bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated workflows for the morphological characterization of organelles in electron microscopy image stacks (LB72)
Authors: Perez Alex , Seyedhosseini Mojtaba , Tasdizen Tolga , Ellisman Mark 
Published: June 2021

Advances in three‐dimensional electron microscopy (EM) have facilitated the collection of image stacks with a field‐of‐view that is large enough to cover a significant percentage of anatomical subdivisions at nano‐resolution. When coupled with enhanced staining protocols, such techniques produce data that can be mined to establish the morphologies of all organelles across hundreds of whole cells in their in situ environments. Although instrument throughputs are approaching terabytes of data per day, image segmentation and analysis remain significant bottlenecks in achieving quantitative descriptions of whole cell organellomes. Here we describe computational workflows that achieve the automatic segmentation of organelles from regions of the central nervous system by applying supervised machine learning algorithms to slices of serial block‐face scanning EM (SBEM) datasets. We also demonstrate that our workflows can be parallelized on supercomputing resources, resulting in a dramatic reduction of their run times. These methods significantly expedite the development of anatomical models at the subcellular scale and facilitate the study of how these models may be perturbed following pathological insults.Grant Funding Source: Supported by NIGMS under awards number P41 GM103412‐25 and P41 GM103426, the NINDS under award number 1R01NS07531, and NIDA under award number 5T32DA007315‐10.
NDFIP1: the missing adaptor for aquaporin‐2 regulation by NEDD4 and NEDD4L (LB723)
Authors: de Groot Theun , Trimpert Christiane , Wesche Daniel , Wong Victoria , van den Berg Dennis , Stagljar Igor , Deen Peter 
Published: June 2021

The aquaporin 2 (AQP2) water channel in collecting duct principal cells is essential for renal water reabsorption. Fine‐tuning of its expression in the apical membrane is critical for reabsorption of the proper amount. This fine‐tuning is the result of signals regulating AQP2 exocytosis and endocytosis. Whereas vasopressin‐induced cAMP signaling causes AQP2 translocation to the apical membrane, protein kinase C‐activating hormones stimulate ubiquitination‐dependent internalization of AQP2. The involved E3‐ubiquitin ligase has not been identified yet.HEK293 cells (from human embryonic kidney) and mpkCCD cells (from murine cortical collecting duct) were used to study ubiquitination and degradation of AQP2.SiRNA knockdown of NEDD4 and NEDD4L in mpkCCD cells increased AQP2 abundance, while both proteins did not interact with AQP2. Yeast Two‐Hybrid assay using full‐length AQP2 as bait identified NEDD4 family interacting protein 2 (NDFIP2). NDFIP2 and its homologue NDFIP1 are adaptor proteins, which bind NEDD4 ubiquitin ligases via their PY‐motifs and bring them close to target proteins. In HEK293 cells, NDFIP1/2 bound AQP2 and were essential for NEDD4/NEDD4L‐mediated ubiquitination and degradation of AQP2, an effect not observed with PY‐lacking NDFIP1/2 proteins. In mpkCCD cells, downregulation of NDFIP1, NEDD4 and NEDD4L, but not NDFIP2, increased AQP2 abundance, but did not affect the extent of AQP2 internalization. In mouse kidney, NDFIP1, but not NDFIP2, co‐localized and co‐immuno‐precipated with AQP2.Our results reveal NDFIP1 as a potent and rate‐limiting regulator of NEDD4/NEDD4L‐mediated ubiquitination and degradation of AQP2.Grant Funding Source: Supported by a Marie Curie Intra European Fellowship grant for CT and a VICI grant for PD.
Voluntary wheel running is necessary for hepatic PGC‐1α adenovirus overexpression to increase hepatic mitochondria in LCR rats (LB741)
Authors: Meers Grace , Morris E. Matthew , Koch Lauren , Britton Steve , Thyfault John 
Published: June 2021

The hepatic adenoviral overexpression (o/e) of peroxisome proliferator‐activated receptor‐γ coactivator‐1α adenovirus (PGC‐1α) in sedentary (SED) low capacity running (LCR) rats increases PGC‐1α mRNA, but does not induce increased PGC‐1α protein, increased mitochondrial content or fatty acid oxidation, as we have previously observed in SED Sprague‐Dawley rats. It is well known that PGC‐1α expression is highly regulated post‐transcriptionally leading us to believe that LCR possess an unknown “brake” that blocks the impact of increased PGC‐1α mRNA. We hypothesized that increased energy expenditure via voluntary wheel running (VWR) would result in increased hepatic PGC‐1α protein in the LCR following PGC‐1α o/e. LCR rats (age=20 wks; n=4‐8) were assigned to SED+PGC‐1α or VWR+PGC‐1α for 4 weeks while β‐galactosidase adenovirus groups served as controls. VWR reduced fat pad mass (~ 50%; p<0.05) but not body mass compared to SED. Both the SED+PGC‐1α and the VWR+PGC‐1α increased hepatic PGC‐1α mRNA, but only the VWR group displayed increased citrate synthase activity and complete palmitate oxidation (p<0.05). The lack of an increase in PGC‐1α protein and mitochondrial function following PGC‐1α o/e cannot be explained by known regulators of PGC‐1α transcriptional activity, SIRT3 or GCN5, as they did not differ between groups. The micro RNA, MiR‐23A, is known to lower PGC‐1α mRNA and protein content in muscle. We observed that MiR‐23A was unexpectedly higher in VWR vs. SED suggesting that this was also not a brake on PGC‐1α function. In conclusion, hepatic adenoviral o/e of PGC‐1α only increases mitochondrial function in running but not SED LCR rats, and the improved function is independent of increased PGC‐1α protein content.Grant Funding Source: Supported by: NIH DK‐088940, NIH T32 AR‐048523, and HSTMVA resources and facilities
Glia maturation factor regulates 1‐methyl‐4‐phenylpyridinium‐induced neuron loss and oxidative damage in primary neuron‐glia cells (LB75)
Authors: Zaheer Smita , Khan Mohammad , Nehman John , Zaheer Asgar 
Published: June 2021

Inflammation mediated by glial activation appears to play critical role in the pathogenesis of Parkinson disease (PD). Glia maturation factor (GMF), a proinflammatory protein localized in the central nervous system, was isolated, sequenced and cloned in our laboratory. In the present investigation, we demonstrate that altered expression of GMF has direct consequences on the survival of dopaminergic neurons and the production of reactive oxygen species (ROS) and NF‐κB mediated production of inflammatory mediators by 1‐methyl‐4‐phenylpyridinium (MPP+). We examined MPP+‐ induced dopaminergic neuronal loss in primary cultures of mouse mesencephalic neuron/glia obtained from GMF‐deficient (GMF‐KO) and GMF‐containing wild type (Wt) mice. Our results demonstrate that overexpression of GMF induced dopaminergic neurodegeneration, whereas GMF downregulation by GMF‐specific shRNA protected dopaminergic neurons from MPP‐induced toxicity. Additionally, deficiency of GMF in GMF‐KO neuron/glia led to decrease production of ROS and downregulation of NF‐κB mediated production of TNF‐α and IL‐1β as compare to Wt neuron/glia. GMF deficiency ameliorates antioxidant balance, as evidenced by the decreased level of lipid peroxidation, less ROS production along with increased level of glutathione; and attenuated the dopaminergic neuronal loss via the downregulation of NF‐κB mediated inflammatory responses. In conclusion, our overall data indicate that GMF modulates oxidative stress and release of deleterious agents by MPP+ leading to loss of dopaminergic neurons. Our study provides new insights into the potential role of GMF and identifies targets for therapeutic interventions in neurodegenerative diseases.Grant Funding Source: Supported by the NINDS grants NS073670
Gestational high‐fat feeding impairs female offspring energy metabolism in mice (LB777)
Authors: Guidotti Stefano , Qiao Liping , Sun Yoo Hyung , Shao Jianhua 
Published: June 2021

Maternal obesity and excessive gestational weight gain increase the risk of offspring to the development of obesity and metabolic defects later in life. The present study aimed to elucidate the effects of gestational high‐fat (HF) feeding on offspring energy metabolism and its underlying mechanisms. Pregnant C57BL/6J mice received HF diet (60% calories from fat) or chow from conception until parturition. After delivery, all dams and offspring were fed with chow. Body composition was monitored by echoMRI throughout the study.At 3 months of age, significantly increased body adiposity and reduced lean body mass (LBM) were observed in female offspring from HF‐fed dams without changes in body weight. Female offspring displayed similar energy intake with reduced energy expenditure (EE). When normalized by LBM, EE was no different between groups. No difference was found in UCP‐1 protein levels in brown adipose tissue and in expression of mitochondrial markers in skeletal muscle. Investigating the molecular mechanism underlying this metabolic phenotype, we found a significant reduction in β‐catenin protein levels in skeletal muscle and white adipose tissue. We also observed a reduction in GSK3‐β phosphorylation and other downstream targets of wnt signaling.Together our data indicate that gestational HF‐feeding increases body adiposity in expense of LBM in female offspring. Suppression of the wnt/ β‐catenin signaling in skeletal muscle could potentially lead to deranged muscle development and hence be related to the reduction in LBM. This defect in muscle development may ultimately lead to reduced energy needs, supporting a mechanism aimed at energy conservation that favors the storage of fat.
Theobromine, the primary methylxanthine found in Theobroma cacao, inhibits malignant glioblastoma cell growth by negatively regulating Akt/mammalian target of rapamycin kinase (LB836)
Authors: Sugimoto Naotoshi , Miwa Shinji , Katakura Masanori , Matsuzaki Kentaro , Shido Osamu , Tsuchiya Hiroyuki , Yachie Akihiro 
Published: June 2021

Theobromine, a caffeine derivative, is the primary methylxanthine produced by Theobroma cacao. We previously showed that methylxanthines, including caffeine and theophylline, have anti‐tumor and anti‐inflammatory effects, which are in part mediated by their inhibition of phosphodiesterase (PDE) [1‐3]. A member of the PDE family, PDE4, is widely expressed in and promotes the growth of glioblastoma, the most common type of brain tumor. Here, we investigate whether theobromine could exert growth inhibitory effects on U87‐MG, a cell line derived from human malignant glioma.We show that theobromine treatment elevates intracellular cAMP levels, indicating the prevention of PDE4 by theobromine, whereas it attenuates the Akt/mammalian target of rapamycin kinase pathway. Theobromine also inhibits cell growth. These results suggest that theobromine might be extremely effective in preventing human glioblastoma.[1] Miwa S, Sugimoto N et al. Int J Oncol., 2011; 39: 465‐472.[2] Miwa S, Sugimoto N et al. Anticancer Res., 2012; 32: 3643‐3649.[3] Saito T, Sugimoto N et al. ScientificWorldJournal, 2012; 2012:748572 (8pages).
Myoglobin: O2 or not O2襃 that is the question (LB90)
Authors: Bord Evan , Laughlin Robert , LeMense Andrew , Marable Chad , Mielke Suzie , Poniewaz Brett , Tuncel Virginia , Wade Gina , Weeden Mike , Wisth Ryan , Sampe David , Wagie Hannah , Geissinger Peter 
Published: June 2021

Free divers can’t hold their breath as long as whales, but they train their bodies to maximize their oxygen (O2) storing potential using the protein myoglobin. Myoglobin’s structure has been known for decades, but researchers are still trying to determine just how myoglobin functions. Found in muscle tissue, myoglobin stores O2, a molecule needed to produce chemical energy. Toxic ligands, such as carbon monoxide (CO) and cyanide, also bind to myoglobin. When CO binds to a free heme group, the heme's binding affinity for CO is 20,000 times that for O2. When heme is surrounded by myoglobin, that binding affinity ratio drops to only 25. The decrease was thought to be due to steric interactions which prevented CO from occupying the same space as His64. Recent evidence suggests that electrostatic interactions and hydrogen bonds play a more important role. The O2 is stabilized as opposed to the CO being pushed out. Several amino acids (His64, Val68, Phe43, Phe46, and Leu29,) seem to stabilize the ligand. With 3D printing technology, the Brown Deer SMART (Students Modeling a Research Topic) Team created a model of myoglobin. If researchers can fully understand ligand discrimination by heme proteins, not only will divers be able to hold their breath longer, but we may be able to cure diseases like anemia where there is a lack of O2 in the blood.Grant Funding Source: The SMART team program is supported by a grant from NIH‐CTSA.
The Anthrax Toxin Heterotrimer: Explorations of the Protective Antigen and Edema and Lethal Factors (LB98)
Authors: Andrews Jannelle , Chick Austin , Chao Tiffany , Chogada Vashu , Douglas Amy , Florack Allison , McCormick Samantha , Kessler Eric , Tuel Kelley , Whalen Joseph , Fisher Mark 
Published: June 2021

Anthrax is a disease caused by the bacterium Bacillus anthracis which received media attention when several senators and news outlets were sent letters containing anthrax endospores in 2001. Five individuals died in this bioterrorist act. In nature, anthrax endospores can remain dormant in the soil for decades where they more regularly infect herbivorous animals through ingestion, inhalation, or injured skin. In their activated form the bacteria releases a tripartite protein toxin consisting of three protein components: Protective Antigen (PA), Edema Factor (EF), and Lethal Factor (LF). The Blue Valley CAPS SMART (Students Modeling A Research Topic) Team modeled each toxin component using Jmol and 3D printing technology. During initial infection by the toxin, a single PA binds to one of two surface receptors, CMG2 or ATR/TEM8. Upon cleavage of PA by a host furin protease, the remaining P63 oligomerizes forming a ring‐shaped heptameric pre‐pore. Once formed, three to four molecules of EF and/or LF bind and are translocated by endocytosis into the cell’s endosome. Subsequent lowering of endosomal pH initiates conformational changes in the PA heptamer forming a pore which facilitates the entry of EF (an adenyl cyclase) and LF (a protease) into the cytosol. Collectively these enzymes significantly disrupt cell signaling, growth and metabolism.Grant Funding Source: Supported by grants from the NIH‐SEPA and NIH‐CTSA.
Real-life studies in allergen immunotherapy
Authors: Passalacqua Giovanni , Bagnasco Diego 
Published: June 2021

Purpose of review
Real-life (or real-world) studies can provide information that cannot be derived from randomized controlled trials. This approach is currently becoming of relevance for many treatments. In recent years, the real-life method has been applied also to allergen immunotherapy, providing new insights on it. We reviewed herein the available literature on the argument.

Recent findings
Several prospective and retrospective studies on allergen immunotherapy in the real-world setting have been published, mostly in the last 5 years. Most of them focused on adverse events, compliance, and the long term/preventive effects, and evidenced an overall favorable profile for different products and different allergens.

Summary
Real life study provided novel information and evidenced those aspects of immunotherapy that worth a more detailed approach, without the strict limitations usually imposed by controlled randomized trials.
Does Inpatient Mobilization Predict 1-Year Mortality After Femoral Neck Fracture Treated With Hemiarthroplasty?
Authors: Gannon Nicholas P. , Kampa John , Westberg Jerald R. , Baer Michael R. , Pietrini Nicholas , Schmidt Andrew H. , Kyle Richard F. 
Published: June 2021

Objective:
To determine whether inpatient mobilization (defined as ambulation before hospital discharge) is associated with 1-year mortality and 90-day hospital readmission in patients treated with a hip hemiarthroplasty for a femoral neck fracture.

Design:
Retrospective case–control.

Setting:
Academic Level 1 trauma center.

Patients/Participants:
Two hundred twelve consecutive femoral neck fractures were treated with hip hemiarthroplasties with a minimum of 1 year of follow-up.

Intervention:
All study patients were treated with a hip hemiarthroplasty and weight-bearing as tolerated postoperative day 1. Patients were prescribed daily physical therapy with the goal of mobilization before discharge from hospital.

Main Outcome Measures:
Mortality at 1 year; hospital readmission within 90 days.

Results:
Two hundred twelve patients were included in the study. One-year mortality was 29%. One hundred thirty-two (62%) patients were able to ambulate before hospital discharge. Ambulation with physical therapy before discharge from hospital was a significant predictor of 1-year mortality when compared with patients who were unable to ambulate (hazard ratio 0.57; 95% confidence interval, 0.34–0.94; P = 0.03), which equates to 43% reduction in risk of mortality. There was no difference in the 90-day readmission rates for ambulatory versus nonambulatory patients.

Conclusions:
Ambulation with physical therapy before discharge reduced the risk of 1-year mortality by 43%, without an effect on 90-day readmission. Sixty-two percentage of our cohort was able to ambulate before discharge. Future investigations are warranted to further identify those patients at heightened risk of mortality and readmission and the role of early rehabilitation in recovery.

Level of Evidence:
Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Assessing the Efficacy and Safety of Tirofiban in Combination With Dual-antiplatelet Therapy in Progressive Ischemic Stroke Patients
Authors: Zhang Haiqi , Lin Feng , Zhao Yanjun , Chang Wansheng , Liu Hui , Yin Jijun , Li Long 
Published: June 2021

Abstract:
This study assessed the efficacy and safety of tirofiban in combination with dual-antiplatelet therapy (DAPT) in progressive ischemic stroke. One hundred and four patients equally divided into a tirofiban group or DAPT group were enrolled from June 2018 to December 2019. Efficacy outcomes included National Institutes of Health Stroke Scale score for 14 days, and modified Rankin scale (mRs) scores as excellent (mRs 0–1) or favorable (mRs 0–2) measured 90 days after stroke. At 14 days, the tirofiban group had a lower National Institutes of Health Stroke Scale score compared with the DAPT group (F = 14.959, P = 0.000). The mRS scores of the 2 groups at 90 days after treatment were significantly different from those before treatment. At 90 days, excellent favorable functional outcome (mRS ≤ 2) was achieved in 33 of 52 (63.43%) patients in the tirofiban group compared with 25 of 52 (48.08%) patients in the DAPT group. The incidence of bleeding was 5.77% in the tirofiban group, compared with 0% in DAPT group. Intravenous (IV) tirofiban alone or combined with DAPT was shown to be safe and effectively improved clinical outcome in progressive ischemic stroke patients. IV tirofiban was shown to be superior to the DAPT regimen.
Tacrolimus Therapy in Adult Heart Transplant Recipients: Evaluation of a Bayesian Forecasting Software
Authors: Kirubakaran Ranita , Stocker Sophie L. , Carlos Lilibeth , Day Richard O. , Carland Jane E. 
Published: June 2021

Background:
Therapeutic drug monitoring is recommended to guide tacrolimus dosing because of its narrow therapeutic window and considerable pharmacokinetic variability. This study assessed tacrolimus dosing and monitoring practices in heart transplant recipients and evaluated the predictive performance of a Bayesian forecasting software using a renal transplant–derived tacrolimus model to predict tacrolimus concentrations.

Methods:
A retrospective audit of heart transplant recipients (n = 87) treated with tacrolimus was performed. Relevant data were collected from the time of transplant to discharge. The concordance of tacrolimus dosing and monitoring according to hospital guidelines was assessed. The observed and software-predicted tacrolimus concentrations (n = 931) were compared for the first 3 weeks of oral immediate-release tacrolimus (Prograf) therapy, and the predictive performance (bias and imprecision) of the software was evaluated.

Results:
The majority (96%) of initial oral tacrolimus doses were guideline concordant. Most initial intravenous doses (93%) were lower than the guideline recommendations. Overall, 36% of initial tacrolimus doses were administered to transplant recipients with an estimated glomerular filtration rate of <60 mL/min/1.73 m despite recommendations to delay the commencement of therapy. Of the tacrolimus concentrations collected during oral therapy (n = 1498), 25% were trough concentrations obtained at steady-state. The software displayed acceptable predictions of tacrolimus concentration from day 12 (bias: −6%; 95%confidence interval, −11.8 to 2.5; imprecision: 16%; 95% confidence interval, 8.7–24.3) of therapy.

Conclusions:
Tacrolimus dosing and monitoring were discordant with the guidelines. The Bayesian forecasting software was suitable for guiding tacrolimus dosing after 11 days of therapy in heart transplant recipients. Understanding the factors contributing to the variability in tacrolimus pharmacokinetics immediately after transplant may help improve software predictions.
Chronotropic Responses to Exercise and Recovery in Myocardial Infarction Patients Taking β-Blockers Following Aerobic High-Intensity Interval Training
Authors: Jayo-Montoya Jon Ander , Jurio-Iriarte Borja , Aispuru G. Rodrigo , Villar-Zabala Beatriz , Blanco-Guzman Sonia , Maldonado-Martín Sara 
Published: June 2021

Purpose:
The objectives of this study were to compare the effects of two different high-intensity interval training (HIIT) programs (low-volume vs high-volume) on chronotropic responses during exercise and recovery, and to contrast the results of the HIIT groups together to only physical activity recommendations in post-myocardial infarction (MI) patients taking β-blockers.

Methods:
Resting heart rate (HRrest), peak HR (HRpeak), HR reserve (HRreserve = HRpeak-HRrest), HR recovery (HRR) as the difference between HRpeak and post-exercise HR, and chronotropic incompetence were assessed in 70 patients (58 ± 8 yr) following MI with a cardiopulmonary exercise test to peak exertion before and after a 16-wk exercise intervention period. All participants were randomized to either attention control (AC) (physical activity recommendations) or one of the two supervised HIIT groups (2 d/wk).

Results:
After the intervention, no significant between-HIIT group differences were observed. The HRpeak increased (P < .05) in low- (Δ= 8 ± 18%) and high-volume HIIT (Δ= 6 ± 9%), with a small decrease in AC (Δ=− 2 ± 12%, P > .05) resulting in large differences (P < .05) between HIIT and AC. The HRreserve increased (P < .05) in high-volume HIIT. The HRR slightly increased (P < .05) in low-volume (5th min, Δ= 19 ± 31%) and high-volume HIIT (2nd min, Δ= 15 ± 29%, and 5th min, Δ= 19 ± 28%).

Conclusion:
These findings suggest that both low- and high-volume HIIT elicit similar improvements in chronotropic responses after MI, independent of β-blocker treatment. Supervised HIIT was more effective than giving physical activity recommendations alone. Low-volume HIIT is presented as a potent and time-efficient exercise strategy that could enhance the sympathovagal balance in this population.