bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance and Reliable Operation of Physiological Controllers Under Various Cardiovascular Models: In Silico and In Vitro Study
Authors: Gwosch Thomas , Magkoutas Konstantinos , Kaiser David , Schmid Daners Marianne
Published: February 2024

The evaluation of control schemes for left ventricular assist devices (LVADs) requires the utilization of an appropriate model of the human cardiovascular system. Given that different patients and experimental data yield varying performance of the cardiovascular models (CVMs) and their respective parameters, it becomes crucial to assess the reliable operation of controllers. This study aims to assess the performance and reliability of various LVAD controllers using two state-of-the-art CVMs, with a specific focus on the impact of interpatient variability. Extreme test cases were employed for evaluation, incorporating both in silico and in vitro experiments. The differences observed in response between the studied CVMs can be attributed to variations in their structures and parameters. Specifically, the model with smaller compartments exhibits higher overload rates, whereas the other model demonstrates increased sensitivity to changes in preload and afterload, resulting in more frequent suction events (34.2% vs. 8.5% for constant speed mode). These findings along with the varying response of the tested controllers highlight the influence of the selected CVM emphasizing the need to test each LVAD controller with multiple CVMs or, at least, a range of parameter sets. This approach ensures sufficient evaluation of the controller’s efficacy in addressing interpatient variability.
Using the Stratum-Specific Likelihood Ratio Method to Derive Outcome-Based Hospital Volume Categories for Total Knee Replacement
Authors: Ghomrawi Hassan M.K. , Huang Lynn W. , Hiredesai Annika N. , French Dustin D.
Published: February 2024

Background:

Evidence of higher hospital volume being associated with improved outcomes for patients undergoing total knee replacement (TKR) is mostly based on arbitrary distribution-based thresholds.

Objective:

We aimed to define outcome-based volume thresholds using data from a national database.

Methods:

We used the MedPAR Limited Data Set inpatient data from 2010-2015 to identify patients who had undergone primary TKR. Surgical and TKR specific complications occurring within the index hospitalization and all-cause readmission within 90 days were considered adverse events. We derived an average annual TKR case volume for each hospital and applied the stratum-specific likelihood ratio method to determine volume categories indicative of a similar likelihood of 90-day post-operative complications. Hierarchical multivariable logistic regression with a random intercept for hospital nested within study year and adjusted for patient and hospital characteristics was performed to determine if these volume thresholds were still associated with the odds of 90-day readmission for complications after adjustment.

Results:

SSLR analysis yielded 4 hospital volume categories based on the likelihood of 90-day postoperative complications: 1–31 (low), 32–127 (medium), 128–248 (high), and 429+ (very high) TKRs performed per year. The results of the hierarchical multivariable logistic regression showed significantly increased odds of 90-day complications at lower volume categories. Sensitivity analyses confirmed our main findings.

Conclusions:

This study is the first to provide national-level volume categories that are evidence-based. Publicizing these thresholds may enhance quality measures available to patients, providers, and payors.
Evaluation of bone marrow invasion on the machine learning of 18F-FDG PET texture analysis in lower gingival squamous cell carcinoma
Authors: Fukushima Yasuhiro , Suzuki Keisuke , Kim Mai , Gu Wenchao , Yokoo Satoshi , Tsushima Yoshito
Published: February 2024

Objectives

Lower gingival squamous cell carcinoma (LGSCC) has the potential to invade the alveolar bone. Traditionally, the diagnosis of LGSCC relied on morphological imaging, but inconsistencies between these assessments and surgical findings have been observed. This study aimed to assess the correlation between LGSCC bone marrow invasion and PET texture features and to enhance diagnostic accuracy by using machine learning.

Methods

A retrospective analysis of 159 LGSCC patients with pretreatment 18F-fluorodeoxyglucose (FDG) PET/computed tomography (CT) examination from 2009 to 2017 was performed. We extracted radiomic features from the PET images, focusing on pathologic bone marrow invasion detection. Extracted features underwent the least absolute shrinkage and selection operator algorithm-based selection and were then used for machine learning via the XGBoost package to distinguish bone marrow invasion presence. Receiver operating characteristic curve analysis was performed.

Results

From the 159 patients, 88 qualified for further analysis (59 men; average age, 69.2 years), and pathologic bone marrow invasion was identified in 69 (78%) of these patients. Three significant radiological features were identified: Gray level co-occurrence matrix_Correlation, INTENSITY-BASED_IntensityInterquartileRange, and MORPHOLOGICAL_SurfaceToVolumeRatio. An XGBoost machine-learning model, using PET radiomic features to detect bone marrow invasion, yielded an area under the curve value of 0.83.

Conclusion

Our findings highlighted the potential of 18F-FDG PET radiomic features, combined with machine learning, as a promising avenue for improving LGSCC diagnosis and treatment. Using 18F-FDG PET texture features may provide a robust and accurate method for determining the presence or absence of bone marrow invasion in LGSCC patients.
Novice Preceptors Facilitating Nursing Student Clinicals
Authors: Wolfe Shelley M. , Joswiak M. Ellen
Published: February 2024

Nursing professional development practitioners rely on nurse preceptors to guide the development of nursing staff and students. A lack of experienced preceptors may require individuals who have limited to no experience in precepting to serve in the preceptor role. Nursing professional development practitioners should be prepared to effectively support and develop novice preceptors. This article analyzes the development and implementation of a novel educational resource that assists the novice preceptor in facilitating nursing student clinicals.
Intracranial Hypertension Associated With Poly-Cranio-Radicular-Neuropathies
Authors: Eaton James E. , Oguz Ipek , Kazimuddin Habeeb , Bagnato Francesca
Published: February 2024

Introduction:

We present the case of a gentleman who developed rapidly progressive vision loss, ophthalmo-paresis, and flaccid quadriparesis in the context of severe intracranial hypertension. We reviewed the available cases in the literature to increase awareness of this rare clinical entity.

Case Report:

A 36-year-old man developed rapidly progressive vision loss, ophthalmo-paresis, and flaccid quadriparesis. He had an extensive workup, only notable for severe intracranial hypertension, >55 cm of H2O. No inflammatory features were present, and the patient responded to CSF diversion. Few similar cases are available in the literature, but all show markedly elevated intracranial pressure associated with extensive neuroaxis dysfunction. Similarly, these patients improved with CSF diversion but did not appear to respond to immune-based therapies.

Conclusions:

We term this extensive neuroaxis dysfunction intracranial hypertension associated with poly-cranio-radicular-neuropathy (IHP) and distinguish it from similar immune-mediated clinical presentations. Clinicians should be aware of the different etiologies of this potentially devastating clinical presentation to inform appropriate and timely treatment.
The Effectiveness of Public Awareness Initiatives Aimed at Encouraging the Use of Evidence-Based Recommendations by Health Professionals: A Systematic Review
Authors: Tian Esther Jie , Nguyen Cathy , Chung Lilian , Morris Chloe , Kumar Saravana
Published: February 2024

Objectives

Public awareness initiatives have attracted growing attention globally, as a strategy to reduce low-value care and disinformation. However, knowledge gap remains in determining their effects. The aim of this systematic review was to summarize existing evidence to date on global effectiveness of public awareness initiatives.

Methods

Primary quantitative studies focusing on passive delivery of public awareness initiatives that targeted health professionals were included. Eligible studies were identified through search of MEDLINE, Embase, Emcare, the Cochrane Library, PsycINFO, Business Source Complete, Emerald Insight, and Google (initially on December 19, 2018, followed by updated search between July 8–10, 2019, and then between March 8–9, 2022) and the reference list of relevant studies. Methodological quality of included studies was assessed using modified McMaster critical appraisal tool. A narrative synthesis of the study outcomes was conducted.

Results

Twenty studies from United States, United Kingdom, Canada, Australia, and multicountry were included. Nineteen studies focused on Choosing Wisely initiative and one focused on National Institute of Clinical Excellence reminders. Most studies investigated one recommendation of a specialty. The findings showed conflicting evidence on the effectiveness of public awareness initiatives, suggesting passive delivery has limited success in reducing low-value care among health professionals.

Conclusions

This review highlights the complexity of change in an established practice pattern in health care. As passive delivery of public awareness initiatives has limited potential to initiate and sustain change, wide-ranging intervention components need to be integrated for a successful implementation.
Endosonography Elastography and Magnetic Resonance Imaging in the Restaging and Response Assessment of Rectal Cancer After Neoadjuvant Therapy
Authors: Tang Xuemei , Yuan Hongmei , Mu Xurong , Gu Peng , Kong Pengfei
Published: February 2024

The objective of this academic research is to assess the efficacy of conventional endorectal ultrasound (ERUS), ultrasonic shear wave elastography (SWE), and magnetic resonance imaging (MRI) techniques in evaluating the impact of neoadjuvant therapy (nCRT). Forty-five patients with advanced low rectal cancer (T ≥ 3) were included. Before and after nCRT, ERUS, SWE, and MRI evaluations were conducted. The T staging of ultrasound (uT) and MRI (mT) were evaluated and compared with the pathological T staging (ypT). The accuracy of the 2 diagnostic methods for T staging, and T downstaging was evaluated. The ultrasound elasticity difference and relative elasticity before and after treatment and pathological T downstaging were compared, and its cutoff value and the area under the curve were assessed. In terms of T staging accuracy after chemoradiotherapy, the values for ERUS, ERUS combined with SWE, and MRI were 64.4%, 71.1%, and 62.2%, respectively. No significant difference was observed among these groups (P> 0.05). The accuracy of uT downstaging was 84.4%, and that of mT downstaging was 88.9%. The receiver operating characteristic curve of uLD and elastic differences and relative elasticity of T downstaging after treatment were 0.754, 0.817, and 0.886, respectively (allP< 0.05). Both ERUS and MRI can evaluate ypT downstaging. The indicators for evaluating T downstaging are uLD, elasticity difference, and relative elasticity, providing more reference for clinical assessment of nCRT efficacy.
Update on the Selection Criteria of Plastic Surgery Residents
Authors: Asghari Arya , Hines Eric , Mocharnuk Joseph , Leis Amber , Wang Eric D.
Published: February 2024

Background

Plastic and reconstructive surgery (PRS) is recognized as a highly competitive specialty. Since the first assessment of resident selection criteria in 2007, PRS residency programs have adopted holistic review processes and adapted to changes such as a decline in medical schools participating in the Alpha Omega Alpha Honor Medical Society as well as the recent transition to pass/fail grading for the United States Medical Licensing Examination (USMLE) step 1 examination (Schultz et al. Plast Reconstr Surg Glob Open. 2020;8:e2892; Tadisina et al. Plast Reconstr Surg. 2017;139:330e–331e). This study was devised to evaluate current PRS residency criteria in light of these changes.

Methods

An anonymous, 12-item, electronic survey was generated and distributed using Alchemer. An email was sent to 171 program directors (PDs) and associate program directors (APDs) of PRS residency programs. Survey questions were developed to collect data regarding respondent demographics and their desired criteria when assessing residency applicants. Complete responses were collected and analyzed with summary statistics and multivariate logistic regression using RStudio (version 1.3.109).

Results

In total, 44 (25.7% response rate) of the 171 PDs and APDs completed the survey. Of the 16 programs (36.4%) with a USMLE cutoff score, 7 (43.8%) reported a range of 230 to 239 and 6 (37.5%) reported a range of 240 to 249. Without a score for step 1, the majority (48.8%) of respondents believe that step 2 scores will replace step 1 scores in terms of assessment criteria, and the content of recommendation letters was selected as the criterion with the greatest increase in weight (66.7%). In addition, 27.3% of programs require a step 2 score at the time of interview. The top 3 academic criteria in order of decreasing importance were the content of recommendation letters, clinical grades, and letter writers, whereas the top 3 nonacademic criteria were subinternship performance, maturity, and interview performance.

Conclusions

Plastic and reconstructive surgery remains a highly competitive specialty for residency applicants. Our findings suggest that Alpha Omega Alpha membership remains diminished in importance, whereas USMLE cutoff scores have increased. With recent changes in the step 1 grading system, PDs and APDs will rely more heavily on step 2 scores and the content of recommendation letters.
ACETATE RINGER'S SOLUTION VERSUS NORMAL SALINE SOLUTION IN SEPSIS: A RANDOMIZED, CONTROLLED TRIAL
Authors: Zhang Jing , Liu Fang , Wu Ziyi , Jiang Jun , Wang Bingqing , Qian Yaoyao , Suo Jinmeng , Li Yiming , Peng Zhiyong
Published: February 2024

Background: Normal saline solution (NSS) and Ringer's acetate solution (RAS) are commonly given to critically ill patients as a fundamental fluid therapy. However, the effect of RAS and NSS on sepsis patient outcomes remains unknown. Methods: We conducted a single-center prospective open-label parallel controlled trial to enroll adult patients (>18 years old) diagnosed with sepsis. Participants received either RAS or NSS for intravenous infusion for 5 days. The primary outcome was the incidence of major adverse kidney events within 28 days (MAKE28). Secondary outcomes included 30−/90-day mortality, acute kidney injury, and hyperchloremia. The patients were then reclassified as NSS-only, RAS-only, and RAS + NSS groups according to the type of fluid they had received before enrollment. Thereafter, a secondarypost hocanalysis was performed. Results: Two hundred fifty-five septic patients were screened, and 143 patients (51.0% in RAS group and 49.0% in NSS group) were enrolled in the study. Each group received a median of 2 L of fluid administration during five interventional days. Of the patients, 39.3% had received 500 mL (500–1,000 mL) of balanced salt solutions (BSSs) before intensive care unit (ICU) admission. There was no statistical difference among the RAS and NSS group on the primary outcome MAKE28 in the initial analysis (23.3% vs. 20.0%; OR, 1.2 [0.6 to 2.2];P= 0.69). MAKE28 was observed in 23.3% of RAS-only versus 27.3% of NSS-only group patients (0.82 [0.35–1.94],P= 0.65) in the secondarypost hocanalysis. The patients in the NSS-only group had a longer invasive mechanical ventilation days and a trend toward the accumulation of serum chloride. Conclusion: This study observed no statistically significant difference on MAKE28 and secondary outcomes among sepsis patients receiving RAS and NSS. However, it is unclear whether the large amount of fluid resuscitation before ICU admission and carrier NSS narrowed the difference between BSSs and NSSs.
Private Equity Investment in Surgical Care
Authors: Sievers Maxwell T. , Neevel Andrew , Diaz Adrian , Rouanet Eva , Sheetz Kyle , Brophy David , Dimick Justin B. , Chhabra Karan R.
Published: February 2024

Objective:

To characterize the extent of private equity (PE) investment affecting surgical care.

Background:

Over the last decade, investor-backed, for-profit PE groups have invested in health care at an unprecedented rate, but the breadth of these investments affecting surgical practice remains largely unknown.

Methods:

Four nationally representative databases were used to identify all merger/acquisitions involving surgical practices between 2015 and 2019, determine PE investment in those transactions, and link the acquisitions with a physician data set.

Results:

A total of 1542 unique transactions were identified, of which 539 were financed by PE. Fifty-eight transactions were then classified into their respective categories within surgical care: digestive disease, orthopedics, urology, vascular surgery, and plastic/cosmetic surgery. These transactions accounted for 199 practice sites and 1405 physicians, averaging 24.2 physicians per transaction. Acquisition activity peaked in 2017, with a total of 63 practices involved. Digestive disease, urology, and orthopedic surgery accounted for the most activity. General surgeons were involved in a small share of the digestive disease practice acquisitions. Three “surgery-adjacent” categories were also identified: anesthesiology, ambulatory surgery centers, and surgical staffing firms. Among these, anesthesia was the largest category in terms of practices (194) and physicians (2660) involved in transactions across the study period. Medical Service Organizations were a key mechanism through which PE firms invested in surgical care.

Conclusions:

PE has engaged in substantial investment within surgical specialties, creating increased practice consolidation. These investments affect all levels of medical care and have notable implications for patients, practitioners, and policymakers.
Effectiveness and Safety of Flumazenil Augmentation During Electroconvulsive Therapy
Authors: Gistelinck Lennart , Van de Velde Nele , Tandt Hannelore , Verslype Pieter , Lemmens Gilbert
Published: February 2024

Introduction

Benzodiazepines are considered to negatively affect seizure quality and duration during electroconvulsive therapy (ECT). Several researchers have advocated the use of flumazenil, a competitive benzodiazepine receptor antagonist, for patients treated with benzodiazepines during ECT. However, clinical evidence regarding flumazenil use in ECT remains sparse. The aim of this study is to investigate the effects of flumazenil on seizure duration and adverse effects.

Methods

All patients with depressive disorders, treated with flumazenil during a course of ECT in 2019 in a tertiary hospital, were identified through a retrospective chart review. Seizure duration was recorded before and after flumazenil administration. Effectiveness of ECT was assessed using the Inventory of Depressive Symptomatology and the Bush-Francis Catatonia Rating Scale. Postictal agitation was ascertained by identifying patients who received additional sedatives immediately after ECT or who needed physical restraint.

Results

Twenty-six patients were included, receiving a total of 363 treatments, of which 263 were augmented with flumazenil. Flumazenil administration increased electroencephalogram seizure duration on average with 10.5 seconds comparing ECT with or without flumazenil (P = 0.003). In 21.8% of the cases, no increase in seizure duration was observed. Postictal agitation occurred at least once in 34.6% of the patients receiving flumazenil during their course of ECT.

Conclusion

Our results show that flumazenil increases seizure duration, albeit with limited clinical implications. Noteworthy, the prevalence of postictal agitation is high. When confronted with short seizures, clinicians should therefore deploy other available techniques to lower seizure threshold before considering flumazenil.
Functional characterization of
SORL1
variants in cell-based assays to investigate variant pathogenicity
Authors: Fazeli Elnaz , Fazeli Elham , Fojtík Petr , Holstege Henne , Andersen Olav M.
Published: February 2024

SORLA, the protein encoded by the
SORL1
gene, has an important role in recycling cargo proteins to the cell surface. While SORLA loss-of-function variants occur almost exclusively in Alzheimer's disease cases, the majority of
SORL1
variants are missense variants that are individually rare and can have individual mechanisms how they impair SORLA function as well as have individual effect size on disease risk. However, since carriers mostly come from small pedigrees, it is challenging to determine variant penetrance, leaving clinical significance associated with most missense variants unclear. In this article, we present functional approaches to evaluate the pathogenicity of a
SORL1
variant, p.D1105H. First, we generated our mutant receptor by inserting the D1105H variant into the full-length SORLA-WT receptor. Then using western blot analysis we quantified the effect of the mutation on maturation and shedding of the receptor for transfected cells, and finally applied a flow cytometry approach to quantify SORLA expression at the cell surface. The results showed decreased maturation, decreased shedding, and decreased cell surface expression of D1105H compared with wild-type SORLA. We propose how these approaches can be used to functionally assess the pathogenicity of
SORL1
variants in the future.

This article is part of a discussion meeting issue ‘Understanding the endo-lysosomal network in neurodegeneration’.
Lysosomal storage, impaired autophagy and innate immunity in Gaucher and Parkinson's diseases: insights for drug discovery
Authors: Hull Alexander , Atilano Magda L. , Gergi Laith , Kinghorn Kerri J.
Published: February 2024

Impairment of autophagic–lysosomal pathways is increasingly being implicated in Parkinson's disease (PD).
GBA1
mutations cause the lysosomal storage disorder Gaucher disease (GD) and are the commonest known genetic risk factor for PD.
GBA1
mutations have been shown to cause autophagic–lysosomal impairment. Defective autophagic degradation of unwanted cellular constituents is associated with several pathologies, including loss of normal protein homeostasis, particularly of α-synuclein, and innate immune dysfunction. The latter is observed both peripherally and centrally in PD and GD. Here, we will discuss the mechanistic links between autophagy and immune dysregulation, and the possible role of these pathologies in communication between the gut and brain in these disorders. Recent work in a fly model of neuronopathic GD (nGD) revealed intestinal autophagic defects leading to gastrointestinal dysfunction and immune activation. Rapamycin treatment partially reversed the autophagic block and reduced immune activity, in association with increased survival and improved locomotor performance. Alterations in the gut microbiome are a critical driver of neuroinflammation, and studies have revealed that eradication of the microbiome in nGD fly and mouse models of PD ameliorate brain inflammation. Following these observations, lysosomal–autophagic pathways, innate immune signalling and microbiome dysbiosis are discussed as potential therapeutic targets in PD and GD.

This article is part of a discussion meeting issue ‘Understanding the endo-lysosomal network in neurodegeneration’.
Differential effects of
SORL1
deficiency on the endo-lysosomal network in human neurons and microglia
Authors: Mishra Swati , Jayadev Suman , Young Jessica E.
Published: February 2024

The endosomal gene
SORL1
is a strong Alzheimer's disease (AD) risk gene that harbours loss-of-function variants causative for developing AD. The
SORL1
protein SORL1/SORLA is an endosomal receptor that interacts with the multi-protein sorting complex retromer to traffic various cargo through the endo-lysosomal network (ELN). Impairments in endo-lysosomal trafficking are an early cellular symptom in AD and a novel therapeutic target. However, the cell types of the central nervous system are diverse and use the ELN differently. If this pathway is to be effectively therapeutically targeted, understanding how key molecules in the ELN function in various cell types and how manipulating them affects cell-type specific responses relative to AD is essential. Here, we discuss an example where deficiency of SORL1 expression in a human model leads to stress on early endosomes and recycling endosomes in neurons, but preferentially leads to stress on lysosomes in microglia. The differences observed in these organelles could relate to the unique roles of these cells in the brain as neurons are professional secretory cells and microglia are professional phagocytic cells. Experiments to untangle these differences are fundamental to advancing the understanding of cell biology in AD and elucidating important pathways for therapeutic development. Human-induced pluripotent stem cell models are a valuable platform for such experiments.

This article is part of a discussion meeting issue ‘Understanding the endo-lysosomal network in neurodegeneration’.
Genome sequence of the bialaphos producer Streptomyces sp. DSM 41527 and two putative phosphonate antibiotic producers Streptomyces sp. DSM 41014 and DSM 41981 from the DSMZ strain collection
Authors: Zimmermann Alina , Nouioui Imen , Mast Yvonne
Published: February 2024

Streptomyces sp. DSM 41014, DSM 41527, and DSM 41981 are three strains from the DSMZ strain collection. Here, we present the draft genome sequences of DSM 41014, DSM 41527, and DSM 41981 with a size of 9.09 Mb, 8,45 Mb, and 9,23 Mb, respectively.
Hindlimb kinematics, kinetics, and muscle dynamics during sit-to-stand and sit-to-walk transitions in emus (Dromaius novaehollandiae)
Authors: LIn Yuting , Rankin Jeffery W , Lamas Luis P , Moazen Mehran , Hutchinson John R
Published: February 2024

Animals not only need to walk and run but also lie prone to rest and then stand up. Sit-to-stand (STS) and sit-to-walk (STW) transitions are vital behaviours little studied in species other than humans so far, but likely impose biomechanical constraints on limb design because they involve near-maximal excursions of limb joints that should require large length changes and force production from muscles. By integrating data from experiments into musculoskeletal simulations, we analysed joint motions, ground reaction forces, and muscle dynamics during the STS and STW transitions in a large terrestrial, bipedal, and cursorial bird: the emu (Dromaius novaehollandiae, approximately 30 kg). Simulation results suggest that in both STS and STW, emus operate near the functional limits (> 50 % of shortening/lengthening) of some of their hindlimb muscles, particularly in distal muscles with limited capacity for length change and leverage. Both movements involved high muscle activations (> 50 %) and force generation of major joint extensor muscles early in the transition. STW also required larger net joint moments and non-sagittal motions, entailing greater demands for muscle capacity. Whilst our study involves multiple assumptions, our findings lay the groundwork for future studies to understand, for example, how tendon contributions may reduce excessive muscle demands, especially in the distal hindlimb. As the first investigation into how an avian species stands up, this study provides a foundational framework for future comparative studies investigating organismal morphofunctional specialisations and evolution, offering potential robotics and animal welfare applications.
High-precision photoacoustic neural modulation uses a non-thermal mechanism
Authors: Chen Guo , Yu Feiyuan , Shi Linli , Marar Carolyn , Du Zhiyi , Jia Danchen , Cheng Ji-Xin , Yang Chen
Published: February 2024

Neuromodulation is a powerful tool for fundamental studies in neuroscience and potential treatments of neurological disorders. Both photoacoustic (PA) and photothermal (PT) effects have been harnessed for non-genetic high-precision neural stimulation. Using a fiber-based device excitable by a nanosecond pulsed laser and a continuous wave laser for PA and PT stimulation, respectively, we systematically investigated PA and PT neuromodulation at the single neuron level. Our results show that to achieve the same level of cell activation recorded by Ca2+ imaging the laser energy needed for PA neurostimulation is 1/40 of that needed for PT stimulation. The threshold energy for PA stimulation is found to be further reduced in neurons overexpressing mechano-sensitive channels, indicating direct involvement of mechano-sensitive channels in PA stimulation. Electrophysiology study of single neurons upon PA and PT stimulation was performed by patch clamp recordings. Electrophysiological features stimulated by PA are distinct from those induced by PT, confirming that PA and PT stimulations operate through distinct mechanisms. These insights offer a foundation for rational design of more efficient and safer non-genetic neural modulation approaches.
Synthesis, Structure and Anticancer Activity of a Dinuclear Organoplatinum(IV) Complex Stabilized by Adenine
Authors: O'Brien Alisha M. , Howard William A , Wheeler Kraig A.
Published: February 2024

The dinuclear organoplatinum(IV) compound {Pt(CH3)3}2(μ-I)2(μ-adenine) (abbreviated Pt2ad), obtained by treating cubic [Pt(CH3)3(μ3-I)]4 with two equivalents of adenine, was isolated and structurally characterized by single crystal X-ray diffraction. The National Cancer Institute Developmental Therapeutics Program′s in vitro sulforhodamine B assays showed Pt2ad to be particularly cytotoxic against central nervous system cancer cell line SF-539, and human renal carcinoma cell line RXF-393. Furthermore, Pt2ad displayed some degree of cytotoxicity against non-small cell lung cancer (NCI-H522), colon cancer (HCC-2998, HCT-116, HT29, and SW-620), melanoma (LOX-IMVI, MALME-3M, M14, MDA-MB-435, SK-MEL-28, and UACC-62), ovarian cancer (OVCAR-5), renal carcinoma (A498), breast cancer (BT-549 and MDA-MB-468), and triple-negative breast cancer (MDA-MB-231).
Transport properties of canonical PIN-FORMED proteins and the role of the loop domain in auxin transport
Authors: Janacek Dorina Pia , Kolb Martina , Schulz Lukas , Mergner Julia , Kuster Bernhard , Glanc Matous , Friml Jiri , ten Tusscher Kirsten , Schwechheimer Claus , Hammes Ulrich Zeno
Published: February 2024

Indole-3-acetic acid (IAA), the most abundant endogenous auxin is transported in plants in a polar fashion by PIN-FORMED (PIN) transporters and controls virtually all plant growth and developmental processes. Canonical PINs possess a long and largely disordered cytosolic loop domain which is shorter in non-canonical PINs. Auxin transport by canonical PINs is activated loop phosphorylation by kinases. While the structure of the transmembrane domains of these transporters was recently solved, their transport properties remained poorly characterized and particularly the relative roles of the transmembrane and loop domain therein. In this study we used flux studies to obtain quantitative kinetic parameters of IAA transport mediated by canonical PINs as well as of chimeras between transmembrane and loop domains of different PINs upon their activation by D6 PROTEIN KINASE or PINOID. We found that the transporters possess distinct transport properties that are due to both the transmembrane and loop domain. To demonstrate the physiological relevance of these distinct transport properties, we modelled root tip IAA distribution patterns and investigated the potential of different PINs to complement the agravitropic root growth phenotype of the pin2 mutant when expressed in the PIN2 domain. We found a strong correlation between transport parameters and physiological output indicating that in addition to PIN polarity a low transport rate in the PIN2 expression domain is required for gravitropic growth. Overall, the data show that the loop domain is not only required for activation of PIN-mediated auxin transport but has an additional role in the transport cycle by a currently unknown mechanism.
Effects of phosphorylation on protein backbone dynamics and conformational preferences
Authors: Bickel David , Vranken Wim
Published: February 2024

Phosphorylations are the most common and extensively studied post-translational modification (PTM) of proteins in eukaryotes. They constitute a major regulatory mechanism, modulating protein function, protein-protein interactions, as well as subcellular localization. Phosphorylation sites are preferably located in intrinsically disordered regions and have been shown to trigger structural rearrangements and order-to-disorder transitions. They can therefore have a significant effect on protein backbone dynamics or conformation, but only sparse experimental data are available. To obtain a more general description of how and when phosphorylations have a significant effect on protein behavior, molecular dynamics (MD) currently provides the only suitable framework to study these effects at a large scale in atomistic detail.

This study develops a systematic MD simulation framework to explore the influence of phosphorylations on the local backbone dynamics and conformational propensities of proteins. Through a series of glycine-backbone peptides, we studied the effects of amino acid residues including the three most common phosphorylations (Ser, Thr, and Tyr), on local backbone dynamics and conformational propensities. We further extended our study to investigate the interactions of all such residues between positionito positionsi+1,i+2,i+3, andi+4 in such peptides. The final dataset is comprised of structural ensembles for 3,393 sequences with more than 1 µs of sampling for each ensemble. To validate the relevance of the results, the structural and conformational properties extracted from the MD simulations are compared to NMR data from the Biological Magnetic Resonance Data Bank.

The systematic nature of this study enables the projection of the gained knowledge onto any phosphorylation-site in the proteome and provides a general framework for the study of further PTMs. The full dataset is publicly available, as a training and reference set.
Developmental effects of barium in planaria
Authors: Molano Alberto
Published: February 2024

An investigation was carried out of the stage-specific effects of barium, a wide spectrum potassium channel blocker that depolarizes cells, on planaria embryologic development. Barium exposure triggered a variety of axes abnormalities in planaria, including dorsoventral malformations (formation of pigmented dorsal bulges, suggestive of BMP up-regulation), anteroposterior abnormalities (two-headed worms with two eyes or a single eye on each end, worms with an ectopic anterior partial body embedded diagonally within the main body of the planaria), and other congenital anomalies (baby worms with extremely short bodies, worms with multiple eyes or with a strange tubular structure emerging from the malformed eyes). The implications of these findings for current understanding of planaria development are discussed.
Degron-based bioPROTACs for controlling signaling in CAR T cells
Authors: Kim Matthew S , Bhargava Hersh K , Shavey Gavin E , Lim Wendell A , El-Samad Hana , Ng Andrew H
Published: February 2024

Chimeric antigen receptor (CAR) T cells have made a tremendous impact in the clinic, but potent signaling through the CAR can be detrimental to treatment safety and efficacy. The use of protein degradation to control CAR signaling can address these issues in pre-clinical models. Existing strategies for regulating CAR stability rely on small molecules to induce systemic degradation. In contrast to small molecule regulation, genetic circuits offer a more precise method to control CAR signaling in an autonomous, cell-by-cell fashion. Here, we describe a programmable protein degradation tool that adopts the framework of bioPROTACs, heterobifunctional proteins that contain a target recognition domain fused to a domain that recruits the endogenous ubiquitin proteasome system. We develop novel bioPROTACs that utilize a compact four residue degron and demonstrate degradation of cytosolic and membrane protein targets using either a nanobody or synthetic leucine zipper as a protein binder. Our bioPROTACs exhibit potent degradation of CARs and can inhibit CAR signaling in primary human T cells. We demonstrate the utility of our bioPROTACs by constructing a genetic circuit to degrade the tyrosine kinase ZAP70 in response to recognition of a specific membrane-bound antigen. This circuit is able to disrupt CAR T cell signaling only in the presence of a specific cell population. These results suggest that bioPROTACs are a powerful tool for expanding the cell engineering toolbox for CAR T cells.
TomoNet: A streamlined cryoET software pipeline with automatic particle picking on flexible lattices
Authors: Wang Hui , Liao Shiqing , Yu Xinye , Zhang Jiayan , Zhou Z. Hong
Published: February 2024

Cryogenic electron tomography (cryoET) is capable of determining in situ biological structures of molecular complexes at near atomic resolution by averaging half a million subtomograms. While abundant complexes/particles are often clustered in arrays, precisely locating and seamlessly averaging such particles across many tomograms present major challenges. Here, we developed TomoNet, a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution. TomoNet features built-in automatic particle picking and 3D classification functions and integrates commonly used packages to streamline high-resolution subtomogram averaging for structures in one-, two- or three-dimensional arrays. Automatic particle picking is accomplished in two complementary ways: one based on template matching and the other employing deep learning. TomoNet's hierarchical file organization and visual display facilitate efficient data management as required for large cryoET datasets. Applications of TomoNet to three types of datasets demonstrate its capability of efficient and accurate particle picking on flexible and imperfect lattices to obtain high-resolution 3D biological structures: virus-like particles, bacterial surface layers within cellular lamellae, and membranes decorated with nuclear egress protein complexes. These results demonstrate TomoNet's potential for broad applications to various cryoET projects targeting high-resolution in situ structures.
The Cryptic Bacterial Microproteome
Authors: Fesenko Igor , Sahakyan Harutyun , Shabalina Svetlana A. , Koonin Eugene V.
Published: February 2024

Microproteins encoded by small open reading frames (smORFs) comprise the dark matter of proteomes. Although functional microproteins were identified in diverse organisms from all three domains of life, bacterial smORFs remain poorly characterized. In this comprehensive study of intergenic smORFs (ismORFs, 15 to 70 codons) in 5,668 bacterial genomes of the family Enterobacteriaceae, we identified 67,297 clusters of ismORFs subject to purifying selection. The ismORFs mainly code for hydrophobic, potentially transmembrane, unstructured, or minimally structured microproteins. Using AlphaFold Multimer, we predicted interactions of some of the predicted microproteins encoded by transcribed ismORFs with proteins encoded by neighboring genes, revealing the potential of microproteins to regulate the activity of various proteins, particularly, under stress. We compiled a catalog of predicted microprotein families with different levels of evidence from synteny analysis, structure prediction, and transcription and translation data. This study offers a resource for investigation of biological functions of microproteins.
A chloroplast cell-free system for measuring ribosome binding site strengths
Authors: Clark Lauren , Voigt Christopher , Jewett Michael C
Published: February 2024

Plastid engineering offers the potential to carry multi-gene traits in plants, however, it requires reliable genetic parts to balance expression. The difficulty of chloroplast transformation and slow plant growth make it challenging to build plants just to characterize genetic parts. To address these limitations, we developed a cell-free system from Nicotiana tabacum chloroplast extracts for prototyping genetic parts. Our cell-free system uses combined transcription and translation driven by T7 RNA polymerase and works with plasmid or linear template DNA. To develop our system, we optimized lysis, extract preparation procedures (e.g., runoff reaction, centrifugation, and dialysis), and the physiochemical reaction conditions. Our cell-free system can synthesize 34 +/- 1 micrograms per milliliter luciferase in batch reactions. We apply our system to test a library of 104 ribosome binding site (RBS) variants and rank them based on cell-free gene expression. We observe a 1300-fold range of luciferase expression normalized by mRNA expression, as assessed by the malachite green aptamer (relative luminescence units per relative fluorescence units). We also find a positive correlation between the observed expression in chloroplast extracts and the predictions made by the RBS calculator. We anticipate that chloroplast cell-free systems will increase the speed and reliability of building genetic programs in plant chloroplasts for diverse applications.
Sildenafil amplifies calcium influx and insulin secretion in pancreatic β cells
Authors: Murao Naoya , Morikawa Risa , Seino Yusuke , Shimomura Kenju , Maejima Yuko , Yamada Yuichiro , Suzuki Atsushi
Published: February 2024

Sildenafil, a phosphodiesterase-5 (PDE5) inhibitor, has been shown to improve insulin sensitivity in animal models and prediabetic patients. However, its other metabolic effects remain poorly investigated. This study examines the impact of sildenafil on insulin secretion in MIN6-K8 mouse clonal β cells. Sildenafil is shown to amplify insulin secretion by enhancing Ca2+influx, an effect that requires other depolarizing stimuli in MIN6-K8 cells but not in KATPchannel-deficient β cells, which are already depolarized. These results indicate that the action of sildenafil is dependent on depolarization and is independent of KATPchannels. Furthermore, sildenafil-amplified insulin secretion is not inhibited by nifedipine or PDE5 knockdown. Thus, sildenafil stimulates Ca2+influx independently of L-type voltage-dependent Ca2+channels (VDCCs) and PDE5, a mechanism that differs from the known pharmacology of sildenafil and conventional insulin secretory pathways. Our results reposition sildenafil as an insulinotropic agent that can be used as a potential anti-diabetic medicine or a tool to elucidate the molecular mechanism of insulin secretion.
The impact of complement factor H-related protein gene deletions on kidney transplantation
Authors: Salla Markkinen , Inkeri Lokki A. , Ilkka Helanterä , Jarmo Ritari , Jukka Partanen , Seppo Meri , Kati Hyvärinen
Published: February 2024

We recently reported that a homozygous deletion in the complement factor H-related (CFHR)locus predisposed kidney transplant patients to rejection. As donors carried intact genes, the susceptibility may have resulted from alloimmune reaction to FHR proteins. However, we found no evidence for anti-FH response. It is therefore possible thatCFHRdeletions as such affect the rejection risk. Here, we used MLPA and WGS to fine-map and sequence theCFHRregion in rs7542235-GG patients, a SNP tagging for ΔCFHR311 deletion. Our results confirmed that all patients with this SNP harboured deletions of various sizes encompassingCFHR1. Furthermore, patients with homozygous ΔCFHR311 were homozygous for rs6677604-A, a SNP tagging for deletions of CFHR311 locus, confirming that allele A tags for deletion of bothCFHR3andCFHR1. Proteomics analyses in a larger population demonstrated that rs7542235-G and rs6677604-A associate with expression levels of several proteins involved in regulating alloimmune response. We observed that while increasing the rejection risk, the ΔCFHR311 did not associate to baseline disease or specific clinical characteristics. To conclude, the various deletion types found in patients shared the deletion ofCFHR1gene confirming its association to variant rs7542235. Also, both deletion-tagging alleles are associated with altered expression of FHR proteins.
Simulation of neutron dark-field data for grating-based interferometers
Authors: Wolf Caitlyn M. , Kim Youngju , Kienzle Paul , Sathe Pushkar S. , Daugherty M. Cyrus , Bajcsy Peter , Hussey Daniel S. , Weigandt Katie M.
Published: February 2024

Hierarchical structures and heterogeneous materials are found in many natural and engineered systems including additive manufacturing, alternative energy, biology and polymer science. Though the structure–function relationship is important for developing more advanced materials, structural characterization over broad length scales often requires multiple complementary measurements. Neutron far-field interferometry aims to enable multi-scale characterization by combining the best of neutron imaging with small-angle neutron scattering (SANS) via dark-field imaging. The microstructure, nominally from 1 nm to 10 µm, is averaged over each volume element ∼(50 µm)3 in the sample, resulting in a `tomographic SANS' measurement. Unlike in small-angle scattering, there are few analytical models to fit dark-field imaging data to extract properties of the microstructure. Fortunately, the dark field and SANS are related through a single Hankel transform. In this work, we discuss the development of a Python-based library, correlogram-tools, that makes use of existing small-angle scattering models and a numerical implementation of the Hankel transform to simulate dark-field interferometry data. We demonstrate how this software can be used to inform researchers of viable sample sets for interferometry experiments, analyze interferometry data, and simulate raw and reconstructed interferometry images for the training of more advanced segmentation models and analysis protocols.
Determination of optimal experimental conditions for accurate 3D reconstruction of the magnetization vector via XMCD-PEEM
Authors: Cascales-Sandoval Miguel A. , Hierro-Rodriguez A. , Ruiz-Gómez S. , Skoric L. , Donnelly C. , Niño M. A. , McGrouther D. , McVitie S. , Flewett S. , Jaouen N. , Belkhou R. , Foerster M. , Fernandez-Pacheco A.
Published: February 2024

This work presents a detailed analysis of the performance of X-ray magnetic circular dichroism photoemission electron microscopy (XMCD-PEEM) as a tool for vector reconstruction of magnetization. For this, 360° domain wall ring structures which form in a synthetic antiferromagnet are chosen as the model to conduct the quantitative analysis. An assessment is made of how the quality of the results is affected depending on the number of projections that are involved in the reconstruction process, as well as their angular distribution. For this a self-consistent error metric is developed which allows an estimation of the optimum azimuthal rotation angular range and number of projections. This work thus proposes XMCD-PEEM as a powerful tool for vector imaging of complex 3D magnetic structures.