bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular architecture and conservation of an immature human endogenous retrovirus
Authors: Krebs Anna-Sophia , Liu Hsuan-Fu , Zhou Ye , Rey Juan S. , Levintov Lev , Shen Juan , Howe Andrew , Perilla Juan R. , Bartesaghi Alberto , Zhang Peijun 
Published: August 2023

AbstractThe human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus in the human genome and is activated and expressed in many cancers and amyotrophic lateral sclerosis. We present the immature HERV-K capsid structure at 3.2 Å resolution determined from native virus-like particles using cryo-electron tomography and subtomogram averaging. The structure shows a hexamer unit oligomerized through a 6-helix bundle, which is stabilized by a small molecule analogous to IP6 in immature HIV-1 capsid. The HERV-K immature lattice is assembled via highly conserved dimer and trimer interfaces, as detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the linker between the N-terminal and the C-terminal domains of CA occurs during HERV-K maturation. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.
Interplay of structural chirality, electron spin and topological orbital in chiral molecular spin valves
Authors: Adhikari Yuwaraj , Liu Tianhan , Wang Hailong , Hua Zhenqi , Liu Haoyang , Lochner Eric , Schlottmann Pedro , Yan Binghai , Zhao Jianhua , Xiong Peng 
Published: August 2023

AbstractChirality has been a property of central importance in physics, chemistry and biology for more than a century. Recently, electrons were found to become spin polarized after transmitting through chiral molecules, crystals, and their hybrids. This phenomenon, called chirality-induced spin selectivity (CISS), presents broad application potentials and far-reaching fundamental implications involving intricate interplays among structural chirality, topological states, and electronic spin and orbitals. However, the microscopic picture of how chiral geometry influences electronic spin remains elusive, given the negligible spin-orbit coupling (SOC) in organic molecules. In this work, we address this issue via a direct comparison of magnetoconductance (MC) measurements on magnetic semiconductor-based chiral molecular spin valves with normal metal electrodes of contrasting SOC strengths. The experiment reveals that a heavy-metal electrode provides SOC to convert the orbital polarization induced by the chiral molecular structure to spin polarization. Our results illustrate the essential role of SOC in the metal electrode for the CISS spin valve effect. A tunneling model with a magnetochiral modulation of the potential barrier is shown to quantitatively account for the unusual transport behavior.
Outer membrane vesicles from a mosquito commensal mediate targeted killing of Plasmodium parasites via the phosphatidylcholine scavenging pathway
Authors: Gao Han , Jiang Yongmao , Wang Lihua , Wang Guandong , Hu Wenqian , Dong Ling , Wang Sibao 
Published: August 2023

AbstractThe gut microbiota is a crucial modulator of Plasmodium infection in mosquitoes, including the production of anti-Plasmodium effector proteins. But how the commensal-derived effectors are translocated into Plasmodium parasites remains obscure. Here we show that a natural Plasmodium blocking symbiotic bacterium Serratia ureilytica Su_YN1 delivers the effector lipase AmLip to Plasmodium parasites via outer membrane vesicles (OMVs). After a blood meal, host serum strongly induces Su_YN1 to release OMVs and the antimalarial effector protein AmLip into the mosquito gut. AmLip is first secreted into the extracellular space via the T1SS and then preferentially loaded on the OMVs that selectively target the malaria parasite, leading to targeted killing of the parasites. Notably, these serum-induced OMVs incorporate certain serum-derived lipids, such as phosphatidylcholine, which is critical for OMV uptake by Plasmodium via the phosphatidylcholine scavenging pathway. These findings reveal that this gut symbiotic bacterium evolved to deliver secreted effector molecules in the form of extracellular vesicles to selectively attack parasites and render mosquitoes refractory to Plasmodium infection. The discovery of the role of gut commensal-derived OMVs as carriers in cross-kingdom communication between mosquito microbiota and Plasmodium parasites offers a potential innovative strategy for blocking malaria transmission.
Severe COVID-19 patients exhibit elevated levels of autoantibodies targeting cardiolipin and platelet glycoprotein with age: a systems biology approach
Authors: Fonseca Dennyson Leandro M. , Filgueiras Igor Salerno , Marques Alexandre H. C. , Vojdani Elroy , Halpert Gilad , Ostrinski Yuri , Baiocchi Gabriela Crispim , Plaça Desirée Rodrigues , Freire Paula P. , Pour Shahab Zaki , Moll Guido , Catar Rusan , Lavi Yael Bublil , Silverberg Jonathan I. , Zimmerman Jason , Cabral-Miranda Gustavo , Carvalho Robson F. , Khan Taj Ali , Heidecke Harald , Dalmolin Rodrigo J. S. , Luchessi Andre Ducati , Ochs Hans D. , Schimke Lena F. , Amital Howard , Riemekasten Gabriela , Zyskind Israel , Rosenberg Avi Z. , Vojdani Aristo , Shoenfeld Yehuda , Cabral-Marques Otavio 
Published: August 2023

AbstractAge is a significant risk factor for the coronavirus disease 2019 (COVID-19) severity due to immunosenescence and certain age-dependent medical conditions (e.g., obesity, cardiovascular disorder, and chronic respiratory disease). However, despite the well-known influence of age on autoantibody biology in health and disease, its impact on the risk of developing severe COVID-19 remains poorly explored. Here, we performed a cross-sectional study of autoantibodies directed against 58 targets associated with autoimmune diseases in 159 individuals with different COVID-19 severity (71 mild, 61 moderate, and 27 with severe symptoms) and 73 healthy controls. We found that the natural production of autoantibodies increases with age and is exacerbated by SARS-CoV-2 infection, mostly in severe COVID-19 patients. Multiple linear regression analysis showed that severe COVID-19 patients have a significant age-associated increase of autoantibody levels against 16 targets (e.g., amyloid β peptide, β catenin, cardiolipin, claudin, enteric nerve, fibulin, insulin receptor a, and platelet glycoprotein). Principal component analysis with spectrum decomposition and hierarchical clustering analysis based on these autoantibodies indicated an age-dependent stratification of severe COVID-19 patients. Random forest analysis ranked autoantibodies targeting cardiolipin, claudin, and platelet glycoprotein as the three most crucial autoantibodies for the stratification of severe COVID-19 patients ≥50 years of age. Follow-up analysis using binomial logistic regression found that anti-cardiolipin and anti-platelet glycoprotein autoantibodies significantly increased the likelihood of developing a severe COVID-19 phenotype with aging. These findings provide key insights to explain why aging increases the chance of developing more severe COVID-19 phenotypes.
Plant and microbial science and technology as cornerstones to Bioregenerative Life Support Systems in space
Authors: De Micco Veronica , Amitrano Chiara , Mastroleo Felice , Aronne Giovanna , Battistelli Alberto , Carnero-Diaz Eugenie , De Pascale Stefania , Detrell Gisela , Dussap Claude-Gilles , Ganigué Ramon , Jakobsen Øyvind Mejdell , Poulet Lucie , Van Houdt Rob , Verseux Cyprien , Vlaeminck Siegfried E. , Willaert Ronnie , Leys Natalie 
Published: August 2023

AbstractLong-term human space exploration missions require environmental control and closed Life Support Systems (LSS) capable of producing and recycling resources, thus fulfilling all the essential metabolic needs for human survival in harsh space environments, both during travel and on orbital/planetary stations. This will become increasingly necessary as missions reach farther away from Earth, thereby limiting the technical and economic feasibility of resupplying resources from Earth. Further incorporation of biological elements into state-of-the-art (mostly abiotic) LSS, leading to bioregenerative LSS (BLSS), is needed for additional resource recovery, food production, and waste treatment solutions, and to enable more self-sustainable missions to the Moon and Mars. There is a whole suite of functions crucial to sustain human presence in Low Earth Orbit (LEO) and successful settlement on Moon or Mars such as environmental control, air regeneration, waste management, water supply, food production, cabin/habitat pressurization, radiation protection, energy supply, and means for transportation, communication, and recreation. In this paper, we focus on air, water and food production, and waste management, and address some aspects of radiation protection and recreation. We briefly discuss existing knowledge, highlight open gaps, and propose possible future experiments in the short-, medium-, and long-term to achieve the targets of crewed space exploration also leading to possible benefits on Earth.
Deep formation of Earth’s earliest continental crust consistent with subduction
Authors: Hastie Alan R. , Law Sally , Bromiley Geoffrey D. , Fitton J. Godfrey , Harley Simon L. , Muir Duncan D. 
Published: August 2023

AbstractAbout four billion years ago, Earth’s outer layer is thought to have been composed mostly of a 25- to 50-km-thick basaltic crust that differentiated to form the oldest stable continental crust. However, the tectonic processes responsible for the formation of this continental material remain controversial. Suggested explanations include convergent plate boundary processes akin to subduction operating today and a variety of relatively shallow (<50 km) non-plate-tectonic intracrustal mechanisms. Here we perform high-pressure–temperature melting experiments on an oceanic plateau analogue for the early basaltic crust and show that magmas with the composition of the early continental crust cannot form at pressures <1.4 GPa (~50 km depth). This suggests that Eoarchaean continental magmas are formed in deep (>50 km) subduction-like environments. Our results support previous Eoarchaean field evidence and analyses of igneous rocks that date to 4.0–3.6 billion years ago, which are consistent with subduction-like processes and suggest a primitive type of plate tectonics operated as long as 4 billion years ago on early Earth.
Therapeutically useful mycobacteriophages BPs and Muddy require trehalose polyphleates
Authors: Wetzel Katherine S. , Illouz Morgane , Abad Lawrence , Aull Haley G. , Russell Daniel A. , Garlena Rebecca A. , Cristinziano Madison , Malmsheimer Silke , Chalut Christian , Hatfull Graham F. , Kremer Laurent 
Published: August 2023

AbstractMycobacteriophages show promise as therapeutic agents for non-tuberculous mycobacterium infections. However, little is known about phage recognition of Mycobacterium cell surfaces or mechanisms of phage resistance. We show here that trehalose polyphleates (TPPs)—high-molecular-weight, surface-exposed glycolipids found in some mycobacterial species—are required for infection of Mycobacterium abscessus and Mycobacterium smegmatis by clinically useful phages BPs and Muddy. TPP loss leads to defects in adsorption and infection and confers resistance. Transposon mutagenesis shows that TPP disruption is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss by mutation, and some M. abscessus clinical isolates are naturally phage-insensitive due to TPP synthesis gene mutations. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, and M. abscessus mutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.
A Multi-Stain Breast Cancer Histological Whole-Slide-Image Data Set from Routine Diagnostics
Authors: Weitz Philippe , Valkonen Masi , Solorzano Leslie , Carr Circe , Kartasalo Kimmo , Boissin Constance , Koivukoski Sonja , Kuusela Aino , Rasic Dusan , Feng Yanbo , Sinius Pouplier Sandra , Sharma Abhinav , Ledesma Eriksson Kajsa , Latonen Leena , Laenkholm Anne-Vibeke , Hartman Johan , Ruusuvuori Pekka , Rantalainen Mattias 
Published: August 2023

AbstractThe analysis of FFPE tissue sections stained with haematoxylin and eosin (H&E) or immunohistochemistry (IHC) is essential for the pathologic assessment of surgically resected breast cancer specimens. IHC staining has been broadly adopted into diagnostic guidelines and routine workflows to assess the status of several established biomarkers, including ER, PGR, HER2 and KI67. Biomarker assessment can also be facilitated by computational pathology image analysis methods, which have made numerous substantial advances recently, often based on publicly available whole slide image (WSI) data sets. However, the field is still considerably limited by the sparsity of public data sets. In particular, there are no large, high quality publicly available data sets with WSIs of matching IHC and H&E-stained tissue sections from the same tumour. Here, we publish the currently largest publicly available data set of WSIs of tissue sections from surgical resection specimens from female primary breast cancer patients with matched WSIs of corresponding H&E and IHC-stained tissue, consisting of 4,212 WSIs from 1,153 patients.
Iridocorneal angle imaging of a human donor eye by spectral-domain optical coherence tomography
Authors: Luo Shangbang , Holland Guy , Khazaeinezhad Reza , Bradford Samantha , Joshi Rohan , Juhasz Tibor 
Published: August 2023

AbstractIridocorneal angle (ICA) details particularly the trabecular meshwork (TM), Schlemm’s canal (SC), and collector channels (CCs) play crucial roles in the regulation of the aqueous outflow in the eyes and are closely associated with glaucoma. Current clinical gonioscopy imaging provides no depth information, and studies of 3D high-resolution optical coherence tomography (OCT) imaging of these structures are limited. We developed a custom-built spectral-domain (SD-) OCT imaging system to fully characterize the angle details. Imaging of a human cadaver eye reveals the visibility of details in the TM/SC/CC region via a ’crossline’ scanning and a series of image processing. This shows that ICA imaging can be used for preoperative glaucoma inspections in the clinical setting with the proposed prototype.
Perception, performance, and detectability of conversational artificial intelligence across 32 university courses
Authors: Ibrahim Hazem , Liu Fengyuan , Asim Rohail , Battu Balaraju , Benabderrahmane Sidahmed , Alhafni Bashar , Adnan Wifag , Alhanai Tuka , AlShebli Bedoor , Baghdadi Riyadh , Bélanger Jocelyn J. , Beretta Elena , Celik Kemal , Chaqfeh Moumena , Daqaq Mohammed F. , Bernoussi Zaynab El , Fougnie Daryl , Garcia de Soto Borja , Gandolfi Alberto , Gyorgy Andras , Habash Nizar , Harris J. Andrew , Kaufman Aaron , Kirousis Lefteris , Kocak Korhan , Lee Kangsan , Lee Seungah S. , Malik Samreen , Maniatakos Michail , Melcher David , Mourad Azzam , Park Minsu , Rasras Mahmoud , Reuben Alicja , Zantout Dania , Gleason Nancy W. , Makovi Kinga , Rahwan Talal , Zaki Yasir 
Published: August 2023

AbstractThe emergence of large language models has led to the development of powerful tools such as ChatGPT that can produce text indistinguishable from human-generated work. With the increasing accessibility of such technology, students across the globe may utilize it to help with their school work—a possibility that has sparked ample discussion on the integrity of student evaluation processes in the age of artificial intelligence (AI). To date, it is unclear how such tools perform compared to students on university-level courses across various disciplines. Further, students’ perspectives regarding the use of such tools in school work, and educators’ perspectives on treating their use as plagiarism, remain unknown. Here, we compare the performance of the state-of-the-art tool, ChatGPT, against that of students on 32 university-level courses. We also assess the degree to which its use can be detected by two classifiers designed specifically for this purpose. Additionally, we conduct a global survey across five countries, as well as a more in-depth survey at the authors’ institution, to discern students’ and educators’ perceptions of ChatGPT’s use in school work. We find that ChatGPT’s performance is comparable, if not superior, to that of students in a multitude of courses. Moreover, current AI-text classifiers cannot reliably detect ChatGPT’s use in school work, due to both their propensity to classify human-written answers as AI-generated, as well as the relative ease with which AI-generated text can be edited to evade detection. Finally, there seems to be an emerging consensus among students to use the tool, and among educators to treat its use as plagiarism. Our findings offer insights that could guide policy discussions addressing the integration of artificial intelligence into educational frameworks.
Preparation of fast-swelling porous superabsorbent hydrogels with high saline water absorbency under pressure by foaming and post surface crosslinking
Authors: Zhai Naihua , Wang Baogui 
Published: August 2023

AbstractSuperabsorbent hydrogels have wide applications in many fields because of their unique water absorbing performance. In spite of decades of research about superabsorbent hydrogels, high water absorbency under pressure and fast-swelling are still challenging and highly desired for their applications in hygienic products and others. Here, we report preparation of fast-swelling porous starch-g-poly(acrylic acid)/poly(vinyl alcohol) superabsorbent hydrogels with high saline water absorbency under pressure by foaming and post surface crosslinking. 2,2′-Azobis(2-amidinopropane) dihydrochloride (AIBA) was used as a new porogen instead of conventional porogens like NaHCO3. Post surface crosslinking of the hydrogel was achieved using glycerol via the esterification reaction. AIBA is a better porogen than NaHCO3 regarding porosity and swelling performance of the hydrogels, and its content has great influences on structure and swelling performance of the hydrogels including water absorbency and swelling rate. Also, the surface crosslinking using glycerol can significantly enhance the saline water absorbency under pressure (2 kPa) but at the sacrifice of the swelling rate. Consequently, the hydrogels show high water absorbencies for deionized water (560 g/g), 0.9 wt% NaCl solution (58 g/g), 0.9 wt% NaCl solution under 2 kPa pressure (28 g/g) and fast-swelling (31 s to achieve a highly swelling state).
Lifelong effects of prenatal and early postnatal stress on the hippocampus, amygdala, and psychological states of Holocaust survivors
Authors: Fňašková Monika , Říha Pavel , Nečasová Markéta , Preiss Marek , Rektor Ivan 
Published: August 2023

AbstractThis study focuses on hippocampal and amygdala volume, seed-based connectivity, and psychological traits of Holocaust survivors who experienced stress during prenatal and early postnatal development. We investigated people who lived in Central Europe during the Holocaust and who, as Jews, were in imminent danger. The group who experienced stress during their prenatal development and early postnatal (PreP) period (n = 11) were compared with a group who experienced Holocaust-related stress later in their lives: in late childhood, adolescence, and early adulthood (ChA) (n = 21). The results of volumetry analysis showed significantly lower volumes of both hippocampi and the right amygdala in the PreP group. Seed-based connectivity analysis revealed increased connectivity from the seed in the right amygdala to the middle and posterior cingulate cortex, caudate, and inferior left frontal operculum in the PreP group. Psychological testing found higher levels of traumatic stress symptoms (TCS-40) and lower levels of well-being (SOS-10) in the PreP group than in the ChA group. The results of our study demonstrate that extreme stress experienced during prenatal and early postnatal life has a profound lifelong impact on the hippocampus and amygdala and on several psychological characteristics.
A randomized trial on differential changes in thought and affect after mindfulness versus dyadic practice indicates phenomenological fingerprints of app-based interventions
Authors: Petzold Paul , Silveira Sarita , Godara Malvika , Matthaeus Hannah , Singer Tania 
Published: August 2023

AbstractContemplative practice has demonstrated benefits for mental health and well-being. Most previous studies, however, implemented in-person trainings containing a mix of different, mostly solitary, practices and focused on pre- to post-training outcomes. In this randomized trial, we explore the immediate differential efficacy of two daily app-delivered practices in shifting emotional (valence, arousal) and thinking patterns (thought content on future-past, self-other, positive–negative dimensions). For 10 weeks of daily training, 212 participants (18–65 years) performed either a novel 12-min partner-based socio-emotional practice (Affect Dyad) or a 12-min attention-focused solitary mindfulness-based practice. Using ordinal Bayesian multilevel modeling, we found that both practice types led to more positive affect and higher arousal. However, whereas mindfulness-based practice partly led to a decrease in active thoughts, particularly in future-, other-related and negative thoughts, the Dyad in contrast led to increases in other-related, and positive thoughts. This shift towards more social and positive thoughts may specifically support overcoming ruminative thinking patterns associated with self-related and negative thought content. Overall, these differential findings may help inform the adaptation of scalable app-based mental trainings in different segments of the population with the goal to improve mental health and well-being.
Formalizing psychological interventions through network control theory
Authors: Stocker Julia Elina , Koppe Georgia , Reich Hanna , Heshmati Saeideh , Kittel-Schneider Sarah , Hofmann Stefan G. , Hahn Tim , van der Maas Han L. J. , Waldorp Lourens , Jamalabadi Hamidreza 
Published: August 2023

AbstractDespite the growing deployment of network representation to comprehend psychological phenomena, the question of whether and how networks can effectively describe the effects of psychological interventions remains elusive. Network control theory, the engineering study of networked interventions, has recently emerged as a viable methodology to characterize and guide interventions. However, there is a scarcity of empirical studies testing the extent to which it can be useful within a psychological context. In this paper, we investigate a representative psychological intervention experiment, use network control theory to model the intervention and predict its effect. Using this data, we showed that: (1) the observed psychological effect, in terms of sensitivity and specificity, relates to the regional network control theoretic metrics (average and modal controllability), (2) the size of change following intervention negatively correlates with a whole-network topology that quantifies the “ease” of change as described by control theory (control energy), and (3) responses after intervention can be predicted based on formal results from control theory. These insights assert that network control theory has significant potential as a tool for investigating psychological interventions. Drawing on this specific example and the overarching framework of network control theory, we further elaborate on the conceptualization of psychological interventions, methodological considerations, and future directions in this burgeoning field.