bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical efficacy of acupuncture combined with Western medicine in the treatment of mild to moderate Alzheimer disease: A protocol of a randomized controlled trial
Authors: Zhou Kangmei , He Jierong , Quan Lin , Guo Rong
Published: September 2022

Background:

Alzheimer disease (AD) is a common cause of dementia, and there are still a lack of treatment options to reverse or prevent disease progression. Existing evidence shows that acupuncture has advantages in the treatment of AD, but whether the efficacy of acupuncture belongs to the placebo effect remains controversial, and there is no strict placebo-controlled clinical study to evaluate the efficacy and safety of acupuncture combined with Western medicine in the treatment of AD.

Methods:

This is a prospective randomized, a single-blind, sham-acupuncture controlled trial to study the clinical efficacy of acupuncture combined with Western medicine in the treatment of mild to moderate AD. Participants will be randomly divided into treatment and control groups. The treatment group using acupuncture combined with donepezil hydrochloride orally, and the control group using sham acupuncture combined with donepezil hydrochloride orally, followed up for 24 weeks after 24 weeks of continuous treatment. Outcome measures included: AD assessment scale-cognitive subscale, mini-mental state examination, activities of daily living, neuropsychiatric inventory questionnaire, serum superoxide dismutase, and homocysteine levels. Finally, SPASS 21.0 software was used for statistical analysis of the data.

Discussion:

This study will evaluate the efficacy of acupuncture combined with Western medicine in improving cognitive function and activities of daily living in AD patients. The results of this study will verify whether the efficacy of acupuncture in the treatment of AD belongs to the placebo effect, which will also provide a reference for the clinical use of acupuncture combined with Western medicine in the treatment of AD.

Trial registration:

The TCTR identification number is TCTR20220817004.
Durable response to olaparib combined low-dose cisplatin in advanced hepatocellular carcinoma with FANCA mutation: A case report
Authors: Lai Yi-Hsuan , Tung Kai-Che , Chen San-Chi
Published: September 2022

Rationale:

To date, there is no actionable gene has been discovered in hepatocellular carcinoma (HCC). Tumor cells with DNA damage response and repair (DDR) gene loss-of-function mutation is sensitivity to poly-ADP-ribose polymerase (PARP) inhibitors and platinum chemotherapy in ovarian, prostate and pancreatic cancers. There is a case report demonstrated the efficacy of PARP inhibitor for BRCA2 mutation that belongs to DDR gene in HCC, which suggested the potential role of PARP inhibitor for HCC with DDR gene mutation.

Patient concerns:

We reported a 44-year-old woman with non-viral HCC who was refractory to multiple treatment including target therapy, immunotherapy, and chemotherapy. The tumor tissue was submitted to next-generation sequencing using the commercially available ACTOnco®+ (ACT Genomics, Taiwan) assay that interrogates 440 and 31 cancer-related genes and fusion genes, respectively.

Diagnosis:

A truncating mutation FANCA p.Q1307fs was also observed. The tumor was microsatellite stable and had low tumor mutational burden of 4.5 muts/Mb.

Interventions and outcomes:

Given FANCA belongs to DDR genes, the inactivation evoked the idea of using PARP inhibitor and cisplatin. Therefore, the patient started to use olaparib combined with low-dose cisplatin (30 mg/m2, every 4 weeks) therapy in December 2019. Significant reduction in the tumor marker level in 1 month (PIVKA-II from 17,395 to 411 ng/dL) and follow-up CT scan showed stable disease. Her tumor did not progress until December 2020 with a progression-free survival of 12 months.

Lessons:

We report the first case of FANCA-mutated HCC that responded well to olaparib and low-dose cisplatin. This addressed the potential therapeutic role of DDR gene mutation in HCC and the possible synergistic effect of PARP inhibitor and cisplatin. These findings highlight areas where further investigation and effort are needed.
Correlation of muscle mass and bone mineral density in the NHANES US general population, 2017–2018
Authors: Qin Hailin , Jiao Wenyong
Published: September 2022

The appendicular skeletal muscle mass index (ASMI) is commonly used to evaluate human skeletal muscle mass. Muscle, an adjacent tissue of bone, is closely related to bone growth and development. The purpose of this study was to explore the association between the ASMI and lumbar bone mineral density (BMD) to identify potential risk factors for osteoporosis. We analyzed the data collected by the NHANES from 2017 to 2018, and finally included 948 participants aged 40 to 59 years. We evaluated the correlation between the ASMI and lumbar spine BMD using univariate and multiple linear regression models. The ASMI was calculated from height and appendicular skeletal muscle mass obtained by dual energy X-ray absorptiometry. Lumbar spine BMD was obtained by dual energy X-ray absorptiometry and used as an observation in our study. In all the models, ASMI was significantly associated with lumbar spine BMD (model 1: β = 0.013, P < .001; model 2: β = 0.013, P < .001). In the subgroup analysis stratified by sex, this positive correlation was present in both sexes (male: β = 0.023, P < .001, β = 0.022, < 0.001; female: β = 0.030, P < .001, β = 0.031, P < .001). This study showed that the ASMI was positively associated with lumbar BMD, and that this correlation is present in both men and women.
Factors influencing caregiver burden in chronic pain patients: A retrospective study
Authors: Tsuji Hironori , Tetsunaga Tomoko , Tetsunaga Tomonori , Misawa Haruo , Oda Yoshiaki , Takao Shinichiro , Nishida Keiichiro , Ozaki Toshifumi
Published: September 2022

Chronic pain coexists with disability, anxiety, depression, and sleep disturbances, which are factors of pain chronicity in the fear-avoidance model. Self-efficacy for managing pain plays a protective role against pain chronicity. For chronic pain sufferers, social support from caregivers is important. However, such caregivers face enormous physical and mental burdens. This study aimed to assess how self-efficacy and factors related to the fear-avoidance model affect caregiver burden. Participants were 135 chronic pain patients and their caregivers who visited our outpatient pain special clinic. In clinical assessments, numeric rating scale (NRS), pain catastrophizing scale (PCS), hospital anxiety and depression scale (HADS), Athens insomnia scale (AIS), pain disability assessment scale (PDAS), pain self-efficacy questionnaire (PSEQ) for the patients and Zarit Burden Interview (ZBI) for their caregivers were evaluated. Participants were divided into 2 groups (L group ZBI < 24 points and H group ZBI ≥ 24 points) and compared. Regression analyses were conducted to identify factors correlated with the ZBI scores. Compared to L group, H group showed significantly higher NRS and HADs depression scores, and lower PSEQ scores. In univariate regression analysis, ZBI scores were significantly correlated with NRS, PCS, HADS anxiety, HADS depression, PDAS and PSEQ. Multiple linear regression analysis revealed that ZBI scores were significantly correlated with PSEQ. The caregivers who perceived high caregiver burden had significantly higher patients’ pain intensity, depression, and lower self-efficacy than those who perceived low caregiver burden. Caregiver burden correlated with the pain intensity, pain catastrophizing, anxiety, depression, disability, and self-efficacy of chronic pain patients. Among these factors, self-efficacy was the most negatively correlated with caregiver burden. Treatments focused on increasing self-efficacy for managing pain have the potential to reduce caregiver burden.
A case report of severe adverse reaction of exenatide: Anaphylactic shock
Authors: Liu Xujing , Zhai Aihua , Zhang Bai
Published: September 2022

Background:

Anaphylactic shock is the severe state of the allergic reaction, which is rapid in onset and fatal. This is the first study that discusses the anaphylactic shock of exenatide reexposure in the patient who has interrupted exenatide treatment.

Patient concerns:

A 47-year-old man was treated with exenatide owing to high blood glucose and obesity. Then he developed localized urticarial on the face, white lip, hands tremble, nausea, vomit, chest stuffiness, dizziness, accompanying with confusion and dyspnea. His blood glucose was 4.6 millimole per liter (mmol/L) and blood pressure was 85/50 millimeters of mercury (mm Hg).

Diagnosis:

Exenatide-induced anaphylactic shock was considered.

Interventions:

The emergency electrocardiogram was performed. The patient was treated with dexamethasone sodium phosphate and calcium gluconate, combined with exenatide withdrawal. He also received oral antiallergic agents and intravenous nutrition treatment.

Outcomes:

After antishock treatment, the clinical response gradually alleviated.

Lessons:

Although exenatide is not prone to anaphylaxis, it is the synthetic peptide that can induce antibody formation. Exenatide has immunogenicity with the potential to elicit an allergic reaction upon administration. Clinicians should always pay more attention to the anaphylactic shock of exenatide, when prescribing for diabetics.
Network pharmacology-based screening of the active ingredients and mechanisms of evodiae fructus anti-glioblastoma multiforme
Authors: Wu Gang , Hao Qingpei , Liu Bo , Zhou Jingru , Fan Cungang , Liu Ruen
Published: September 2022

Background:

Evodiae fructus has been shown to have anti-glioblastoma multiforme (GBM) effects. However, its anti-GBM active components and mechanism remain unclear. In this study, the active components of evodiae fructus were screened by network pharmacology to explore the possible molecular mechanism of resistance to GBM.

Materials and methods:

The main active ingredients of evodiae fructus were derived from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Batch-traditional Chinese medicine (TCM). TCMSP and Swiss absorption, distribution, metabolism and elimination (ADME) predict genetic targets for ingredients that meet pharmacological criteria. GBM-related targets were obtained from DisGeNet, GeneCards, Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), and TCGA. A Venn diagram was used to obtain the common targets of evodiae fructus and GBM. Protein–protein interaction (PPI) networks and component-disease target networks were constructed using Cytoscape 3.8.1 software for visualization. GBM gene differential expression was visualized by VolcaNoseR, and potential targets were enriched by Gene Ontology (GO) function and annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway by SRplot. Molecular docking verification was conducted using AutoDock Vina software.

Results:

According to the screening conditions, 24 active components and 80 drug targets were obtained. The PPI network contains 80 proteins. The molecular docking verification showed the molecular docking affinity of the core active compounds in evodiae fructus with CASP3, JUN, EGFR, and AKT1.

Conclusions:

This study preliminarily identified the various molecular targets and multiple pathways of evodiae fructus against GBM.
Research status, hotspots and trends of acupuncture and moxibustion in the treatment of Alzheimer’s disease: A bibliometric analysis
Authors: Yue Jinhuan , Li Xiao-Ling , Gao Rui-Xue , Zhang Qinhong , Li Ang , Zhao Wei-Wei , Li Yan , Li Shu-Lin
Published: September 2022

Background:

Acupuncture and moxibustion (AM) are utilized to treat Alzheimer’s disease (AD). However, no bibliometric analysis has explored this issue. Thus, this study investigated the status, hotspots and trends of AM in the treatment of AD.

Methods:

CiteSpace and VOSviewer softwares were used to analyze the literature on the AM for AD in the Web of Science Core Collection database. We analyzed the data of countries/regions, institutions, journals, authors, keywords, and cited references.

Results:

After removing duplicates, 193 articles were retrieved. The number of publications on this topic has increased gradually. The most productive and collaborative country was China (143 documents), followed by South Korea (19). The top 3 active academic institutions were Beijing University of Chinese Medicine, Capital Medicine University, and Guangzhou University of Chinese Medicine. The most productive journal was Evidence-based Complementary and Alternative Medicine (13 documents), followed by the Frontiers in Aging Neuroscience (10), Medicine (10), and Neural Regeneration Research (10). The top 3 co-cited journals were Evidence-based Complementary and Alternative Medicine (156 citations), Acupuncture Electro-therapeutics Research (152), and Acupuncture in Medicine (146). The research hotspots in this domain are dementia, memory, hippocampus, mouse models, and Parkinson’s disease. Major frontiers are comparing the therapeutic effects of acupuncture and donepezil and electroacupuncture at different frequencies in this field.

Conclusion:

This bibliometric study identified relevant hotspots and trends in research on AM in the treatment of AD, which can provide researchers with key information in this domain and help further explore new research directions.
Depression and anxiety in individuals with axial spondyloarthritis and nonspecific low back pain who are interested in non-pharmacological therapy options: Cross-sectional study
Authors: Hušáková Markéta , Levitová Andrea , Domluvilová Daniela , Dad’ová Klára , Pavelka Karel
Published: September 2022

Psychological burden, such as depression and anxiety, may be associated with axial spondyloarthritis (axSpA) and poor prognosis of nonspecific low back pain (NSLBP). Non-pharmacological therapy is a substantial part of the management of both illnesses. Our study describes the psychological outcomes in patients with axSpA and NSLBP who were actively looking for non-pharmacological therapy. A total of 60 participants (34 with axSpA and 26 with NSLBP) were included in this cross-sectional study. Anxiety and depression were examined using the Beck Anxiety Inventory (BAI) and Beck Depression Inventory (BDI-II), respectively. The relationships between BAI and BDI-II and quality of life (EQ-5D), pain intensity (NRS pain), disease activity (AS disease activity score, ASDAS-CRP), and function (Bath AS Functional Index, BASFI) were determined. The intensity of anxiety and depression did not differ between patients with and without axSpA. In both, axSpA and NSLBP, BAI, and BDI-II scores were inversely correlated with EQ-5D, R = −0.268 (P ˂ .05) and R = −0.486 (P ˂ .0001), respectively. We found a variation in the relationship between pain intensity and psychological outcomes in NSLBP and axSpA. The pain intensity score was correlated with the BDI-II (R = 0.542, P = .001) and BAI (R = 0.489, P = .003) scores only in patients with axSpA. In patients with axSpA, BAI was inversely correlated with disease duration (R = −0.356, P = .039) and positively correlated with increased disease activity and poor function, ASDAS-CRP (R = 0.431, P = .012) and BASFI (R = 0.621, P ˂ .0001) scores. The ASDAS-CRP score was positively correlated with BDI-II (R = 0.562, P = .001), and both disease activity and female sex were identified as risk factors for poor BDI-II outcomes in axSpA patients according to multiple regression analysis. Experiences of anxiety and depression seem to be similar for patients with axSpA and NSLBP in this selected group of participants. However, pain intensity may influence psychological outcomes, mainly in patients with axSpA. Disease activity, impaired function, and female sex were risk factors for anxiety and depression in patients with axSpA.
The effectiveness of multimedia combined with teach-back method on the level of knowledge, confidence and behavior of professional caregivers in preventing falls in elderly patients: A randomized non-blind controlled clinical study
Authors: Wang Qinqin , Zou Huixiang , Wang Qin
Published: September 2022

Background:

Teach-back is a teaching method that can quickly improve the acknowledge of target audience and change their behaviors effectively. However, this approach has not been reported in previous studies that were dedicated to reducing the incidence of falls in elderly inpatients. Therefore, we aimed to evaluate the effectiveness of the teach-back method for improving the knowledge, confidence, and behaviors (KCB) of professional caregivers on the fall prevention in elderly inpatients and to provide practical evidence for reducing the incidence of falls.

Methods:

This is a prospective study. At the recruitment, the demographic data of the professional caregivers were completely collected. Questionnaire about KCB of professional caregivers on fall prevention in elderly inpatients was used as an assessment scale, and the differences between the scores were analyzed. At the end of the study, the fall rate of the patients cared by different groups was counted and analyzed.

Results:

A total of 100 professional caregivers were recruited, all of which participated in the whole study process. There was no statistical differences in demographic data. Three or six months after the courses, the knowledge scores, confidence scores, and behavior scores of the two groups were significantly improved, and the observation group scores were significantly higher than it was in the control group (P < .05). During the study period, the incidence of falls in the observation group was 1.32%, while it was 0.30% in the control group (P < .05).

Conclusion:

Teach-back method can rapidly improve KCB of professional caregivers about fall prevention in elderly inpatients, which is worthy of clinical practice.
Hyperkalemia in a Hemolyzed Sample in Pediatric Patients
Authors: Kaila Rahul , Hendrickson Marissa , Avendano Pablo , Davey Cynthia , Cullen Ryan , Colbenson Gretchen , Louie Jeffery
Published: September 2022

Objective

The aim of the study is to analyze whether repeat testing is necessary in healthy children presenting to a pediatric emergency department (ED) who are found to have hyperkalemia on a hemolyzed specimen.

Methods

A 5-year retrospective analysis of pediatric ED patients found to have elevated potassium values on laboratory testing of a sample reported to be hemolyzed. All patients aged 0 to 17 years who had an elevated potassium level after an intravenous draw resulted from a serum sample that was reported as hemolyzed during an ED visit were included in the study.

Results

One hundred eighty-seven patients with some degree of both hemolysis and hyperkalemia were included in the final analysis. The median age was 1.9 years of age. The most common race among all patients was White, followed by African American, and Asian. One hundred forty-five children had repeat sampling for hemolyzed hyperkalemia, 142 children, 97.9% (95% confidence interval, 95.6%–100%) had a normal potassium on repeat and 3 children, 2.1% (95% confidence interval, 0.0%–4.4%) had true hyperkalemia. The frequency of true hyperkalemia in our study population was 2% (3/145). All 3 of these patients had underlying conditions that would appropriately have raised clinician suspicion for hyperkalemia.

Conclusions

It may be unnecessary to obtain repeat samples to confirm normal potassium in a hemolyzed sample with normal blood urea nitrogen and creatinine.
Sinus Augmentation Using Caldwell-Luc Technique in the Existence of Ectopic Tooth in the Maxillary Sinus: A Multidisciplinary Approach
Authors: Çelik Osman E. , Ceylan Mehmet E.
Published: September 2022

Ectopic maxillary third molar teeth can often be located in the maxillary sinus, and the region necessarily requires a multidisciplinary approach due to its proximity to the oral cavity. Ectopic third molar tooth in the maxillary sinus was detected by oral and radiological examination in a 26-year-old male patient. The tooth was removed, and sinus augmentation was performed through the Caldwell-Luc procedure, and a dental implant was placed afterward. The treatment was ended by making a prosthetic metal-supported ceramic crown. Both removals of the ectopic tooth from the maxillary sinus, sinus augmentation, and implant operation can be achieved in a single operation of a single-window opened in the bone. As a result, because of the adjacency of the regions in operations related to the maxillary sinus, both the dental practitioner and the otolaryngologist should evaluate the operation, and multidisciplinary work should be done when necessary.
Donor Side Preference in Maxillary Reconstruction With the Free Fibula Flap
Authors: Weitgasser Laurenz , Barton Richard , Ricketts Sophie , Murray Simon S. , Matros Evan , Morrison Edwin J.
Published: September 2022

Background:

The implications on the choice of donor side when using the free fibula flap for reconstruction of unilateral maxillectomy defects has not been discussed in the literature so far.

Methods:

A unilateral maxillectomy reconstruction was replicated using a 3D-printed skull model and fresh cadaveric dissections of left and right osteomyocutaneous fibula flaps for comparison. Detailed photo documentation was conducted to analyze and illustrate the anatomical differences of performing a reconstruction using the ipsilateral or contralateral sides and their relative benefits and risks.

Results:

A more favorable lie of the septum and skin paddle and flexor hallucis longus muscle is attainable depending on which donor side is used and the planned direction of the pedicle.

Conclusion:

This study demonstrates why it is preferable to use the ipsilateral fibula if anastomosis is to the ipsilateral facial or neck recipient vessels, or the contralateral fibula where the contralateral recipient vessels are preferred.
Horizontal detection of post-translational modifications to an amino acid with a nanopore based on analyte volume and translocation-time
Authors: Sampath G.
Published: September 2022

A method is proposed for the detection of post-translational modifications (PTMs) in single amino acids (AAs) for three types of PTMs (methylation, acetylation, and phosphorylation). It is preceded by a precursor step in which the terminal residue cleaved from a peptide is identified with a set of transfer RNAs (tRNAs) in a method proposed earlier (doi: 10.36227/techrxiv.19318145.v3). The identified AA (unmodified or modified) is separated from its cognate tRNA and translocated through a nanopore under electrophoresis. The resulting current blockade level (a proxy for analyte volume) and its width (a proxy for analyte translocation time) are measured and used to identify any PTM that might be present. The theoretical volumes of the 20 proteinogenic AAs and their PTMs are computed from crystallographic data and the ratio of the volume of a modified AA to that of an unmodified one obtained. The theoretical translocation time for the 20 AAs and their PTMs through a nanopore with a bilevel voltage profile is calculated with a Fokker-Planck drift-diffusion model. A 2-D scatter plot with these two quantities is generated for each AA type. Experimentally measured blockade levels and widths for an AA, modified or unmodified, can now be compared with the AA’s scatter plot to assign a PTM for a modified AA. PTM assignment is horizontal across the PTMs for the AA because the latter has already been identified from its cognate tRNA in the precursor step, the other 19 AA types and their PTMs are not involved. Computational results are presented for 49 PTMs covering all 20 AAs and the three PTM types mentioned above.
Temperature-triggeredin situforming lipid mesophase gel for local treatment of ulcerative colitis
Authors: Carone Marianna , Spalinger Marianne R. , Gaultney Robert A. , Mezzenga Raffaele , Mookhoek Aart , Krebs Philippe , Rogler Gerhard , Luciani Paola , Aleandri Simone
Published: September 2022

Ulcerative colitis (UC) is a chronic inflammatory bowel disease affecting the colonic mucosa. There is no cure for UC and its chronic relapsing/remitting nature strongly affects patient quality of life. Current treatment options frequently have significant side effects and remission rates are limited raising a demand for new treatment strategies. Novel therapeutic approaches that could maximize the drug concentration at the site of inflammation with minimal systemic exposure, like topical applications, would address this unmet clinical need. To date, few drug delivery systems (DDSs) have been designed to topically convey small molecules to the rectum and left-sided colon. Here, we developed and tested a drug delivery platform for topical treatment of UC based on a temperature-triggeredin situforming adhesive lipid gel (TIF-Gel). Due to its soft, gel-like consistency, its high encapsulation efficacy, and its drug-controlled release, TIF-Gel suggests a more patient-friendly and effective application with respect to the rectal formulations currently available.

Capitalizing on the biocompatible and biodegradable self-assembled structure of lipid mesophases (LMPs), we loaded TIF-Gel with tofacitinib (TOFA; a hydrophilic inhibitor of the enzymes Janus kinase 1 and 3) or TAC (a hydrophobic immunosuppressive drug), both of which are indicated in the treatment of UC. We designed and fully characterized our biocompatible lipid formulationin vitroand tested itin vivousing two different murine models of inflammatory bowel disease: chemically-induced and T cell transfer-mediated. Both approaches (TIF-Gel-TOFA and TIF-Gel-TAC) led to reductions in colitis disease severity and intestinal inflammation compared to vehicles, therefore showing therapeutic efficacy.

Overall, our findings show that TIF-Gel can deliver drugs locally to the colonic mucosa to mitigate intestinal inflammatory disease in a pre-clinical model. They also suggest that, in a clinical setting, TIF-Gel might provide a patient-friendly approach to improve colitis while allowing for a reduction of the adverse effects associated with a systemic therapy.
Metabolic plasticity of T-cell therapies: multi-omic profiling of interacting human tumor-infiltrating lymphocytes and autologous tumor adoptive cell therapy
Authors: Martinez-Paniagua Melisa , Haymaker Cara , Robinson Jonathan , Harel Michal , Creasy Caitlin , Adolacion Jay R T. , An Xingyue , Fathi Mohsen , Rezvan Ali , Kumar Monish , Amritkar Amit , Woodman Scott E. , Amaria Rodabe N. , Geiger Tamar , Hwu Patrick , Bernatchez Chantale , Varadarajan Navin
Published: September 2022

Adoptive cell therapy (ACT) based onex vivoexpanded autologous tumor-infiltrating lymphocytes (TILs) can mediate durable antitumor responses even in heavily pretreated patients. However, only a subset of patients responds to ACT; efforts to identify correlates of response have focused on profiling the tumor or the TIL but rarely in an interactive environment. Interactive profiling can provide unique insights into the clinical performance of TILs since the fate, function, and metabolism of TILs are influenced by autologous tumor-derived factors. Here, we performed a suite of cell-sparing assays dubbed holistic analysis of the bioactivity of interacting T cells and autologous tumor cells (HABITAT). HABITAT profiling of TILs used for human ACT and their autologous tumor cells included function-based single-cell profiling by timelapse imaging microscopy in nanowell grids (TIMING); multi-omics using RNA-sequencing and proteomics; metabolite inference using genome-scale metabolic modeling, and pulse-chase assays based on confocal microscopy to profile the uptake and fate of fatty acids (FA). Phenotypically, the ACT TILs from both responders (Rs) and nonresponders (NRs) were comprised of predominantly effector memory T cells (TEMcells) and did not express a high frequency of programmed death ligand-1 (PD-L1) and showed no differences in TCR diversity. Our results demonstrate that while tumor cells from both Rs and NRs are efficient at uptaking FAs, R TILs are significantly more efficient at utilizing FA through fatty acid oxidation (FAO) than NR TILs under nutrient starvation conditions. While it is likely that lipid and FA uptake is an inherent adaptation of TIL populations to lipid-rich environments, performing FAO sustains the survival of TILs and allows them to sustain antitumor cytolytic activity. We propose that metabolic plasticity enabling FAO is a desirable attribute of human TILs for ACT leading to clinical responses.
Digital Light Processing 3D printing for biological applications of polydimethylsiloxane-based microfluidics
Authors: Poskus Matthew D. , Wang Tuo , Deng Yuxuan , Borcherding Sydney , Atkinson Jake , Zervantonakis Ioannis K.
Published: September 2022

Soft lithography microfluidics offer many benefits over conventional biological assays; however, the impact this field is inhibited by the lack of widespread adoption of this technology in part due to prohibitive cost and fabrication time. Recent improvements in three-dimensional (3D) printing technologies such as digital light processing (DLP) printing offer a cost-effective and rapid prototyping solution to microfluidic fabrication. Limited information is available about how 3D printing parameters and resin cytocompatibility impact the performance of 3D printed molds for fabrication of polydimethylsiloxane (PDMS)-based microfluidics for cellular studies. Using a low-cost, commercially available DLP 3D printer, we assess the cytocompatibility of several resins, optimize printer settings and characterize minimum feature size of our system. We demonstrate the applications of DLP printing for soft lithography microfluidics by developing four assays to characterize cell viability, drug response, establish concentration gradients, and monitor live-cell 3D invasion into a hydrogel.
Subpopulation Codes Permit Information Modulation Across Cortical States
Authors: Getz Matthew P. , Huang Chengcheng , Doiron Brent
Published: September 2022

Cortical state is modulated by myriad cognitive and physiological mechanisms. Yet it is still unclear how changes in cortical state relate to changes in neuronal processing. Previous studies have reported state dependent changes in response gain or population-wide shared variability, motivated by the fact that both are important determinants of the performance of any population code. However, if the state-conditioned cortical regime is well-captured by a linear input-output response (as is often the case), then the linear Fisher information (FI) about a stimulus available to a decoder is invariant to state changes. In this study we show that by contrast, when one restricts a decoder to a subset of a cortical population, information within the subpopulation can increase through a modulation of cortical state. A clear example of such a subpopulation code is one in which decoders only receive projections from excitatory cells in a recurrent excitatory/inhibitory (E/I) network. We demonstrate the counterintuitive fact that when decoding only from E cells, it is exclusively the I cell response gain and connectivity which govern how information changes. Additionally, we propose a parametrically simplified approach to studying the effect of state change on subpopulation codes. Our results reveal the importance of inhibitory circuitry in modulating information flow in recurrent cortical networks, and establish a framework in which to develop deeper mechanistic insight into the impact of cortical state changes on information processing in these circuits.
Subpopulations of cancer-associated fibroblasts expressing fibroblast activation protein and podoplanin in non-small cell lung cancer are a predictor of poor clinical outcome
Authors: Mathieson Layla , Koppensteiner Lilian , Pattle Samuel , Dorward David A , O’Connor Richard , Akram Ahsan
Published: September 2022

Cancer-associated fibroblasts (CAFs) are the dominant cell type in the stroma of solid organ cancers, including non-small cell lung cancer (NSCLC). Fibroblast heterogeneity is widely recognised in many cancers, with subpopulations of CAFs being identified and potentially being indicative of prognosis and treatment efficacy. Here, the subtypes displayed by CAFs isolated from human NSCLC resections are initially identified by flow cytometry, using the markers FAP, CD29, αSMA, PDPN, CD90, FSP-1 and PDGFRβ, showing five distinct subpopulations, CAF-S1-S5. Our findings show that when comparing fibroblasts from tumour tissue with that from adjacent lung tissue, CAF-S2 and CAF-S3 are found in the normal tissue and marker expression suggests a less activated phenotype whereas CAF-S1, CAF-S4 and CAF-S5 are predominantly found in the tumour tissue and are positive for a combination of markers of fibroblast activation. We focus on these subtypes most associated with fibroblast activation, primarily focussing on a previously unreported CAF-S5 subtype, and comparing to the previously identified CAF-S1. Both these subsets express FAP and PDPN as markers of fibroblast activation, but CAF-S5 lacks expression of the common activation marker αSMA. The spatial relevance of these subtypes in a cohort of 163 NSCLC patients was then investigated by multiplex immunofluorescence on a tumour micro-array of patient samples, revealing CAF-S5 are found further from tumour regions than CAF-S1. To understand the functional role of CAF-S5, scRNA sequencing data was used to compare the subset to the previously identified CAF-S1, finding that CAF-S5 displays an inflammatory phenotype, whereas CAF-S1 displays a contractile phenotype. We demonstrate that presence of either the CAF-S1 or CAF-S5 subtype is correlated to worse survival outcome in NSCLC, highlighting the importance of the identification of CAF subtypes in NSCLC.
Over Two Million Protein Translocations Reveal Optimal Conditions for High Bandwidth Recordings, Studying Transport Energetics, and Unfolding
Authors: Nuwan Y. M. , Bandara D. Y. , Freedman Kevin J.
Published: September 2022

The gradual tapered geometry of nanopipettes offers a unique perspective on protein transport through nanopores since both a gradual and fast confinement is possible depending on translocation direction. Protein capture rate, unfolding, speed of translocation, and clogging probability are studied by toggling the lithium chloride concentration between 4 M and 2 M. Interestingly, the proteins in this study could be transported with or against the electrophoresis and offer vastly different attributes of sensing and affect whether a protein unfolds during pore transit. A ruleset for studying proteins is developed that prevents irreversible pore clogging and yielded upwards of >100,000 events/nanopore. Minimizing clogging also permitted higher quality data via the use of smaller pores (i.e., <2× the size of the protein) including higher SNR recordings and data acquisition at the highest available bandwidth (100 kHz). The extended duration of experiments further revealed that the capture rate takes ~2 hours to reach a steady state with a value ~3x greater than the initial reading, emphasizing the importance of reaching equilibrated transport for studying the energetics of protein transport (i.e., diffusion vs barrierlimited). Even in the equilibrated transport state, improper lowpass filtering was shown to distort the classification of diffusion-limited vs barrier-limited transport. Finally electric-field induced protein unfolding was found to be most prominent in EO dominant transport whereas EP dominant events show no evidence of unfolding. Thus, our findings showcase the optimal conditions for protein translocations and the impact on studying protein unfolding, transport energetics, and acquiring high bandwidth data.
CLPB3 is required for the removal of chloroplast protein aggregates and for thermotolerance in Chlamydomonas
Authors: Kreis Elena , Niemeyer Justus , Merz Marco , Scheuring David , Schroda Michael
Published: September 2022

In the cytosol of plant cells, heat-induced protein aggregates are resolved by ClpB/Hsp100 family member HSP101, which is essential for thermotolerance. For chloroplast family member CLPB3 this is less clear with controversial reports on its role in conferring thermotolerance. To shed light onto this issue, we have characterized two Chlamydomonas reinhardtii clpb3 mutants. We show that chloroplast CLPB3 is required for resolving heat-induced protein aggregates containing stromal TIG1 and the small heat shock proteins HSP22E/F in vivo and for conferring thermotolerance under heat stress. Although CLPB3 accumulates to similarly high levels as stromal HSP70B under ambient conditions, we observed no prominent constitutive phenotypes. However, we found decreased accumulation of the ribosomal subunit PRPL1 and increased accumulation of the stromal protease DEG1C in the clpb3 mutants, suggesting that reduction in chloroplast protein synthesis capacity and increase in protease capacity may compensate for loss of CLPB3 function. Under ambient conditions, CLPB3 was distributed throughout the chloroplast but reorganized into stromal foci upon heat stress, which mostly disappeared during recovery. CLPB3 foci were localized next to signals from HSP22E/F, originating largely to the thylakoid membrane occupied area. This suggests a possible role for CLPB3 in disentangling protein aggregates from the thylakoid membrane system.

Highlight

Chloroplast CLPB3 in Chlamydomonas is required for resolving heat-induced protein aggregates and this activity confers thermotolerance under severe heat stress.

During heat stress, CLPB3 organizes into stromal foci located next to the thylakoid membrane system, indicating a role for CLPB3 in disentangling protein aggregates from there.
Expanded diversity of tfdA harboring bacteria across the natural and built environment
Authors: White Amber M. , Gonzalez Vazquez Amarilys , McDaniel Elizabeth A. , Peterson Benjamin D. , Koch Paul , Remucal Christina K. , McMahon Katherine D.
Published: September 2022

2,4-Dichlorophenoxyacetic acid (2,4-D) is an herbicide commonly used in aquatic and terrestrial environments that is degraded by bacteria through the TFD pathway. Previous work has relied on culture-based methods to develop primers for qPCR analysis of the gene cassette in environmental samples. In this study, we combined molecular and genomic approaches to examine the accuracy of established tfdA qPCR primers on environmental samples and update the phylogeny of tfdA genes detected in bacterial genomes. We found most putative 2,4-D degraders are within the Proteobacteria but also found several novel degraders including members of the phyla Candidatus Rokubacteria and Candidatus Eremiobacteraeota. In silico analysis of established primers showed potential amplification of < 5% of putative degrader sequences but 52-100% of experimentally verified degraders when allowing for three and one mismatches between template and primer sequences, respectively. Overall, our work expands the diversity of putative 2,4-D degraders and demonstrates the limitations of culture-based tools for investigating functional diversity of microorganisms in the environment.

Importance

Cultivation-based methods can misrepresent the diversity of environmental microorganisms. Our work showcases one example of how culture-based development of molecular tools underestimates the full spectrum of 2,4-D degrading microorganisms. Accurately identifying microorganisms with 2,4-D degradation potential is crucial for understanding the biodegradation potential of a commonly used herbicide across terrestrial, aquatic, and subsurface environments. Additionally, this work reinforces well-documented pitfalls associated with relying on cultured representatives when constructing primers and the challenges of translating findings from a few cultured representatives to understudied or unknown microorganisms in complex environments.
Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium
Authors: Ghersi Joey J. , Baldissera Gabriel , Hintzen Jared , Luff Stephanie A. , Cheng Siyuan , Xia Ivan Fan , Sturgeon Christopher M. , Nicoli Stefania
Published: September 2022

Multipotent hematopoietic stem/progenitor cells (HSPCs) generate all mature blood cells in the erythroid, lymphoid, and myeloid lineages. HSPCs are initially produced in the embryo, via transdifferentiation of hemogenic endothelial cells (hemECs) in the aorta-gonad mesonephros (AGM). HSPCs in the AGM are functionally heterogenous in differentiation and proliferative output, but how these intrinsic differences are acquired remains unanswered. This knowledge could inform approaches to overcome the dysregulation of HSPC heterogeneity associated with poor outcomes of autologous transplants. Here we discovered that loss of microRNA (miR)-128 (miR-128Δ/Δ) in zebrafish leads to an expansion of hemECs forming replicative HSPCs in the AGM, and a skew towards the erythroid and lymphoid lineages in larval and adult stages. Furthermore, we found that inhibiting miR-128 during the differentiation of human pluripotent stem cells into hemECs, but not during the endothelial-to-hematopoietic transition, recapitulated the lineage skewing. In vivo, expression of wild-type miR-128 in endothelium restored the blood lineage distribution in miR-128Δ/Δ zebrafish. We found that miR-128 represses the expression of the Wnt inhibitor csnk1a1 and the Notch ligand jag1b, and thus promotes Wnt and Notch signaling in hemECs. De-repression of cskn1a1 resulted in hemECs generating replicative and erythroid-biased HSPCs, whereas de-repression of jag1b resulted in hemECs forming lymphoid-biased HSPCs in the AGM and relative mature blood cells in adult. We propose that HSPC heterogeneity is established in hemogenic endothelium prior to transdifferentiation and is programmed in part by Wnt and Notch signaling modulation.
Accelerated High-throughput Plant Imaging and Phenotyping System
Authors: Kose Talha , Lins Tiago F. , Wang Jessie , O’Brien Anna M. , Sinton David , Frederickson Megan E.
Published: September 2022

The complex web of interactions in biological communities is an area of study that requires large multifactorial experiments with sufficient statistical power. The use of automated tools can reduce the time and labor associated with experiment setup, data collection, and analysis in experiments aimed at untangling these webs. Here we demonstrate tools for high-throughput experimentation (HTE) in duckweeds, small aquatic plants that are amenable to autonomous experimental preparation and image-based phenotyping. We showcase the abilities of our HTE system in a study with 6,000 experimental units grown across 1,000 different nutrient environments. The use of our automated tools facilitated the collection and analysis of time-resolved growth data, which revealed finer dynamics of plant-microbe interactions across environmental gradients. Altogether, our HTE system can run experiments of up to 11,520 experimental units and can be adapted to studies with other small organisms.
ClickArr: a novel, high throughput assay for evaluating β-arrestin isoform recruitment
Authors: French Alexander R. , Meqbil Yazan J. , van Rijn Richard M.
Published: September 2022

Modern methods for quantifying signaling bias at GPCRs rely on using a single β-arrestin isoform. However, it is increasingly appreciated that the two β-arrestin isoforms have unique roles, requiring the ability to assess β-arrestin isoform preference. Herein, we present ClickArr, a live-cell assay that simultaneously reports recruitment of both β-arrestin isoforms as they compete for interaction with GPCRs. We demonstrate that an agonist can have β-arrestin isoform bias, potentially opening up a new dimension for drug development.
Balancing competing effects of tissue growth and cytoskeletal regulation duringDrosophilawing disc development
Authors: Kumar Nilay , Tsai Kevin , Mim Mayesha Sahir , Ambriz Jennifer Rangel , Chen Weitao , Zartman Jeremiah J. , Alber Mark
Published: September 2022

Cytoskeletal structure and force generation within cells must be carefully regulated as the developing organ grows to reach a final size and shape. However, how the complex regulation of multiple features of tissue architecture is simultaneously coordinated remains poorly understood. Through iterations between experiments and novel computational multi-scale model simulations, we investigate the combined regulation of cytoskeletal regulation and proliferation in the growing wing imaginal disc. First, we found through experiments and calibrated model simulations that the local curvature and nuclear positioning of cells in the growing wing disc are defined by patterning of nested spatial domains of peaks in apical and basal contractility. Additionally, predictions from model simulations that incorporate a mechanistic description of interkinetic nuclear migration demonstrate that cell proliferation increases the local basal curvature of the wing disc. This is confirmed experimentally as basal curvature increases when growth and proliferation are increased through insulin signaling. In surprising contrast, we experimentally found that Decapentaplegic (Dpp), the key morphogen involved in both growth control and patterning of the anterior-posterior axis, counteracts increases in tissue bending due to cell proliferation via a combined mechanism that balances the competing impacts of both proliferation and patterning of cell contractility. Overall, the high conservation of these regulatory interactions suggests an important balancing mechanism through dual regulation of proliferation and cytoskeleton to meet the multiple criteria defining tissue morphogenesis.