bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity and Abundance of Fish in The Bone Canal
Authors: Lamangantjo Chairunnisah J. , Valentine Aydalina Regina , Sarniati R. R , Ibrahim Mustamin
Published: July 2023

This study aims to describe the species diversity and abundance of fish in the Gorontalo Bone Canal. This research was conducted in the Bone Canal, Bone Bolango district, Gorontalo province with a survey method. Fish identification was carried out at the Zoology Laboratory of the Biology Department, State University of Gorontalo. The sampling technique was random sampling using nets installed at four observation stations for 24 hours. Station I is the northern part of the canal (upstream), station II is in the middle of the canal, station III is in the southern part of the canal (downstream) and station IV is located at the mouth of the Bone canal. Measurements of the physical and chemical parameters of water were carried out at each station. The fish caught were identified by referring to the book: “Identification of Freshwater Fish in Western Indonesia and Sulawesi” by: Kottelat at al, (1993). Research results and conclusions: 185 individual fish were found consisting of 3 orders, 5 families and 7 species, including: Cyprinus carpio and Barbonimus goionotus (Cypriniformes: Cyprinidae), Hypostamus sp. (Siluriformes: Loriicaridae), Oreocrhomis mosambicus and Oreochromis niloticus (Perciformes: Cichlidae), Oxyeleotris marmorata (Perciformes: Eleotrididae), and Anabas testudineus (Perciformes:Anabantidae). The highest diversity index is at station IV with H’= 1.96 and the lowest is at station I with H’= 1.50. This shows that the level of diversity of fish species in the Bone canal is moderate, the productivity is sufficient, the ecosystem condition is quite balanced and the ecological pressure is moderate. Hypostamus sp. has the highest level of abundance in all stations with an average of K = 30.9%. The lowest abundance was Cyprinus carpio with an average of all stations K= 3.3%, indicating that the abundance in Bone canal was relatively moderate.
Study of The Potential Compound on Leaves of Syzygium samarangense as An Antibacterial to Streptococcus pneumoniae
Authors: Khoirur Rijal M. , Rifda  , Lisdiana Lisa
Published: July 2023

Pneumonia is one of the respiratory infections caused by Streptococcus pneumoniae. Bacterial resistance problems regarding the treatment of pneumonia can be overcome by exploring active compounds in plants that have potential as antibacterials, one of which is water guava (Syzygium samarangense). This study aims to discover active compounds with the antibacterial potential of S. pneumoniae from water guava leaves (S. samarangense). This study was conducted in September 2022 at Universitas Negeri Surabaya with in silico method (blind molecular docking). The method used in this study was in silico approach, including the collection of proteins and compounds, preparation of proteins and ligands, minimization of compounds, blind molecular docking, and visualization of the results of molecular docking. The results showed that the value of binding affinity and RMSD of PBP-2X protein (PDB ID: 1QME) which binds to 1-methyl ethyl acetate, valeraldehyde, and dibutyl phthalate was -5.6 KJ/mol and 2.575 Å, -5 KJ/mol and 1.373 Å, and -6.7 KJ/mol and 1.637 Å, respectively. The result indicates that the selected compounds have the potential as antibacterial to S. pneumoniae. In the near future, this study requires further in vitro and in vivo testing as a step to validate the activity of the active compound of guava leaves as an antibacterial of S. pneumoniae.
The Analysis of SIIR Mathematical Model Time Delay as The Solution of Tuberculosis Transmission in South Sulawesi
Authors: Side Syafruddin , Sanusi Wahidah , Rifandi Muh. , Yusuf Andi Muh. Ridho S.A.P.
Published: July 2023

This study discusses the numerical solution of the Susceptible-Infected-Recovered (SIIR) transmission model for Tuberculosis (TB) transmission in South Sulawesi. The data used is secondary data from the number of Tuberculosis (TB) sufferers in South Sulawesi from the South Sulawesi Provincial Health Office. The discussion begins with a study of the SIIR model, then builds a time delay SIIR model on the spread of tuberculosis. Next, simulate the delay time SIIR model to find out the number of tuberculosis cases in South Sulawesi. Determining the parameters, simulation and analysis of the results in this study obtained a graph of the movement of the SIIR model of time delay of the spread of tuberculosis with real data. After analyzing the numerical simulation, it is seen that there is a tendency for the spread of Tuberculosis (TB) in South Sulawesi. The SIIR model is a four-dimensional non-linear differential equation. The results of the modeling are simulated using MatLab software to predict the number of TB cases so that early prevention measures are the government’s attention to prevent the spread of Tuberculosis (TB) in South Sulawesi.
The Effect of The Problem-Based Learning (PBL) Model with a Multi-Representation Approach on Students’ Critical Thinking Skills in The Buffer Solution Concept
Authors: Mohamad Erni , Paputungan Mardjan , Dahiba Asnita
Published: July 2023

This study aims to determine the effect of the Problem-Based Learning model on students’ critical thinking skills with multi-representation approach on buffer solution concept. The research applied an experimental research method. This type of research is quite experimental. The design used in this study is a non-equivalent control group design. The population in this study were all students of XI IPA. Samples were taken using a purposive sampling technique and involved students of class XI IPA 1 and XI IPA 2. The researcher conducted an essay test with five questions that had been examined for validity and reliability to determine the effect of the problem-based learning model on students’ critical thinking skills with multi-representation approach of the buffer solution concept. The hypothesis testing uses a t-test and obtains a value of tcount = 4.98 > ttable = 1.67655. Thus, Ho is rejected, and Ha is accepted. In conclusion, there is an effect of the problem-based learning model on students’ critical thinking skills with multi-representation approach on the buffer solution concept.
The Effect of Problem-Based Learning Model to Student Learning Outcomes on Colloid Topic
Authors: Mahabu Sintiya , Paputungan Mardjan , Suleman Nita , Rumape Opir , Abdul Rauf Laliyo Lukman , Tangio Julhim S.
Published: July 2023

This research aimed to determine the effect of the problem-based learning model on students’ learning outcomes on the colloid topic. This research applied an experimental method with a quasi-experimental design using a pretest-posttest control group design. The sample in this study was conducted in one of the SMA in The Bone Bolango district. To determine the effect of the problem-based learning model on students’ learning outcomes in the colloid topic, the researcher used a test in the form of an essay with five questions that have been tested for validity and reliability. In the meantime, the hypothesis testing in this study was carried out by employing a t-test. The results of hypothesis testing obtained that the tcount value of 7,7 was higher than 1,67649. Where H0 was rejected and Ha was accepted. Thus, it could be concluded that the problem-based learning model affected students’ learning outcomes in the colloid topic.
Improving Students’ Learning Outcomes Using The Team Based Learning Model With Multi-representation Approach On Electrolyte and Non Electrolyte Solutions
Authors: Pikoli Masrid , Botuihe Nurmeyla U. , Lukum Astin
Published: July 2023

This study aims to improve student learning outcomes on electrolyte and non-electrolyte solution materials of class X IPA 2 SMA Negeri 1 Suwawa using a Team-Based learning model with Multi-representation approach. This class action research by Kemmis and Taggart model which is carried out in the stages of planning, acting, observing, and reflecting. The research is conducted in two cycles by applying the Team-Based Learning model with a Multi-representation approach in each cycle. The finding shows that the Team-Based learning model with a multi-representation approach can improve students’ learning outcomes in electrolyte and non-electrolyte solution materials. The improvement can be seen during the learning of cycle I and cycle II. Students’ completeness is 62.9% in cycle I and 100% in cycle II. As well as having met ≥ 80% of success indicators. In addition, there is also an improvement in student activity and learning participation in electrolyte and non-electrolyte solution materials using a Team-Based learning model with a multi-representation approach. Student learning activity also improves with the average percentage of student activity at 90% in cycle I and 92.5% in cycle II with very good categories.
Palliativmedizinische Aspekte in der klinischen Akut- und Notfallmedizin sowie Intensivmedizin: Konsensuspapier der DGIIN, DGK, DGP, DGHO, DGfN, DGNI, DGG, DGAI, DGINA und DGPalliativmedizin
Authors: Michels Guido , John Stefan , Janssens Uwe , Raake Philip , Schütt Katharina Andrea , Bauersachs Johann , Barchfeld Thomas , Schucher Bernd , Delis Sandra , Karpf-Wissel Rüdiger , Kochanek Matthias , von Bonin Simone , Erley Christiane M. , Kuhlmann Susanne D. , Müllges Wolfgang , Gahn Georg , Heppner Hans Jürgen , Wiese Christoph H. R. , Kluge Stefan , Busch Hans-Jörg , Bausewein Claudia , Schallenburger Manuela , Pin Martin , Neukirchen Martin
Published: July 2023

Die zeitgerechte Integration der Palliativmedizin ist ein wichtiger Bestandteil in der medizinischen Behandlung von verschiedenen Erkrankungen im fortgeschrittenen Stadium. Während eine erweiterte S3-Leitlinie zur Palliativmedizin für Patienten mit einer nicht heilbaren Krebserkrankung existiert, fehlt bis dato eine Leitlinie für nicht-onkologische Patienten bzw. eine konkrete Empfehlung für Patienten, die in der Notaufnahme oder auf Intensivstation behandelt werden. Basierend auf dem vorliegenden Konsensuspapier wird auf die palliativmedizinischen Aspekte der jeweiligen Fachdisziplinen eingegangen. Durch die zeitgerechte Integration der Palliativversorgung soll eine verbesserte Lebensqualität und Symptomlinderung in der klinischen Akut- und Notfallmedizin sowie Intensivmedizin erreicht werden.
CircRNA SCAR Improves High-Glucose-Induced Mitochondrial Dysfunction and Permeability Damage in Retinal Microvascular Endothelial Cells
Authors: Wu Rong , Huang Sheng , Xie Jin-feng , Wen Nian-lian , Wen Min , Zhong Su-e
Published: July 2023

This study was designed to assess the role and mechanism of circRNA SCAR in human retinal microvascular endothelial cells (hRMVECs) treated with high glucose. Quantitative real-time polymerase chain reaction (qRT-PCR) and cell counting kit 8 (CCK-8) were used to detect the effects of different concentrations of glucose on circRNA SCAR expression and cell proliferation in hRMVECs. Cell viability, levels of oxygen species (ROS), malondialdehyde (MDA) and adenosine triphosphate (ATP), as well as activities of antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) in the transfected hRMVECs in each group were detected using CCK-8 and their corresponding detection kits. Changes in mtDNA copy number in high-glucose-induced hRMVECs were observed by qRT-PCR. Additionally, western blot was applied to detect effect of overexpressing circRNA SCAR on the expression levels of mitochondrial function-related proteins (Drp1 and Fis1) and cell permeability-related proteins (claudin-5, occludin and ZO-1) in hRMVECs under high-glucose concentration. According to experimental results, high glucose significantly downregulated circRNA SCAR expression and inhibited cell proliferation in hRMVECs. Instead, overexpression of this circRNA SCAR promoted cell proliferation, reduced levels of ROS, MDA and ATP, and increased SOD and CAT activities in hRMVECs under high-glucose concentration. Also, circRNA SCAR overexpression reversed the high-glucose-induced decrease in mtDNA copy number as well as, high-glucose-induced upregulation of Drp1 and Fis1 protein expression and downregulation of claudin-5, occludin and ZO-1 protein expression in hRMVECs. In summary, circRNA SCAR promotes the proliferation of hRMVECs under high-glucose concentration, alleviates oxidative stress induced by high glucose, and improves mitochondrial function and permeability damage.
Doctors Identify Hemorrhage Better during Chart Review when Assisted by Artificial Intelligence
Authors: Laursen Martin S. , Pedersen Jannik S. , Hansen Rasmus S. , Savarimuthu Thiusius R. , Lynggaard Rasmus B. , Vinholt Pernille J.
Published: July 2023

Objectives This study evaluated if medical doctors could identify more hemorrhage events during chart review in a clinical setting when assisted by an artificial intelligence (AI) model and medical doctors' perception of using the AI model.

Methods To develop the AI model, sentences from 900 electronic health records were labeled as positive or negative for hemorrhage and categorized into one of 12 anatomical locations. The AI model was evaluated on a test cohort consisting of 566 admissions. Using eye-tracking technology, we investigated medical doctors' reading workflow during manual chart review. Moreover, we performed a clinical use study where medical doctors read two admissions with and without AI assistance to evaluate performance when using and perception of using the AI model.

Results The AI model had a sensitivity of 93.7% and a specificity of 98.1% on the test cohort. In the use studies, we found that medical doctors missed more than 33% of relevant sentences when doing chart review without AI assistance. Hemorrhage events described in paragraphs were more often overlooked compared with bullet-pointed hemorrhage mentions. With AI-assisted chart review, medical doctors identified 48 and 49 percentage points more hemorrhage events than without assistance in two admissions, and they were generally positive toward using the AI model as a supporting tool.

Conclusion Medical doctors identified more hemorrhage events with AI-assisted chart review and they were generally positive toward using the AI model.
Assisted documentation as a new focus for artificial intelligence in endoscopy: the precedent of reliable withdrawal time and image reporting
Authors: Lux Thomas J. , Saßmannshausen Zita , Kafetzis Ioannis , Sodmann Philipp , Herold Katja , Sudarevic Boban , Schmitz Rüdiger , Zoller Wolfram G. , Meining Alexander , Hann Alexander
Published: July 2023

Background Reliable documentation is essential for maintaining quality standards in endoscopy; however, in clinical practice, report quality varies. We developed an artificial intelligence (AI)-based prototype for the measurement of withdrawal and intervention times, and automatic photodocumentation.

Method A multiclass deep learning algorithm distinguishing different endoscopic image content was trained with 10 557 images (1300 examinations, nine centers, four processors). Consecutively, the algorithm was used to calculate withdrawal time (AI prediction) and extract relevant images. Validation was performed on 100 colonoscopy videos (five centers). The reported and AI-predicted withdrawal times were compared with video-based measurement; photodocumentation was compared for documented polypectomies.

Results Video-based measurement in 100 colonoscopies revealed a median absolute difference of 2.0 minutes between the measured and reported withdrawal times, compared with 0.4 minutes for AI predictions. The original photodocumentation represented the cecum in 88 examinations compared with 98/100 examinations for the AI-generated documentation. For 39/104 polypectomies, the examiners’ photographs included the instrument, compared with 68 for the AI images. Lastly, we demonstrated real-time capability (10 colonoscopies).

Conclusion Our AI system calculates withdrawal time, provides an image report, and is real-time ready. After further validation, the system may improve standardized reporting, while decreasing the workload created by routine documentation.
Outcome of Emergency Pulmonary Lobectomy under ECMO Support in Patients with COVID-19
Authors: Almeida Ana Beatriz , Schweigert Michael , Spieth Peter , Dubecz Attila , de Abreu Marcelo Gama , Richter Torsten , Kellner Patrick
Published: July 2023

Background Not much is known about the results of nonelective anatomical lung resections in coronavirus disease 2019 (COVID-19) patients put on extracorporeal membrane oxygenation (ECMO). The aim of this study was to analyze the outcome of lobectomy under ECMO support in patients with acute respiratory failure due to severe COVID-19.

Methods All COVID-19 patients undergoing anatomical lung resection with ECMO support at a German university hospital were included into a prospective database. Study period was April 1, 2020, to April 30, 2021 (first, second, and third waves in Germany).

Results A total of nine patients (median age 61 years, interquartile range 10 years) were included. There was virtually no preexisting comorbidity (median Charlson score of comorbidity 0.2). The mean interval between first positive COVID-19 test and surgery was 21.9 days. Clinical symptoms at the time of surgery were sepsis (nine of nine), respiratory failure (nine of nine), acute renal failure (five of nine), pleural empyema (five of nine), lung artery embolism (four of nine), and pneumothorax (two of nine). Mean intensive care unit (ICU) and ECMO days before surgery were 15.4 and 6, respectively. Indications for surgery were bacterial superinfection with lung abscess formation and progressive septic shock (seven of nine) and abscess formation with massive pulmonary hemorrhage into the abscess cavity (two of nine). All patients were under venovenous ECMO with femoral-jugular configuration. Operative procedures were lobectomy (eight) and pneumonectomy (one). Weaning from ECMO was successful in four of nine. In-hospital mortality was five of nine. Mean total ECMO days were 10.3 ± 6.2 and mean total ICU days were 27.7 ± 9.9. Mean length of stay was 28.7 ± 8.8 days.

Conclusion Emergency surgery under ECMO support seems to open up a perspective for surgical source control in COVID-19 patients with bacterial superinfection and localized pulmonary abscess.
Multi-residue analysis of eight veterinary drugs in buffalo milk using liquid chromatography-tandem mass spectrometry†
Authors: Huang Xingchen , Zhu Pingchuan , Sun Qinqiang , Liu Runfeng , Zhang Pengfei , Liu Yuqi , Hu Wei , Xu Huiyan , Lu Yangqing , Fu Qiang
Published: July 2023

Context There are still comparatively few methods for the detection of drug residues in buffalo milk. Aims This study aims to develop a method for the detection of drug residues in buffalo milk. Methods In this study, we developed an analytical method for veterinary drug residues in buffalo milk using liquid chromatography–tandem mass spectrometry. The multi-residue method was established for the simultaneous identification and quantitation of eight common veterinary drugs, including metronidazole, salbutamol, atropine, trimethoprim, hydrocortisone, kitasamycin, roxithromycin and tylosin. Key results The sample processing method for buffalo milk was compared and optimised. The precision, recovery and matrix effects of the method were validated. The precision and accuracy of all analytes ranged from 1.81% to 12.35% and 1.25% to 14.57%, respectively. The average recovery percentages varied between 93.59% and 114.57%, and the average matrix effect ranged from 87.12% to 103.76%. All eight analytes in buffalo milk exhibited stability under different treatment conditions. Conclusions The developed method was successfully applied to laboratory analysis and routine sample analysis. The method was demonstrated to be rapid, sensitive and reliable for the rapid monitoring of veterinary drug residues in buffalo milk. Implications The findings of this study contribute to the risk assessment of veterinary drug residues for preventing the human consumption of contaminated buffalo milk and its derivatives.
Whale sharks as oceanic nurseries for Golden Trevally
Authors: Sheaves M. , Mattone C. , Barnett A. , Abrantes K. , Bradley M. , Sheaves A. , Sheaves J. , Waltham N. J.
Published: July 2023

The Golden Trevally, Gnathanodon speciosus, is a large predatory fish with an extremely broad tropical Indo-Pacific distribution that crosses many biogeographical boundaries. Both published information and freely available imagery suggest that small juvenile G. speciosus are often associated with whale sharks, Rhincodon typus; an association that could explain the unusually widespread distribution of G. speciosus, and suggests a novel nursery relationship. The possibility of such an association has the potential to reshape our understanding of the ecological roles played by long-range migrants such as R. typus and other megafauna, our understanding of the full extent of their conservation value, and how we manage both members of the relationship.
Self-programmed dynamics of T cell receptor condensation
Authors: Chen Hui , Xu Xinyi , Hu Wei , Wu Songfang , Xiao Jianhui , Wu Peng , Wang Xiaowen , Han Xuling , Zhang Yanruo , Zhang Yong , Jiang Ning , Liu Wanli , Lou Changjie , Chen Wei , Xu Chenqi , Lou Jizhong
Published: July 2023

A common event upon receptor–ligand engagement is the formation of receptor clusters on the cell surface, in which signaling molecules are specifically recruited or excluded to form signaling hubs to regulate cellular events. These clusters are often transient and can be disassembled to terminate signaling. Despite the general relevance of dynamic receptor clustering in cell signaling, the regulatory mechanism underlying the dynamics is still poorly understood. As a major antigen receptor in the immune system, T cell receptors (TCR) form spatiotemporally dynamic clusters to mediate robust yet temporal signaling to induce adaptive immune responses. Here we identify a phase separation mechanism controlling dynamic TCR clustering and signaling. The TCR signaling component CD3ε chain can condensate with Lck kinase through phase separation to form TCR signalosomes for active antigen signaling. Lck-mediated CD3ε phosphorylation, however, switched its binding preference to Csk, a functional suppressor of Lck, to cause the dissolvement of TCR signalosomes. Modulating TCR/Lck condensation by targeting CD3ε interactions with Lck or Csk directly affects T cell activation and function, highlighting the importance of the phase separation mechanism. The self-programmed condensation and dissolvement is thus a built-in mechanism of TCR signaling and might be relevant to other receptors.
Intrinsic neural diversity quenches the dynamic volatility of neural networks
Authors: Hutt Axel , Rich Scott , Valiante Taufik A. , Lefebvre Jérémie
Published: July 2023

Heterogeneity is the norm in biology. The brain is no different: Neuronal cell types are myriad, reflected through their cellular morphology, type, excitability, connectivity motifs, and ion channel distributions. While this biophysical diversity enriches neural systems’ dynamical repertoire, it remains challenging to reconcile with the robustness and persistence of brain function over time (resilience). To better understand the relationship between excitability heterogeneity (variability in excitability within a population of neurons) and resilience, we analyzed both analytically and numerically a nonlinear sparse neural network with balanced excitatory and inhibitory connections evolving over long time scales. Homogeneous networks demonstrated increases in excitability, and strong firing rate correlations—signs of instability—in response to a slowly varying modulatory fluctuation. Excitability heterogeneity tuned network stability in a context-dependent way by restraining responses to modulatory challenges and limiting firing rate correlations, while enriching dynamics during states of low modulatory drive. Excitability heterogeneity was found to implement a homeostatic control mechanism enhancing network resilience to changes in population size, connection probability, strength and variability of synaptic weights, by quenching the volatility (i.e., its susceptibility to critical transitions) of its dynamics. Together, these results highlight the fundamental role played by cell-to-cell heterogeneity in the robustness of brain function in the face of change.
A neural probe for concurrent real-time measurement of multiple neurochemicals with electrophysiology in multiple brain regions in vivo
Authors: Chae Uikyu , Woo Jiwan , Cho Yakdol , Han Jeong-Kyu , Yang Soo Hyun , Yang Esther , Shin Hyogeun , Kim Hyun , Yu Hyun-Yong , Lee C. Justin , Cho Il-Joo
Published: July 2023

Real-time monitoring of various neurochemicals with high spatial resolution in multiple brain regions in vivo can elucidate neural circuits related to various brain diseases. However, previous systems for monitoring neurochemicals have limitations in observing multiple neurochemicals without crosstalk in real time, and these methods cannot record electrical activity, which is essential for investigating neural circuits. Here, we present a real-time bimodal (RTBM) neural probe that uses monolithically integrated biosensors and multiple shanks to study the connectivity of neural circuits by measuring multiple neurochemicals and electrical neural activity in real time. Using the RTBM probe, we demonstrate concurrent measurements of four neurochemicals—glucose, lactate, choline, and glutamate without cross-talking each other—and electrical activity in real time in vivo. Additionally, we show the functional connectivity between the medial prefrontal cortex and mediodorsal thalamus through the simultaneous measurement of chemical and electrical signals. We expect that our device will contribute to not only elucidating the role of neurochemicals in neural circuits related to brain functions but also developing drugs for various brain diseases related to neurochemicals.
The RNA-binding proteins hnRNP H and F regulate splicing of a MYC-dependent HRAS exon in prostate cancer cells
Authors: Chen Xinyuan , Yang Harry Taegyun , Zhang Beatrice , Phillips John W. , Cheng Donghui , Rigo Frank , Witte Owen N. , Xing Yi , Black Douglas L.
Published: July 2023

The MYC proto-oncogene contributes to the pathogenesis of more than half of human cancers. Malignant transformation by MYC transcriptionally up-regulates the core pre-mRNA splicing machinery and causes misregulation of alternative splicing. However, our understanding of how splicing changes are directed by MYC is limited. We performed a signaling pathway-guided splicing analysis to identify MYC-dependent splicing events. These included an HRAS cassette exon repressed by MYC across multiple tumor types. To molecularly dissect the regulation of this HRAS exon, we used antisense oligonucleotide tiling to identify splicing enhancers and silencers in its flanking introns. RNA-binding motif prediction indicated multiple binding sites for hnRNP H and hnRNP F within these cis-regulatory elements. Using siRNA knockdown and cDNA expression, we found that both hnRNP H and F activate the HRAS cassette exon. Mutagenesis and targeted RNA immunoprecipitation implicate two downstream G-rich elements in this splicing activation. Analyses of ENCODE RNA-seq datasets confirmed hnRNP H regulation of HRAS splicing. Analyses of RNA-seq datasets across multiple cancers showed a negative correlation of HNRNPH gene expression with MYC hallmark enrichment, consistent with the effect of hnRNP H on HRAS splicing. Interestingly, HNRNPF expression showed a positive correlation with MYC hallmarks and thus was not consistent with the observed effects of hnRNP F. Loss of hnRNP H/F altered cell cycle progression and induced apoptosis in the PC3 prostate cancer cell line. Collectively, our results reveal mechanisms for MYC-dependent regulation of splicing and point to possible therapeutic targets in prostate cancers.
Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria
Authors: Wang Dihao , Fiebig Olivia C. , Harris Dvir , Toporik Hila , Ji Yi , Chuang Chern , Nairat Muath , Tong Ashley L. , Ogren John I. , Hart Stephanie M. , Cao Jianshu , Sturgis James N. , Mazor Yuval , Schlau-Cohen Gabriela S.
Published: July 2023

In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Å and resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Å resulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy.
Having multiple selves helps learning agents explore and adapt in complex changing worlds
Authors: Dulberg Zack , Dubey Rachit , Berwian Isabel M. , Cohen Jonathan D.
Published: July 2023

Satisfying a variety of conflicting needs in a changing environment is a fundamental challenge for any adaptive agent. Here, we show that designing an agent in a modular fashion as a collection of subagents, each dedicated to a separate need, powerfully enhanced the agent’s capacity to satisfy its overall needs. We used the formalism of deep reinforcement learning to investigate a biologically relevant multiobjective task: continually maintaining homeostasis of a set of physiologic variables. We then conducted simulations in a variety of environments and compared how modular agents performed relative to standard monolithic agents (i.e., agents that aimed to satisfy all needs in an integrated manner using a single aggregate measure of success). Simulations revealed that modular agents a) exhibited a form of exploration that was intrinsic and emergent rather than extrinsically imposed; b) were robust to changes in nonstationary environments, and c) scaled gracefully in their ability to maintain homeostasis as the number of conflicting objectives increased. Supporting analysis suggested that the robustness to changing environments and increasing numbers of needs were due to intrinsic exploration and efficiency of representation afforded by the modular architecture. These results suggest that the normative principles by which agents have adapted to complex changing environments may also explain why humans have long been described as consisting of “multiple selves.”
Demographic consequences of phenological asynchrony for North American songbirds
Authors: Youngflesh Casey , Montgomery Graham A. , Saracco James F. , Miller David A. W. , Guralnick Robert P. , Hurlbert Allen H. , Siegel Rodney B. , LaFrance Raphael , Tingley Morgan W.
Published: July 2023

Changes in phenology in response to ongoing climate change have been observed in numerous taxa around the world. Differing rates of phenological shifts across trophic levels have led to concerns that ecological interactions may become increasingly decoupled in time, with potential negative consequences for populations. Despite widespread evidence of phenological change and a broad body of supporting theory, large-scale multitaxa evidence for demographic consequences of phenological asynchrony remains elusive. Using data from a continental-scale bird-banding program, we assess the impact of phenological dynamics on avian breeding productivity in 41 species of migratory and resident North American birds breeding in and around forested areas. We find strong evidence for a phenological optimum where breeding productivity decreases in years with both particularly early or late phenology and when breeding occurs early or late relative to local vegetation phenology. Moreover, we demonstrate that landbird breeding phenology did not keep pace with shifts in the timing of vegetation green-up over a recent 18-y period, even though avian breeding phenology has tracked green-up with greater sensitivity than arrival for migratory species. Species whose breeding phenology more closely tracked green-up tend to migrate shorter distances (or are resident over the entire year) and breed earlier in the season. These results showcase the broadest-scale evidence yet of the demographic impacts of phenological change. Future climate change–associated phenological shifts will likely result in a decrease in breeding productivity for most species, given that bird breeding phenology is failing to keep pace with climate change.
Multimodeling approach to evaluating the efficacy of layering pharmaceutical and nonpharmaceutical interventions for influenza pandemics
Authors: Prasad Pragati V. , Steele Molly K. , Reed Carrie , Meyers Lauren Ancel , Du Zhanwei , Pasco Remy , Alfaro-Murillo Jorge A. , Lewis Bryan , Venkatramanan Srinivasan , Schlitt James , Chen Jiangzhuo , Orr Mark , Wilson Mandy L. , Eubank Stephen , Wang Lijing , Chinazzi Matteo , Pastore y Piontti Ana , Davis Jessica T. , Halloran M. Elizabeth , Longini Ira , Vespignani Alessandro , Pei Sen , Galanti Marta , Kandula Sasikiran , Shaman Jeffrey , Haw David J. , Arinaminpathy Nimalan , Biggerstaff Matthew
Published: July 2023

When an influenza pandemic emerges, temporary school closures and antiviral treatment may slow virus spread, reduce the overall disease burden, and provide time for vaccine development, distribution, and administration while keeping a larger portion of the general population infection free. The impact of such measures will depend on the transmissibility and severity of the virus and the timing and extent of their implementation. To provide robust assessments of layered pandemic intervention strategies, the Centers for Disease Control and Prevention (CDC) funded a network of academic groups to build a framework for the development and comparison of multiple pandemic influenza models. Research teams from Columbia University, Imperial College London/Princeton University, Northeastern University, the University of Texas at Austin/Yale University, and the University of Virginia independently modeled three prescribed sets of pandemic influenza scenarios developed collaboratively by the CDC and network members. Results provided by the groups were aggregated into a mean-based ensemble. The ensemble and most component models agreed on the ranking of the most and least effective intervention strategies by impact but not on the magnitude of those impacts. In the scenarios evaluated, vaccination alone, due to the time needed for development, approval, and deployment, would not be expected to substantially reduce the numbers of illnesses, hospitalizations, and deaths that would occur. Only strategies that included early implementation of school closure were found to substantially mitigate early spread and allow time for vaccines to be developed and administered, especially under a highly transmissible pandemic scenario.
Qualitative metabolomics-based characterization of a phenolic UDP-xylosyltransferase with a broad substrate spectrum from
Lentinus brumalis
Authors: Jeong Eunah , Kim Wonyong , Son Seungju , Yang Sungyeon , Gwon Dasom , Hong Jihee , Cho Yoonhee , Jang Chang-Young , Steinegger Martin , Lim Young Woon , Kang Kyo Bin
Published: July 2023

Wood-decaying fungi are the major decomposers of plant litter. Heavy sequencing efforts on genomes of wood-decaying fungi have recently been made due to the interest in their lignocellulolytic enzymes; however, most parts of their proteomes remain uncharted. We hypothesized that wood-decaying fungi would possess promiscuous enzymes for detoxifying antifungal phytochemicals remaining in the dead plant bodies, which can be useful biocatalysts. We designed a computational mass spectrometry–based untargeted metabolomics pipeline for the phenotyping of biotransformation and applied it to 264 fungal cultures supplemented with antifungal plant phenolics. The analysis identified the occurrence of diverse reactivities by the tested fungal species. Among those, we focused on
O
-xylosylation of multiple phenolics by one of the species tested,
Lentinus brumalis
. By integrating the metabolic phenotyping results with publicly available genome sequences and transcriptome analysis, a UDP-glycosyltransferase designated UGT66A1 was identified and validated as an enzyme catalyzing
O
-xylosylation with broad substrate specificity. We anticipate that our analytical workflow will accelerate the further characterization of fungal enzymes as promising biocatalysts.
MAPK/MAK/MRK overlapping kinase (MOK) controls microglial inflammatory/type-I IFN responses via Brd4 and is involved in ALS
Authors: Pérez-Cabello Jesús A. , Silvera-Carrasco Lucía , Franco Jaime M. , Capilla-González Vivian , Armaos Alexandros , Gómez-Lima María , García-García Raquel , Yap Xin Wen , Leal-Lasarte Magdalena , Lall Deepti , Baloh Robert H. , Martínez Salvador , Miyata Yoshihiko , Tartaglia Gian G. , Sawarkar Ritwick , García-Domínguez Mario , Pozo David , Roodveldt Cintia
Published: July 2023

Amyotrophic lateral sclerosis (ALS) is a fatal and incurable neurodegenerative disease affecting motor neurons and characterized by microglia-mediated neurotoxic inflammation whose underlying mechanisms remain incompletely understood. In this work, we reveal that MAPK/MAK/MRK overlapping kinase (MOK), with an unknown physiological substrate, displays an immune function by controlling inflammatory and type-I interferon (IFN) responses in microglia which are detrimental to primary motor neurons. Moreover, we uncover the epigenetic reader bromodomain-containing protein 4 (Brd4) as an effector protein regulated by MOK, by promoting Ser
492
-phospho-Brd4 levels. We further demonstrate that MOK regulates Brd4 functions by supporting its binding to cytokine gene promoters, therefore enabling innate immune responses. Remarkably, we show that MOK levels are increased in the ALS spinal cord, particularly in microglial cells, and that administration of a chemical MOK inhibitor to ALS model mice can modulate Ser
492
-phospho-Brd4 levels, suppress microglial activation, and modify the disease course, indicating a pathophysiological role of MOK kinase in ALS and neuroinflammation.
Ancient transcriptional regulators can easily evolve new pair-wise cooperativity
Authors: Fowler Kyle R. , Leon Fredrick , Johnson Alexander D.
Published: July 2023

Cells regulate gene expression by the specific binding of transcription regulators to cis-regulatory sequences. Pair-wise cooperativity between regulators—whereby two different regulators physically interact and bind DNA in a cooperative manner—is common and permits complex modes of gene regulation. Over evolutionary timescales, the formation of new combinations of regulators represents a major source of phenotypic novelty, facilitating new network structures. How functional, pair-wise cooperative interactions arise between regulators is poorly understood, despite the abundance of examples in extant species. Here, we explore a protein–protein interaction between two ancient transcriptional regulators—the homeodomain protein Matα2 and the MADS box protein Mcm1—that was gained approximately 200 million y ago in a clade of ascomycete yeasts that includes
Saccharomyces cerevisiae
. By combining deep mutational scanning with a functional selection for cooperative gene expression, we tested millions of possible alternative evolutionary solutions to this interaction interface. The artificially evolved, functional solutions are highly degenerate, with diverse amino acid chemistries permitted at all positions but with widespread epistasis limiting success. Nonetheless, approximately ~45% of the random sequences sampled function as well or better in controlling gene expression than the naturally evolved sequence. From these variants (which are unconstrained by historical contingency), we discern structural rules and epistatic constraints governing the emergence of cooperativity between these two transcriptional regulators. This work provides a mechanistic basis for long-standing observations of transcription network plasticity and highlights the importance of epistasis in the evolution of new protein–protein interactions.
Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors
Authors: Akkapeddi Padma , Hattori Takamitsu , Khan Imran , Glasser Eliezra , Koide Akiko , Ketavarapu Gayatri , Whaby Michael , Zuberi Mariyam , Teng Kai Wen , Lefler Julia , Maso Lorenzo , Bang Injin , Ostrowski Michael C. , O’Bryan John P. , Koide Shohei
Published: July 2023

The G12D mutation is among the most common KRAS mutations associated with cancer, in particular, pancreatic cancer. Here, we have developed monobodies, small synthetic binding proteins, that are selective to KRAS(G12D) over KRAS(wild type) and other oncogenic KRAS mutations, as well as over the G12D mutation in HRAS and NRAS. Crystallographic studies revealed that, similar to other KRAS mutant-selective inhibitors, the initial monobody bound to the S-II pocket, the groove between switch II and α3 helix, and captured this pocket in the most widely open form reported to date. Unlike other G12D-selective polypeptides reported to date, the monobody used its backbone NH group to directly recognize the side chain of KRAS Asp12, a feature that closely resembles that of a small-molecule inhibitor, MTRX1133. The monobody also directly interacted with H95, a residue not conserved in RAS isoforms. These features rationalize the high selectivity toward the G12D mutant and the KRAS isoform. Structure-guided affinity maturation resulted in monobodies with low nM
K
D
values. Deep mutational scanning of a monobody generated hundreds of functional and nonfunctional single-point mutants, which identified crucial residues for binding and those that contributed to the selectivity toward the GTP- and GDP-bound states. When expressed in cells as genetically encoded reagents, these monobodies engaged selectively with KRAS(G12D) and inhibited KRAS(G12D)-mediated signaling and tumorigenesis. These results further illustrate the plasticity of the S-II pocket, which may be exploited for the design of next-generation KRAS(G12D)-selective inhibitors.
A DNA-based hydrogel for exosome separation and biomedical applications
Authors: Tang Jianpu , Jia Xuemei , Li Qian , Cui Zhen , Liang Aiqi , Ke Bin , Yang Dayong , Yao Chi
Published: July 2023

Exosomes (EXOs) have been proven as biomarkers for disease diagnosis and agents for therapeutics. Great challenge remains in the separation of EXOs with high-purity and low-damage from complex biological media, which is critical for the downstream applications. Herein, we report a DNA-based hydrogel to realize the specific and nondestructive separation of EXOs from complex biological media. The separated EXOs were directly utilized in the detection of human breast cancer in clinical samples, as well as applied in the therapeutics of myocardial infarction in rat models. The materials chemistry basis of this strategy involved the synthesis of ultralong DNA chains via an enzymatic amplification, and the formation of DNA hydrogels through complementary base-pairing. These ultralong DNA chains that contained polyvalent aptamers were able to recognize and bind with the receptors on EXOs, and the specific and efficient binding ensured the selective separation of EXOs from media into the further formed networked DNA hydrogel. Based on this DNA hydrogel, rationally designed optical modules were introduced for the detection of exosomal pathogenic microRNA, which achieved the classification of breast cancer patients versus healthy donors with 100% precision. Furthermore, the DNA hydrogel that contained mesenchymal stem cell–derived EXOs was proved with significant therapeutic efficacy in repairing infarcted myocardium of rat models. We envision that this DNA hydrogel–based bioseparation system is promising as a powerful biotechnology, which will promote the development of extracellular vesicles in nanobiomedicine.
Cell surface nucleocapsid protein expression: A betacoronavirus immunomodulatory strategy
Authors: López-Muñoz Alberto Domingo , Santos Jefferson J. S. , Yewdell Jonathan W.
Published: July 2023

We recently reported that SARS-CoV-2 nucleocapsid (N) protein is abundantly expressed on the surface of both infected and neighboring uninfected cells, where it enables activation of Fc receptor-bearing immune cells with anti-N antibodies (Abs) and inhibits leukocyte chemotaxis by binding chemokines (CHKs). Here, we extend these findings to N from the common cold human coronavirus (HCoV)-OC43, which is also robustly expressed on the surface of infected and noninfected cells by binding heparan sulfate/heparin (HS/H). HCoV-OC43 N binds with high affinity to the same set of 11 human CHKs as SARS-CoV-2 N, but also to a nonoverlapping set of six cytokines. As with SARS-CoV-2 N, HCoV-OC43 N inhibits CXCL12β-mediated leukocyte migration in chemotaxis assays, as do all highly pathogenic and common cold HCoV N proteins. Together, our findings indicate that cell surface HCoV N plays important evolutionarily conserved roles in manipulating host innate immunity and as a target for adaptive immunity.
The evolution of archaeal flagellar filaments
Authors: Kreutzberger Mark A. B. , Cvirkaite-Krupovic Virginija , Liu Ying , Baquero Diana P. , Liu Junfeng , Sonani Ravi R. , Calladine Chris R. , Wang Fengbin , Krupovic Mart , Egelman Edward H.
Published: July 2023

Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from
Pyrobaculum calidifontis
with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.