg/serving and represent some of the first reported tSGA concentrations in tomato-based products. Our validation studies indicate that our method is sensitive, robust, and able to be used for a variety of applications where concentrations of biologically relevant tSGAs need to be quantified.
Simulating intervertebral disc cell behavior within 3D multifactorial environments
Authors: Baumgartner L. , Reagh J.J. , González Ballester M.A. , Noailly J.
Published: December 2019

Motivation

Low back pain is responsible for more global disability than any other condition. Its incidence is closely related to intervertebral disc (IVD) failure, which is likely caused by an accumulation of microtrauma within the IVD. Crucial factors in microtrauma development are not entirely known yet, probably because their exploration in vivo or in vitro remains tremendously challenging. In-silico modelling is, therefore, definitively appealing, and shall include approaches to integrate influences of multiple cell stimuli at the microscale. Accordingly, this study introduces a hybrid Agent-based (AB) model in IVD research and exploits network modelling solutions in systems biology to mimic the cellular behavior of Nucleus Pulposus cells exposed to a 3D multifactorial biochemical environment, based on mathematical integrations of existing experimental knowledge. Cellular activity reflected by mRNA expression of Aggrecan, Collagen type I, Collagen type II, MMP-3 and ADAMTS were calculated for inflamed and non-inflamed cells. mRNA expression over long periods of time is additionally determined including cell viability estimations. Model predictions were eventually validated with independent experimental data.

Results

As it combines experimental data to simulate cell behavior exposed to a multifactorial environment, the present methodology was able to reproduce cell death within 3 days under glucose deprivation and a 50% decrease in cell viability after 7 days in an acidic environment. Cellular mRNA expression under non-inflamed conditions simulated a quantifiable catabolic shift under an adverse cell environment, and model predictions of mRNA expression of inflamed cells provide new explanation possibilities for unexpected results achieved in experimental research.

Contact

laura.baumgartner@upf.edu
TheEruca sativagenome and transcriptome: A targeted analysis of sulfur metabolism and glucosinolate biosynthesis pre and postharvest
Authors: Bell Luke , Chadwick Martin , Puranik Manik , Tudor Richard , Methven Lisa , Kennedy Sue , Wagstaff Carol
Published: December 2019

Rocket (Eruca sativa) is a source of health-related metabolites called glucosinolates (GSLs) and isothiocyanates (ITCs) but little is known of the genetic and transcriptomic mechanisms responsible for regulating pre and postharvest accumulations. We present the firstde novoreference genome assembly and annotation, with ontogenic and postharvest transcriptome data relating to sulfur assimilation, transport, and utilization. Diverse gene expression patterns related to sulfur metabolism and GSL biosynthesis are present between inbred lines of rocket. A clear pattern of differential expression determines GSL abundance and the formation of hydrolysis products. One breeding line sustained GSL accumulation and hydrolysis product formation throughout storage. Copies ofMYB28,SLIM1, SDI1andESM1orthologs have increased and differential expression postharvest, and are associated with GSLs and hydrolysis product formation. Two glucosinolate transporter gene orthologs (GTR2) were found to be associated with increased GSL accumulations.
Expression and function of voltage gated proton channels (H V 1) in MDA-MB-231 cells
Authors: Bare Dan , Cherny Vladimir , Abukhdeir Abde , DeCoursey Thomas , morgan deri
Published: December 2019

Expression of the voltage gated proton channel (H v 1) as identified by immunocytochemistry has been previously reported in breast cancer tissue. Increased expression of H V 1 was correlated with poor prognosis and decreases overall and disease-free survival but the mechanism of its involvement in the disease is unknown. Here we present electrophysiological recordings of H V 1 channel activity thus, demonstrating their presence and functional properties in the plasma membrane of a breast cancer cell line, MDA-MB-231. With western blotting we also identify significant levels of H V 1 expression in 3 out of 8 “triple negative” breast cancer cell lines (estrogen, progesterone, and HER2 receptor expression negative). We examine the function of H V 1 in breast cancer using MDA-MB-231 cells as a model by suppressing the expression of H V 1 using shRNA (“knock-down;”“KD”) and by eliminating H V 1 using CRISPR/Cas9 gene editing (“knock-out”; “KO”). However, these two approaches produced different effects. Knock-down of H V 1 using shRNA resulted in slower cell migration in a scratch assay and a significant reduction in H 2 O 2 release. In contrast, H V 1 KO cells do not show reduction in migration or H 2 O 2 release. H V 1 KO but not knock-down cells showed an increased glycolytic rate with an accompanied increase in p-AKT (Phospho-AKT, Ser473) activity. The expression of CD171/LCAM-1, an adhesion molecule and prognostic indicator for breast cancer, was reduced in the absence of H V 1 expression. When we compared MDA-MB-231 xenograft growth rates in immunocompromised mice, tumors from H V 1 KO cells grew less in mass with lower staining for the Ki-67 maker for cell proliferation rate. Therefore, deletion of H V 1 expression in MDA-MB-231 cells limits tumor growth rate. The limited growth thus, appears to be independent of oxidant production by NADPH oxidase molecules and be determined through cell adhesion activity. While H V 1 KO results in cell mechanisms different from KD, both implicate H V 1-mediated pathways for control of tumor growth in the MDA-MB-231 cell line.
Haplotype of the astrocytic water channel AQP4 modulates slow wave energy in human NREM sleep
Authors: Larsen Sara Marie Ulv , Landolt Hans-Peter , Berger Wolfgang , Nedergaard Maiken , Knudsen Gitte Moos , Holst Sebastian Camillo
Published: December 2019

Cerebrospinal fluid (CSF) flow through the brain parenchyma is facilitated by the astrocytic water channel aquaporin 4 (AQP4). Homeostatically regulated electroencephalographic (EEG) slow waves are a hallmark of deep non-rapid-eye-movement (NREM) sleep and have been implicated in the regulation of parenchymal CSF flow and brain clearance. The humanAQP4gene harbors several single nucleotide polymorphisms (SNPs) associated with AQP4 expression, brain-water homeostasis and neurodegenerative diseases. To date, their role in sleep-wake regulation is unknown. To investigate whether functional variants inAQP4modulate human sleep, nocturnal EEG-recordings and cognitive performance were investigated in 123 healthy participants genotyped for a common eight-SNPAQP4-haplotype. We show that thisAQP4-haplotype is associated with distinct modulations of NREM slow wave energy, strongest in early sleep and mirrored by changes in sleepiness and reaction times during extended wakefulness. The study provides the first human evidence for a link between AQP4, deep NREM sleep and cognitive consequences of prolonged wakefulness.
Morphologically and physiologically diverse fruits of twoLepidiumspecies differ in allocation of glucosinolates into immature and mature seed and pericarp
Authors: Mohammed Said , Bhattacharya Samik , Gesing Matthias A. , Klupsch Katharina , Theißen Günter , Mummenhoff Klaus , Müller Caroline
Published: December 2019

The morphology and physiology of diaspores play crucial roles in determining the fate of seeds in unpredictable habitats. In some genera of the Brassicaceae different types of diaspores can be found.Lepidium appelianumproduces non-dormant seeds within indehiscent fruits while inL. campestredormant seeds are released from dehiscent fruits. These different diaspore types offer an excellent model system to analyse the allocation of relevant defence compounds into different tissues, which may maximise diaspore fitness. Total glucosinolate concentration and composition were analysed in immature and mature seeds and pericarps ofL. appelianumandL. campestreusing high-performance liquid chromatography. Moreover, transgenic RNAiL. campestrelines were used for comparison that produce indehiscent fruits due to silencing ofLcINDEHISCENCE, theINDEHISCENCEortholog ofL. campestre. Total glucosinolate concentrations were lower in green compared to mature seeds in all studiedLepidiumspecies and transgenic lines. In contrast, indehiscent fruits ofL. appelianummaintained their total glucosinolate concentration in mature pericarps compared to green ones, while in dehiscentL. campestreand in indehiscent RNAi-LcIND L. campestrea significant decrease in total glucosinolate concentrations from green to mature pericarps could be detected. Regarding the distribution of glucosinolate classes, high concentrations of 4-methoxyindol-3-ylmethyl glucosinolate were found in mature seeds ofL. appelianum, while no indole glucosinolates were detected in mature diaspores ofL. campestre. The diaspores of the latter species may rather depend on aliphatic and aromatic glucosinolates for long-term protection. The allocation patterns of glucosinolates correlate with the morpho-physiologically distinct fruits ofL. appelianumandL. campestreand may be explained by the distinct dispersal strategies and the dormancy status of both species.
Lipin-1 contributes to IL-4 mediated macrophage polarization
Authors: Chandran Sunitha , Schilke Robert M. , Blackburn Cassidy M.R. , Yurochko Aila , Mirza Rusella , Scott Rona S. , Finck Brian N. , Woolard Matthew D.
Published: December 2019

Macrophage responses contribute to a diverse array of pathologies ranging from infectious disease to sterile inflammation. Polarization of macrophages determines their cellular function within biological processes. Lipin-1 is a phosphatidic acid phosphatase in which its enzymatic activity contributes to macrophage pro-inflammatory responses. Lipin-1 also possesses transcriptional co-regulator activity and whether this activity is required for macrophage polarization is unknown. Using mice that lack only lipin-1 enzymatic activity or both enzymatic and transcriptional coregulator activities from myeloid cells, we investigated the contribution of lipin-1 transcriptional co-regulator function towards macrophage wound healing polarization. Macrophages lacking both lipin-1 activities did elicit IL-4 mediated gene expression to levels seen in either wild-type or lipin-1 enzymatically deficient macrophages. Furthermore, we provide evidence that the lack of myeloid-associated lipin-1 transcriptional co-regulator activity leads to impaired full thickness excisional wound healing. Our study demonstrates that lipin-1 transcriptional co-regulatory activity contributes to macrophage polarization and the macrophage contribution to wound healingin vivo.
Model balancing: in search of consistent metabolic states and in-vivo kinetic constants
Authors: Liebermeister Wolfram , Noor Elad
Published: December 2019

Enzyme kinetic constantsin vivoare largely unknown, which limits the construction of large metabolic models. While model fitting, in principle, aims at fitting kinetic constants to measured metabolic fluxes, metabolite concentrations, and enzyme concentrations, the resulting estimation problems are typically non-convex and hard to solve, especially if models are large. Here we assume that metabolic fluxes are known and show how consistent kinetic constants, metabolite concentrations, and enzyme concentrations can be determined simultaneously from data. If one specific term is omitted – a term that penalises small enzyme concentrations – we obtain a convex optimality problem with a unique local optimum. The estimation method with or without this term, called model balancing, applies to models with a wide range of rate laws and accounts for thermodynamic constraints on kinetic constants and metabolite concentrations through thermodynamic forces. It can be used to estimatein-vivokinetic constants from omics data, to complete and adjust available data, or to construct plausible metabolic states with a predefined flux distribution. As a demonstrative case, we balance a model ofE. colicentral metabolism with artificial or experimental data. The tests show what information about kinetic constants can be obtained from omics data, and reveal the practical limits of estimatingin-vivokinetic constants.
The Lands cycle modulates plasma membrane lipid organization and insulin sensitivity in skeletal muscle
Authors: Ferrara Patrick J. , Rong Xin , Maschek J. Alan , Verkerke Anthony R.P. , Siripoksup Piyarat , Song Haowei , Krishnan Karthickeyan C. , Johnson Jordan M. , Turk John , Houmard Joseph A. , Lusis Aldons J. , Cox James E. , Shaikh Saame Raza , Tontonoz Peter , Funai Katsuhiko
Published: December 2019

Aberrant lipid metabolism promotes the development of skeletal muscle insulin resistance, but the exact identity of lipid-mediated mechanisms relevant to human obesity remains unclear. A comprehensive lipidomic analyses of primary myocytes from lean insulin-sensitive (LN) and obese insulin-resistant (OB) individuals revealed several species of lysophospholipids (lyso-PL) that were differentially-abundant. These changes coincided with greater expression of lysophosphatidylcholine acyltransferase 3 (LPCAT3), an enzyme involved in phospholipid transacylation (Lands cycle). Strikingly, mice with skeletal muscle-specific knockout of LPCAT3 (LPCAT3-MKO) exhibited greater muscle lyso-PC/PC, concomitant with greater insulin sensitivityin vivoand insulin-stimulated skeletal muscle glucose uptakeex vivo. Absence of LPCAT3 reduced phospholipid packing of the cellular membranes and increased plasma membrane lipid clustering, suggesting that LPCAT3 affects insulin receptor phosphorylation by modulating plasma membrane lipid organization. In conclusion, obesity accelerates the skeletal muscle Lands cycle, whose consequence might induce the disruption of plasma membrane organization that suppresses muscle insulin action.