bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implications of Instituting an Enhanced Recovery after Surgery Pathway in Patients Receiving Chemotherapy in Microsurgical Breast Reconstruction
Authors: Haddock Nicholas T. , Garza Ricardo , Boyle Carolyn E. , Teotia Sumeet S. 
Published: October 2020

Background:
Neuropathy is a common side effect of chemotherapeutic agents. Manifestations of chemotherapy-induced neuropathy can present in a myriad of fashions, ranging from numbness, tingling, and pain to motor weakness and autonomic dysfunction.
1
Given the nature of breast reconstruction, a significant portion of the patients have a history of chemotherapy exposure; its effect on postoperative pain management has not been previously explored.

Methods:
This study is a retrospective review of patients who underwent deep inferior epigastric perforator flap breast reconstruction performed by the two senior authors from January of 2016 to September of 2019. The patients were separated into two groups, before and after enhanced recovery after surgery. The primary outcome observed was postoperative opioid consumption, measured as oral morphine equivalents; p values were obtained through univariate linear regression.

Results:
In total, 256 patients were analyzed, of which 113 had chemotherapy exposure. The difference between opioid consumption in patients in the pre–enhanced recovery after surgery group without and with chemotherapy exposure was statistically significant (211.5 mg versus 278.5 mg; p = 0.0279). There was no difference between opioid consumption with regard to chemotherapy history in the enhanced recovery after surgery group (137.4 mg versus 133.0 mg; p = 0.7251).

Conclusions:
Patients with chemotherapy exposure required more opioids to be comfortable. It is unknown whether this difference is secondary to increased pain or less effectiveness of opioids. Further research is necessary to assess whether there are better ways to address pain postoperatively in patients with chemotherapy exposure.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Improving In Vitro Cartilage Generation by Co-Culturing Adipose-Derived Stem Cells and Chondrocytes on an Allograft Adipose Matrix Framework
Authors: Ziegler Mary E. , Sorensen Alexandria M. , Banyard Derek A. , Evans Gregory R. D. , Widgerow Alan D. 
Published: October 2020

Background:
Microtia is an inherited condition that results in varying degrees of external ear deformities; the most extreme form is anotia. Effective surgical reconstruction techniques have been developed. However, these usually require multistage procedures and have other inherent disadvantages. Tissue engineering technologies offer new approaches in the field of external ear reconstruction. In this setting, chondrocytes are cultured in the laboratory with the aim of creating bioengineered cartilage matrices. However, cartilage engineering has many challenges, including difficulty in culturing sufficient chondrocytes. To overcome these hurdles, the authors propose a novel model of cartilage engineering that involves co-culturing chondrocytes and adipose-derived stem cells on an allograft adipose-derived extracellular matrix scaffold.

Methods:
Auricular chondrocytes from porcine ear were characterized. Adipose-derived stem cells were isolated and expanded from human lipoaspirate. Then, the auricular chondrocytes were cultured on the allograft adipose matrix either alone or with the adipose-derived stem cells at different ratios and examined histologically.

Results:
Cartilage induction was most prominent when the cells were co-cultured on the allograft adipose matrix at a ratio of 1:9 (auricular chondrocyte–to–adipose-derived stem cell ratio). Furthermore, because of the xenogeneic nature of the experiment, the authors were able to determine that the adipose-derived stem cells contributed to chondrogenesis by means of a paracrine stimulation of the chondrocytes.

Conclusions:
In this situation, adipose-derived stem cells provide sufficient support to induce the formation of cartilage when the number of auricular chondrocytes available is limited. This novel model of cartilage engineering provides a setting for using the patient’s own chondrocytes and adipose tissue to create a customized ear framework that could be further used for surgical reconstruction.
Alterations in Neural Responses and Pain Perception in Older Adults During Distraction
Authors: González-Roldán Ana María , Terrasa Juan Lorenzo , Sitges Carolina , van der Meulen Marian , Anton Fernand , Montoya Pedro 
Published: October 2020

ABSTRACTObjectiveAlthough it is acknowledged that pain may be modulated by cognitive factors, little is known about the effect of aging on these control processes. The present study investigated electroencephalographical correlates of pain processing and its cognitive modulation in healthy older individuals.MethodsFor this purpose, the impact of distraction on pain was evaluated in 21 young (9 men; 20.71 [2.30]) and 20 older (10 men; 66.80 [4.14]) adults. Participants received individually adjusted electrical pain stimuli in a high-distraction condition (one-back task) and in a low-distraction condition (simple letter response task). Pain-related evoked potentials and pain ratings were analyzed.ResultsBoth groups rated pain as less intense (F(1,39) = 13.954,p< .001) and less unpleasant (F(1,39) = 10.111,p= .003) when it was experienced during the high- rather than the low-distraction condition. However, in comparison to younger participants, older adults gave higher unpleasantness ratings to painful stimulation (F(1,39) = 4.233,p= .046), accompanied by attenuated neural responses (N1-P1 and P3 amplitudes), regardless of the distraction condition (F(1,38) = 6.028 [p= .019] andF(1,38) = 6.669 [p= .014], respectively).ConclusionsOlder participants felt pain relief through distraction, like younger participants. However, we also found that aging may enhance affective aspects of pain perception. Finally, our results show that aging is characterized by reduced neural processing of painful stimuli. This phenomenon could be related to the increased vulnerability of older participants to develop chronic pain.
Hydroxychloroquine (HCQ) reverses anti-PD-1 immune murine checkpoint blockade: TCF1 as a marker in humans for COVID-19 and HCQ therapy
Authors: Krueger Janna , Santinon Francois , Kazanova Alexandra , Issa Mark , Larrivee Bruno , Milhalcioiu Catalin , Rudd Christopher E. 
Published: October 2020

AbstractCoronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious threat to global public health. Hydroxychloroquine (HCQ) and the antibiotic azithromycin (AZ) are still being used by thousands and numerous hospitals to treat COVID-19. In a related context, immunotherapy using checkpoint blockade (ICB) with antibodies such as anti-PD-1 has revolutionised cancer therapy. Given that cancer patients on ICB continue to be infected with SARS-CoV-2, an understanding of the effects of HCQ and AZ on the elimination of tumors by anti-PD-1 ICB is urgently needed. In this study, we report that HCQ alone, or in combination with AZ, at doses used to treat COVID-19 patients, reverses the therapeutic benefit of anti-PD-1 in controlling B16 melanoma tumor growth in mice. No deleterious effect was seen on untreated tumors, or in using AZ alone in anti-PD-1 immunotherapy. Mechanistically, HCQ and HCQ/AZ inhibited PD-L1 expression on tumor cells, while specifically targeting the anti-PD-1 induced increase in progenitor CD8+CD44+PD-1+TCF1+tumor infiltrating T-cells (TILs) and the generation of CD8+CD44+PD-1+effectors. Surprisingly, it also blocked the appearance of a subset of terminally exhausted CD8+ TILs. No effect was seen on the presence of CD4+ T-cells, FoxP3+ Tregs, thymic subsets, B-cells, antibody production, myeloid cells, or the vasculature of mice. Lastly, we identified TCF-1 expression in peripheral CD8+ T-cells from cancer or non-cancer human patients infected with SARs CoV2 as a marker for the effects of COVID-19 and HCQ on the immune system. This study indicates for the first time that HCQ and HCQ/AZ negatively impact the ability of anti-PD-1 checkpoint blockade to promote tumor rejection.Graphic Abstract
Nascent prostate cancer heterogeneity drives evolution and resistance to intense hormonal therapy
Authors: Wilkinson Scott , Ye Huihui , Karzai Fatima , Harmon Stephanie A. , Terrigino Nicholas T. , VanderWeele David J. , Bright John R. , Atway Rayann , Trostel Shana Y. , Carrabba Nicole V. , Whitlock Nichelle C. , Walker Stephanie M. , Lis Rosina T. , Sater Houssein A. , Capaldo Brian J. , Madan Ravi A. , Gulley James L. , Chun Guinevere , Merino Maria J. , Pinto Peter A. , Salles Daniela C. , Kaur Harsimar B. , Lotan Tamara L. , Venzon David J. , Choyke Peter L. , Turkbey Baris , Dahut William L. , Sowalsky Adam G. 
Published: October 2020

ABSTRACTLocalized prostate cancer is distinctively characterized by intratumoral heterogeneity, and tumors with more complex evolutionary paths display more aggressive characteristics. In clinical trials of intense neoadjuvant androgen deprivation therapy (inADT), patients with complete or near-complete responses experience durable remissions. However, the molecular characteristics distinguishing exceptional responders and nonresponders at baseline have not been established. Here, we present the integrated histologic and genomic analysis of pre-treatment baseline tissue from our recent Phase 2 clinical study of inADT. Multiregion sampling demonstrated that patients with incomplete and nonresponding tumors demonstrate greater tumor diversity as estimated by phylogenetic tree reconstruction from DNA sequencing and automated analysis of immunohistochemical stains. Development of a four-factor binary model to predict poor response correlated with increased genomic diversity in our 37-patient cohort and a validation cohort of 188 Gleason score 8-10 prostate cancers. Together, these findings demonstrate that even in the primary setting, more highly evolved tumors have increased fitness to resist therapy.
Clinical Validation of a Quantitative HIV-1 DNA Droplet Digital PCR assay: Applications for Detecting Occult HIV-1 Infection and Monitoring Cell-associated HIV-1 Dynamics across Different Subtypes in HIV-1 Prevention and Cure Trials
Authors: Powell Laura , Dhummakupt Adit , Siems Lilly , Singh Dolly , Duff Yann Le , Uprety Priyanka , Jennings Cheryl , Szewczyk Joseph , Chen Ya , Nastouli Eleni , Persaud Deborah 
Published: October 2020

ABSTRACTBackgroundIn HIV-1-exposed infants, nucleic acid testing (NAT) is required to diagnose infection since passively transferred maternal antibodies preclude antibody testing. The sensitivity of clinical NAT assays is lowered with infant antiretroviral prophylaxis and, with empiric very early antiretroviral treatment of high-risk infants, thereby impacting early infant diagnosis. Similarly, adult HIV-1 infections acquired under pre-exposure prophylaxis may occur at low levels (occult infection), with undetectable plasma viremia and indeterminate antibody tests, for which HIV-1 DNA testing maybe a useful adjunct. Cell-associated HIV-1 DNA concentrations are also used to monitor HIV-1 persistence in viral reservoirs with relevance to HIV-1 cure therapeutics, particularly in perinatal infections.MethodsThe analytical sensitivity and specificity of an HIV-1 DNA droplet digital PCR (ddPCR) assay was determined, across different HIV-1 subtypes, using serial dilutions of a plasmid containing a 160-base pair sequence of the HIV-1 LTR-gag spiked into peripheral blood mononuclear cells (PBMCs), with MOLT-4 cells or PBMCs infected with different HIV-1 subtypes (A, B and C), and U1 cells spiked into PBMCs. Inter- and intra-run variability were used to determine assay precision.ResultsThe HIV-1 LTR-gag ddPCR assay was reliable and reproducible, and exhibited high analytical specificity with sensitivity to near single copy level, across multiple HIV-1 subtypes, and a limit of detection of 4.09 copies/million PBMCs.ConclusionsThis assay has applications for detecting occult HIV-1-infection that may occur in the setting of combination and long-acting regimens used for HIV-1 prevention, across different HIV-1 subtypes, in both infants and adults, and in HIV-1 cure interventions, particularly with perinatal infections.
Laboratory evaluation of SARS-CoV-2 antibodies: detectable IgG up to 20 weeks post infection
Authors: Robertson Louise J. , Moore Julie S. , Blighe Kevin , Ng Kok Yew , Quinn Nigel , Jennings Fergal , Warnock Gary , Sharpe Peter , Clarke Mark , Maguire Kathryn , Rainey Sharon , Price Ruth , Burns William , Kowalczyk Amanda , Awuah Agnes , McNamee Sara , Wallace Gayle , Hunter David , Segar Steve , Shern Connie Chao , Nesbit M. Andrew , McLaughlin James , Moore Tara 
Published: October 2020

AbstractBackgroundThe SARS-CoV-2 pandemic necessitated rapid and global responses across all areas of healthcare, including an unprecedented interest in serological immunoassays to detect antibodies to the virus. The dynamics of the immune response to SARS-CoV-2 is still not well understood and requires further investigation into the longevity of humoral immune response that is evoked due to SARS-CoV-2 infection.MethodsWe measured SARS-CoV-2 antibody levels in plasma samples from 880 people in Northern Ireland using Roche Elecsys Anti-SARS-CoV-2 IgG/IgA/IgM, Abbott SARS-CoV-2 IgG and EuroImmun IgG SARS-CoV-2 ELISA immunoassays to analyse immune dynamics over time. We undertook a laboratory evaluation for the UK-RTC AbC-19 rapid lateral flow immunoassay (LFIA), for the target condition of SARS-CoV-2 Spike protein IgG antibodies using a reference standard system to establish a characterised panel of 330 positive and 488 negative SARS-CoV-2 IgG samples.ResultsWe detected persistence of SARS-CoV-2 IgG up to 140 days (20 weeks) post infection, across all three laboratory-controlled immunoassays. On the known positive cohort, the UK-RTC AbC-19 lateral flow immunoassay showed a sensitivity of 97.58% (95.28%-98.95%) and on known negatives, showed specificity of 99.59% (98.53 %-99.95%).ConclusionsThrough comprehensive analysis of a cohort of pre-pandemic and pandemic individuals, we show detectable levels of IgG antibodies, lasting up to 140 days, providing insight to antibody levels at later time points post infection. We show good laboratory validation performance metrics for the AbC-19 rapid test for SARS-CoV-2 Spike protein IgG antibody detection in a laboratory based setting.
Brazilin Removes Toxic alpha-Synuclein and Seeding Competent Assemblies from Parkinson Brain by Altering Conformational Equilibrium
Authors: Nahass George R. , Sun Yuanzi , Xu Yong , Batchelor Mark , Reilly Madeleine , Benilova Iryna , Kedia Niraja , Spehar Kevin , Sobott Frank , Sessions Richard B. , Caughey Byron , Radford Sheena E. , Jat Parmjit , Collinge John , Bieschke Jan 
Published: October 2020

ABSTRACTAlpha-synuclein (α-syn) fibrils, a major constituent of the neurotoxic Lewy Bodies in Parkinson’s disease, form via nucleation dependent polymerization and can replicate by a seeding mechanism. Brazilin, a small molecule derived from red cedarwood trees in Brazil, has been shown to inhibit the fibrillogenesis of amyloid-beta (Aβ) and α-syn, prompting our inquiry in its mechanism of action. Here we test the effects of Brazilin on both seeded and unseeded α-syn fibril formation and show that the natural polyphenol inhibits fibrillogenesis of α-syn by a unique mechanism that is distinct from other polyphenols and is also distinct from its effect on Aβ. Brazilin preserves the natively unfolded state of α-syn by stabilizing the compact conformation of the α-syn monomer over the aggregation-competent extended conformation. Molecular docking of Brazilin shows the molecule to interact both with unfolded α-syn monomers and with the cross-β sheet structure of α-syn fibrils. Brazilin eliminates seeding competence of α-syn assemblies from Parkinson’s disease patient brain tissue, and treatment of pre-formed fibril assemblies with Brazilin significantly reduces their toxicity in primary neurons. Our findings suggest that Brazilin has substantial potential as a neuroprotective and therapeutic agent for Parkinson’s Disease.Highlights- The natural polyphenol Brazilin binds to monomeric, oligomeric and fibrillar α-syn- Brazilin shifts the equilibrium away from aggregation-competent monomer conformations- Brazilin inactivates seeding-competent α-syn isolated from Parkinson patients’ brains- Brazilin detoxifies α-syn aggregation intermediates and stabilizes mature amyloid fibrilsGraphical Abstract
Assembly factors chaperone rRNA folding by isolating helical junctions that are prone to misfolding
Authors: Huang Haina , Karbstein Katrin 
Published: October 2020

AbstractWhile RNAs are known to misfold, the underlying molecular causes remain unclear, and focused on alternative secondary structures. Conversely, how RNA chaperones function in a biological context to promote folding beyond duplex annealing, remains unknown. Here we show in a combination of DMS-MaPseq, structural analyses, biochemical experiments, and yeast genetics that three-way junctions are prone to misfolding during assembly of the small ribosomal subunitin vivo. We identify ubiquitous roles for ribosome assembly factors in chaperoning their folding by preventing the formation of tertiary interactions. In the absence of these assembly factors, tertiary interactions kinetically trap misfolded three-way junctions, thereby blocking further progress in the assembly cascade. While these protein chaperones act indirectly by binding the interaction partners, our analyses also suggest direct roles for snoRNAs in binding and chaperoning three-way junctions during transcription. This work furthermore shows that the dissociation of assembly factors renders reversible folding steps irreversible, thereby setting up a timer that regulates not just the flux of assembly but also dictates the propensity of misfolded intermediates to escape quality control. Finally, the data demonstrate how RNA chaperones act locally to unfold specific tertiary interactions, in contrast to protein chaperones, which globally unfold misfolded proteins.
Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
Authors: Molloy Erin K. , Gatesy John , Springer Mark S. 
Published: October 2020

AbstractA potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e. local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study, provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100 000 parsimony-informative RIs. We found that, when given just 1 000 parsimony-informative RIs as input, ASTRAL BP successfully reconstructed major clades (i.e clades separated by branches > 0.3 CUs) with high support and identified rapid radiations (i.e. shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios.
Puerarin blocks aging phenotype in cultured human dermal fibroblasts
Authors: Kamiya Yuki , Odama Mao , Mizuguti Aki , Murakami Shigeru , Ito Takashi 
Published: October 2020

AbstractDermal fibroblast aging contributes to aging-associated functional defects in the skin since dermal fibroblasts are important to maintain skin homeostasis by interacting with epidermis and extracellular matrix. Here we identified that puerarin, an isoflavone contained inPueraria lobata(Kudzu), can prevent the aging-phenotype of human dermal fibroblasts. Puerarin treatment increased in proliferating cells and decreased in senescence-associated beta-galactosidase positive cells in the high-passage culture of dermal fibroblasts. Moreover, puerarin reduced smooth muscle actin-positive myofibroblasts and the expression of a reticular fibroblast marker, calponin 1 (CNN1), which were induced in high-passage fibroblasts. Fulvestrant, an estrogen receptor antagonist, blocked puerarin-mediated downregulation of SMA and CNN1. Our results suggest that puerarin may be a useful food factor that alleviates aging-related functional defects in the skin.