SRPK2 Mediates HBV Core Protein Phosphorylation and Capsid Assembly via Docking Interaction.

Members of the serine-arginine protein kinase (SRPK) family, SRPK1 and SRPK2, phosphorylate the hepatitis B core protein (Cp) and are crucial for pregenomic RNA encapsidation during viral nucleocapsid assembly. Among them, SRPK2 exhibits higher kinase activity toward Cp. In this study, we identified Cp sites that are phosphorylated by SRPK2 and demonstrated that the kinase utilizes an SRPK-specific docking groove to interact with and regulate the phosphorylation of the C-terminal arginine rich domain of Cp. We determined that direct interaction between the docking groove of SRPK2 and unphosphorylated Cp inhibited premature viral capsid assembly in vitro, whereas the phosphorylation of the viral protein reactivated the process. Pull-down assays together with the new cryo-electron microscopy structure of the HBV capsid in complex with SRPK2 revealed that the kinases decorate the surface of the viral capsid by interacting with the C-terminal domain of Cp, underscoring the importance of the docking interaction in regulating capsid assembly and pregenome packaging. Moreover, SRPK2-knockout in HepG2 cells suppressed Cp phosphorylation, indicating that SRPK2 is an important cellular kinase for HBV life cycle.

Event-Based Clinical Finding Extraction from Radiology Reports with Pre-trained Language Model.

Radiology reports contain a diverse and rich set of clinical abnormalities documented by radiologists during their interpretation of the images. Comprehensive semantic representations of radiological findings would enable a wide range of secondary use applications to support diagnosis, triage, outcomes prediction, and clinical research. In this paper, we present a new corpus of radiology reports annotated with clinical findings. Our annotation schema captures detailed representations of pathologic findings that are observable on imaging ("lesions") and other types of clinical problems ("medical problems"). The schema used an event-based representation to capture fine-grained details, including assertion, anatomy, characteristics, size, and count. Our gold standard corpus contained a total of 500 annotated computed tomography (CT) reports. We extracted triggers and argument entities using two state-of-the-art deep learning architectures, including BERT. We then predicted the linkages between trigger and argument entities (referred to as argument roles) using a BERT-based relation extraction model. We achieved the best extraction performance using a BERT model pre-trained on 3 million radiology reports from our institution: 90.9-93.4% F1 for finding triggers and 72.0-85.6% F1 for argument roles. To assess model generalizability, we used an external validation set randomly sampled from the MIMIC Chest X-ray (MIMIC-CXR) database. The extraction performance on this validation set was 95.6% for finding triggers and 79.1-89.7% for argument roles, demonstrating that the model generalized well to the cross-institutional data with a different imaging modality. We extracted the finding events from all the radiology reports in the MIMIC-CXR database and provided the extractions to the research community.

Site-Selective Lysine Acetylation of Human Immunoglobulin G for Immunoliposomes and Bispecific Antibody Complexes.

Site-selective acetylation of a single lysine residue in a protein that reaches a lysine acetyltransferase's accuracy, precision, and reliability is challenging. Here, we report a peptide-guided, proximity-driven group transfer reaction that acetylates a single lysine residue, Lys 248, of the fragment crystallizable region (Fc region) in the heavy chain of the human Immunoglobulin G (IgG). An Fc-interacting peptide bound with the Fc domain and positioned a phenolic ester close to Lys 248, which induced a nucleophilic reaction and resulted in the transfer of an acetyl group to Lys 248. The acetylation reaction proceeded to a decent yield under the physiological condition without the need for deglycosylation, unnatural amino acids, or catalysts. Along with acetylation, functional moieties such as azide, alkyne, fluorescent molecules, or biotin could also be site-selectively installed on Lys 248, allowing IgG's further derivatization. We then synthesized an antibody-lipid conjugate and constructed antibody-conjugated liposomes (immunoliposomes), targeting HER2-positive (HER2+) cancer cells. We also built a bispecific antibody complex (bsAbC) covalently linking an anti-HER2 antibody and an anti-CD3 antibody. The bsAbC showed in vitro effector-cell-mediated cytotoxicity at nanomolar concentrations. Compared with bispecific antibodies (bsAbs), bsAbCs are constructed based on native IgGs and contain two antigen-binding sites to each antigen, twice that of bsAbs. Altogether, this work reports a method of site-selective acetylation of native antibodies, highlights a facile way of site-selective IgG functionalization, and underscores the potential of bsAbCs in cancer immunotherapy.

Derivation of a Ni bioaccessibility value for screening-level risk assessment of Ni substances in ingested materials including soils.

The objective of the present study was to derive a Ni bioaccessibility value for screening-level risk assessment of Ni substances in ingested materials including soils where multiple Ni substances are expected but not definitively identified. Broad ranges of Ni mass loading and dissolution time of a simple gastric assay were applied to pure Ni substances (removing the confounding factors of soil constituents on dissolution), thus broadening the applicability of the conclusions. The data were also used to support current knowledge of 'read across' for Ni substances. Release of Ni from pure manufactured Ni substances (Ni metal, NiO, NiSO4, Ni3S2, and NiS) was determined relative to Ni mass and substance surface area loading. Mass loadings ranged from 0.33 to 20.0 g Ni per L of 0.15 M HCl, and dissolution time ranged from 1 to 168 h. Proton exhaustion was indicated only at the highest loading (20 g/L) of NiO and Ni-M. Dissolution of substances other than NiSO4 was most likely limited by formation of intermediate products at the particle surface or particle agglomeration, impeding access to the principal Ni substance. The bioaccessibility of Ni for these substances was consistent with previously published data: substances other than NiSO4 were < 48% bioaccessible for a variety of gastric assays, which is much lower than all data for NiSO4, the usual reference substance. Thus, we suggest that Ni bioaccessibility data from gastric assays that are most relevant to human exposure can be relied upon to develop scientifically sound screening-level human health RA decisions for Ni contamination in soils and sediments in the absence of detailed Ni speciation.

Morphological Diversity, Protein Adsorption, and Cellular Uptake of Polydopamine-Coated Gold Nanoparticles.

Polydopamine (PDA)-coated nanoparticles are adhesive bionanomaterials widely utilized in intracellular applications, yet how their adhesiveness affects their colloidal stability and their interactions with serum proteins and mammalian cells remain unclear. In this work, we systematically investigate the combined effects of dopamine (DA) concentration and polymerization time (both reaction parameters spanning 2 orders of magnitude) on the morphological diversity of PDA-coated nanoparticles by coating PDA onto gold nanoparticle cores. Independent of the DA concentration, Au@PDA NPs remain largely aggregated upon several hours of limited polymerization; interestingly, extended polymerization for 2 days or longer yield randomly aggregated NPs, nearly monodisperse NPs, or worm-like NP chains in the ascending order of DA concentration. Upon exposure to serum proteins, the specific type of proteins adsorbed to the Au@PDA NPs strongly depends upon the DA concentration. As DA concentration increases, less albumin and more hemoglobin subunits adhere. Moreover, cellular uptake is a strong function of polymerization time. Serum-stabilized Au@PDA NPs prepared by limited polymerization enter Neuro-2a and HeLa cancer cells more abundantly than those prepared by extended polymerization. Our data underscore the importance of DA concentration and polymerization time for tuning the morphology and degree of intracellular delivery of PDA-coated nanostructures.

Chaperonin TRiC/CCT Modulates the Folding and Activity of Leukemogenic Fusion Oncoprotein AML1-ETO.

AML1-ETO is the most common fusion oncoprotein causing acute myeloid leukemia (AML), a disease with a 5-year survival rate of only 24%. AML1-ETO functions as a rogue transcription factor, altering the expression of genes critical for myeloid cell development and differentiation. Currently, there are no specific therapies for AML1-ETO-positive AML. While known for decades to be the translational product of a chimeric gene created by the stable chromosome translocation t(8;21)(q22;q22), it is not known how AML1-ETO achieves its native and functional conformation or whether this process can be targeted for therapeutic benefit. Here, we show that the biosynthesis and folding of the AML1-ETO protein is facilitated by interaction with the essential eukaryotic chaperonin TRiC (or CCT). We demonstrate that a folding intermediate of AML1-ETO binds to TRiC directly, mainly through its ß-strand rich, DNA-binding domain (AML-(1-175)), with the assistance of HSP70. Our results suggest that TRiC contributes to AML1-ETO proteostasis through specific interactions between the oncoprotein's DNA-binding domain, which may be targeted for therapeutic benefit.

Modulation of STAT3 folding and function by TRiC/CCT chaperonin.

Signal transducer and activator of transcription 3 (Stat3) transduces signals of many peptide hormones from the cell surface to the nucleus and functions as an oncoprotein in many types of cancers, yet little is known about how it achieves its native folded state within the cell. Here we show that Stat3 is a novel substrate of the ring-shaped hetero-oligomeric eukaryotic chaperonin, TRiC/CCT, which contributes to its biosynthesis and activity in vitro and in vivo. TRiC binding to Stat3 was mediated, at least in part, by TRiC subunit CCT3. Stat3 binding to TRiC mapped predominantly to the ß-strand rich, DNA-binding domain of Stat3. Notably, enhancing Stat3 binding to TRiC by engineering an additional TRiC-binding domain from the von Hippel-Lindau protein (vTBD), at the N-terminus of Stat3, further increased its affinity for TRiC as well as its function, as determined by Stat3's ability to bind to its phosphotyrosyl-peptide ligand, an interaction critical for Stat3 activation. Thus, Stat3 levels and function are regulated by TRiC and can be modulated by manipulating its interaction with TRiC.

Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase.

Ion-translocating rotary ATPases serve either as ATP synthases, using energy from a transmembrane ion motive force to create the cell's supply of ATP, or as transmembrane ion pumps that are powered by ATP hydrolysis. The members of this family of enzymes each contain two rotary motors: one that couples ion translocation to rotation and one that couples rotation to ATP synthesis or hydrolysis. During ATP synthesis, ion translocation through the membrane-bound region of the complex causes rotation of a central rotor that drives conformational changes and ATP synthesis in the catalytic region of the complex. There are no structural models available for the intact membrane region of any ion-translocating rotary ATPase. Here we present a 9.7 Å resolution map of the H(+)-driven ATP synthase from Thermus thermophilus obtained by electron cryomicroscopy of single particles in ice. The 600-kilodalton complex has an overall subunit composition of A(3)B(3)CDE(2)FG(2)IL(12). The membrane-bound motor consists of a ring of L subunits and the carboxy-terminal region of subunit I, which are equivalent to the c and a subunits of most other rotary ATPases, respectively. The map shows that the ring contains 12 L subunits and that the I subunit has eight transmembrane helices. The L(12) ring and I subunit have a surprisingly small contact area in the middle of the membrane, with helices from the I subunit making contacts with two different L subunits. The transmembrane helices of subunit I form bundles that could serve as half-channels across the membrane, with the first half-channel conducting protons from the periplasm to the L(12) ring and the second half-channel conducting protons from the L(12) ring to the cytoplasm. This structure therefore suggests the mechanism by which a transmembrane proton motive force is converted to rotation in rotary ATPases.

Intermittent versus continuous erlotinib with concomitant modified "XELOX" (q3W) in first-line treatment of metastatic colorectal cancer: correlation with serum amphiregulin and transforming growth factor alpha.

BACKGROUND: This study evaluated the activity of 2 schedules of erlotinib in combination with chemotherapy, and the prognostic significance of serum amphiregulin (AREG) and transforming growth factor alpha (TGFa) in metastatic colorectal cancer. METHODS: A total of 60 untreated patients were randomized to a "continuous" (CON; erlotinib 100 mg daily) or an "intermittent" (INT; erlotinib 150 mg on alternate day on day 2 to 14, then 150 mg daily on days 15 to 21) schedule of erlotinib with a modified XELOX (capecitabine plus oxaliplatin) regimen. Serum levels of AREG and TGFa were determined serially. RESULTS: Baseline characteristics were similar between the 2 arms. Of the 58 patients evaluated for response, there was a nonsignificant trend toward a slightly higher overall response rate in the INT arm (66.7%) versus the CON arm (56.7%). At a median follow-up of 2.8 years, the median overall survival was 18.8 months (95% confidence interval = 11.3-22.9 months) and 20.7 months (95% confidence interval = 12.5-31 months, P = .19) for the CON and INT arm, respectively. KRAS mutation did not predict drug response. The 2 arms did not differ significantly in toxicity. Baseline serum TGFa was an independent predictor of progression-free survival, whereas a drop in serum TGFa and AREG levels following 3 to 4 cycles of treatment were associated with shorter progression-free survival and overall survival, respectively. CONCLUSIONS: The intermittent erlotinib schedule was associated with a higher response rate, although this is not statistically significant. Serum TGFa and AREG levels have prognostic significance in erlotinib-treated patients with colorectal cancer, and further studies are warranted.

Structure of intact Thermus thermophilus V-ATPase by cryo-EM reveals organization of the membrane-bound V(O) motor.

The eubacterium Thermus thermophilus uses a macromolecular assembly closely related to eukaryotic V-ATPase to produce its supply of ATP. This simplified V-ATPase offers several advantages over eukaryotic V-ATPases for structural analysis and investigation of the mechanism of the enzyme. Here we report the structure of the complex at approximately 16 A resolution as determined by single particle electron cryomicroscopy (cryo-EM). The resolution of the map and our use of cryo-EM, rather than negative stain EM, reveals detailed information about the internal organization of the assembly. We could separate the map into segments corresponding to subunits A and B, the threefold pseudosymmetric C-subunit, a central rotor consisting of subunits D and F, the L-ring, the stator subcomplex consisting of subunits I, E, and G, and a micelle of bound detergent. The architecture of the V(O) region shows a remarkably small area of contact between the I-subunit and the ring of L-subunits and is consistent with a two half-channel model for proton translocation. The arrangement of structural elements in V(O) gives insight into the mechanism of torque generation from proton translocation.

Emotion-behaviour decoupling and experiential pleasure deficits predict negative symptoms and functional outcome in first-episode schizophrenia patients.

BACKGROUND: Emotion-behaviour decoupling refers to the failure to translate emotion into motivated behaviour, and is a putative marker for schizophrenia. The heterogeneity of experiential pleasure and emotion expressivity deficits has been reported in schizophrenia patients. These three constructs are believed to contribute to negative symptoms, but very few studies have examined their predictive ability for clinical and functional outcome of schizophrenia. This study aimed to clarify whether these three constructs influence clinical and functional outcome of schizophrenia. METHOD: At baseline, 127 first-episode schizophrenia patients completed a behavioural paradigm for emotion-behaviour decoupling, and self-report scales for experiential pleasure and emotion expressivity deficits. Cluster-analysis was applied to characterize schizophrenia subgroups based on these three constructs. At end-point (mean follow-up = 5.37 years, SD = 1.03 years), 85 schizophrenia patients were reassessed using the Clinical Assessment Interview for Negative Symptoms (CAINS) and a clinician-rated social functioning scale. RESULTS: Cluster 1 (n = 74) did not show emotion-behaviour decoupling, and had intact experiential pleasure and emotion expressivity. Cluster 2 (n = 29) showed emotion-behaviour decoupling and experiential pleasure deficits. Cluster 3 (n = 24) showed emotion expressivity deficits. At endpoint, the three clusters differed significantly in CAINS MAP factor (p = 0.016) and social functioning (p = 0.019), but not CAINS EXP factor. Specifically, Cluster 2 (n = 18) showed more severe negative symptoms of CAINS MAP factor (p = 0.046) and poorer social functioning (p = 0.022) than Cluster 1 (n = 49). Cluster 3 (n = 18) did not differ from Cluster 1 and Cluster 2 in negative symptoms and social functioning. DISCUSSION: Emotion-behaviour decoupling and experiential pleasure deficits predicted clinical and functional outcome of schizophrenia.

The beauty and complexity of the small heat shock proteins: a report on the proceedings of the fourth workshop on small heat shock proteins.

The Fourth Cell Stress Society International workshop on small heat shock proteins (sHSPs), a follow-up to successful workshops held in 2014, 2016 and 2018, took place as a virtual meeting on the 17-18 November 2022. The meeting was designed to provide an opportunity for those working on sHSPs to reconnect and discuss their latest work. The diversity of research in the sHSP field is reflected in the breadth of topics covered in the talks presented at this meeting. Here we summarise the presentations at this meeting and provide some perspectives on exciting future topics to be addressed in the field.

The Important Role of Motivation and Pleasure Deficits on Social Functioning in Patients With Schizophrenia: A Network Analysis.

Negative symptoms, particularly the motivation and pleasure (MAP) deficits, are associated with impaired social functioning in patients with schizophrenia (SCZ). However, previous studies seldom examined the role of the MAP on social functioning while accounting for the complex interplay between other psychopathology. This network analysis study examined the network structure and interrelationship between negative symptoms (at the "symptom-dimension" and "symptom-item" levels), other psychopathology and social functioning in a sample of 269 patients with SCZ. The psychopathological symptoms were assessed using the Clinical Assessment Interview for Negative Symptoms (CAINS) and the Positive and Negative Syndrome Scale (PANSS). Social functioning was evaluated using the Social and Occupational Functioning Assessment Scale (SOFAS). Centrality indices and relative importance of each node were estimated. The network structures between male and female participants were compared. Our resultant networks at both the "symptom-dimension" and the "symptom-item" levels suggested that the MAP factor/its individual items were closely related to social functioning in SCZ patients, after controlling for the complex interplay between other nodes. Relative importance analysis showed that MAP factor accounted for the largest proportion of variance of social functioning. This study is among the few which used network analysis and the CAINS to examine the interrelationship between negative symptoms and social functioning. Our findings supported the pivotal role of the MAP factor to determine SCZ patients' social functioning, and as a potential intervention target for improving functional outcomes of SCZ.

Prospective Memory Influences Social Functioning in People With First-Episode Schizophrenia: A Network Analysis and Longitudinal Study.

Background: Prospective memory (PM) impairment is associated with impaired social functioning, but evidence is limited to chronic schizophrenia samples and cross-sectional design. The aim of this study was to utilize network analysis to address the complex interplay between PM, psychopathology, and functional outcome.Methods: This longitudinal study recruited 119 people with first-episode DSM-IV schizophrenia and followed up with them for 2 to 6 years. PM and working memory were assessed at baseline (in 2010-2015) using valid computerized tasks and the Letter-Number Span Test, respectively. Psychopathology and social functioning were assessed at endpoint (in 2016-2017) using the Positive and Negative Syndrome Scale (PANSS) and the Social and Occupational Functioning Assessment Scale (SOFAS), respectively. Network analysis examined the effect of baseline PM on SOFAS while accounting for the effects of psychopathology.Results: The resultant network showed that social functioning, PANSS positive symptoms, and PANSS general symptoms clustered together, whereas time-based and event-based PM and working memory formed another cluster. Time-based PM linked event-based PM and working memory with social functioning. Time-based PM (expected influence [EI] = 0.69), event-based PM (EI = 0.65), and working memory (EI = 0.83) demonstrated high values of expected influence, but social functioning (variance explained = 0.685) and PANSS negative (variance explained = 0.657) and general (variance explained = 0.583) subscales demonstrated high values of predictability.Conclusions: Time-based PM is the central node linking neurocognitive functions with social functioning. PM and working memory are "target" nodes for interventions bringing changes to the network, whereas social functioning and psychopathology are "malleable" nodes. PM and working memory are promising intervention targets for functional recovery in schizophrenia.

Automatic Assignment of Radiology Examination Protocols Using Pre-trained Language Models with Knowledge Distillation.

Selecting radiology examination protocol is a repetitive, and time-consuming process. In this paper, we present a deep learning approach to automatically assign protocols to computed tomography examinations, by pre-training a domain-specific BERT model (BERTrad). To handle the high data imbalance across exam protocols, we used a knowledge distillation approach that up-sampled the minority classes through data augmentation. We compared classification performance of the described approach with n-gram models using Support Vector Machine (SVM), Gradient Boosting Machine (GBM), and Random Forest (RF) classifiers, as well as the BERTbase model. SVM, GBM and RF achieved macro-averaged F1 scores of 0.45, 0.45, and 0.6 while BERTbase and BERTrad achieved 0.61 and 0.63. Knowledge distillation boosted performance on the minority classes and achieved an F1 score of 0.66.

Gastric bioaccessibility is a conservative measure of nickel bioavailability after oral exposure: Evidence from Ni-contaminated soil, pure Ni substances and Ni alloys.

Oral bioaccessibility (BAc) is a surrogate for the bioavailability (BAv) of a broad range of substances, reflecting the value that the approach offers for assessing oral exposure and risk. BAc is generally considered to have been validated as a proxy for oral BAv for the important soil contaminants Pb, Cd, and As. Here, using literature data for Ni BAc and BAv, we confirmed that Ni BAc (gastric only, with HCl mimicking stomach conditions) is a conservative measure of BAv for the oral exposure pathway. Measured oral BAv of Ni in soil was shown to be 50-100 times less than the simplest oral BAc estimates (%BAv = 0.012(%BAc) - 0.023 (r = 0.701, 95%CI [0.456, 0.847], n = 30)) in rats, demonstrating a significant conservatism for exposure assessment. The relationship between the oral BAv and BAc of nickel sulfate hexahydrate (NSHH) was comparable to that of soil, with measured oral BAv of NSHH (1.94%) being a small fraction of NSHH gastric BAc (91.1%). BAc and BAv reflect the underlying Ni speciation of the sample, with the bioaccessible leaching limits being represented by the highly soluble Ni salts and the poorly soluble Ni monoxide, and the environmental (e.g. soil properties) or gastric (e.g. food present) conditions. BAc has potential utility for chemical classification purposes because pure Ni substances can be grouped by %BAc values(using standardized methodologies for the relevant exposure routes), these groupings reflecting the underlying chemistry and speciation of the samples of substances tested here, with 0.008% %BAc for alloys (SS304, SS316, Inconel, Monel), <1% in green NiO and Ni metal massives, 0.9-23.6% for Ni powders, 9.8-22.7% for Ni sulfides, 26.3-29.6% for black oxidic Ni, and 82-91% for the soluble Ni salts. Oral BAc provides realistic yet conservative estimates of BAv for the hazard classification and risk assessment of Ni substances.

Non-coplanar VMAT plans for postoperative primary brain tumour to reduce dose to hippocampus, temporal lobe and cochlea: a planning study.

OBJECTIVES: This study aimed to compare radiotherapy plan quality of coplanar volumetric modulated arc therapy (CO-VMAT) and non-coplanar VMAT (NC-VMAT) for post-operative primary brain tumour. METHODS: A total of 16 patients who were treated for primary brain tumours were retrospectively selected for this study. For each patient, identical CT sets with structures were used for both CO-VMAT and NC-VMAT planning. For CO-VMAT, one full arc and two coplanar half arcs were used. For NC-VMAT, one full coplanar and two non-coplanar half arcs with couch rotation of 315° or 45° were used. Dose constraints were adhered to the RTOG 0614, RTOG 0933 and TMH protocol. Dose volumetric parameters were collected for statistical analysis. RESULTS: .NC-VMAT achieved significant dose reduction in contralateral hippocampus, both temporal lobes and cochleae, and other OARs while the plan qualities remained the same. In particular, NC-VMAT decreased contralateral hippocampus mean dose by 1.67Gy. Similarly, the NC-VMAT decreased temporal lobe mean dose by 6.29Gy and 2.8Gy for ipsilateral and contralateral side respectively. Furthermore, it decreased cochlea mean dose by 5.34Gy and 0.97Gy for ipsilateral and contralateral side respectively. Overall, there was a reduction of 5.4% of normal brain tissue volume receiving low dose irradiation. CONCLUSION: The proposed NC-VMAT showed more favourable plan quality than the CO-VMAT for primary brain tumours, in particular to hippocampus, temporal lobes, cochleae and OARs located to the contralateral side of tumours. ADVANCES IN KNOWLEDGE: For primary brain tumours radiotherapy, NC-VMAT can reduce doses to the hippocampus, both temporal lobes, and cochleae, as well as OARs located to the contralateral side of tumours.

A distinct giant coat protein complex II vesicle population in Arabidopsis thaliana.

Plants live as sessile organisms with large-scale gene duplication events and subsequent paralogue divergence during evolution. Notably, plant paralogues are expressed tissue-specifically and fine-tuned by phytohormones during various developmental processes. The coat protein complex II (COPII) is a highly conserved vesiculation machinery mediating protein transport from the endoplasmic reticulum to the Golgi apparatus in eukaryotes1. Intriguingly, Arabidopsis COPII paralogues greatly outnumber those in yeast and mammals2-6. However, the functional diversity and underlying mechanism of distinct COPII paralogues in regulating protein endoplasmic reticulum export and coping with various adverse environmental stresses are poorly understood. Here we characterize a novel population of COPII vesicles produced in response to abscisic acid, a key phytohormone regulating abiotic stress responses in plants. These hormone-induced giant COPII vesicles are regulated by an Arabidopsis-specific COPII paralogue and carry stress-related channels/transporters for alleviating stresses. This study thus provides a new mechanism underlying abscisic acid-induced stress responses via the giant COPII vesicles and answers a long-standing question on the evolutionary significance of gene duplications in Arabidopsis.

Structural basis of substrate recognition and thermal protection by a small heat shock protein.

Small heat shock proteins (sHsps) bind unfolding proteins, thereby playing a pivotal role in the maintenance of proteostasis in virtually all living organisms. Structural elucidation of sHsp-substrate complexes has been hampered by the transient and heterogeneous nature of their interactions, and the precise mechanisms underlying substrate recognition, promiscuity, and chaperone activity of sHsps remain unclear. Here we show the formation of a stable complex between Arabidopsis thaliana plastid sHsp, Hsp21, and its natural substrate 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) under heat stress, and report cryo-electron microscopy structures of Hsp21, DXPS and Hsp21-DXPS complex at near-atomic resolution. Monomeric Hsp21 binds across the dimer interface of DXPS and engages in multivalent interactions by recognizing highly dynamic structural elements in DXPS. Hsp21 partly unfolds its central α-crystallin domain to facilitate binding of DXPS, which preserves a native-like structure. This mode of interaction suggests a mechanism of sHsps anti-aggregation activity towards a broad range of substrates.

Extraction and Analysis of Clinically Important Follow-up Recommendations in a Large Radiology Dataset.

Communication of follow-up recommendations when abnormalities are identified on imaging studies is prone to error. In this paper, we present a natural language processing approach based on deep learning to automatically identify clinically important recommendations in radiology reports. Our approach first identifies the recommendation sentences and then extracts reason, test, and time frame of the identified recommendations. To train our extraction models, we created a corpus of 1367 radiology reports annotated for recommendation information. Our extraction models achieved 0.93 f-score for recommendation sentence, 0.65 f-score for reason, 0.73 f-score for test, and 0.84 f-score for time frame. We applied the extraction models to a set of over 3.3 million radiology reports and analyzed the adherence of follow-up recommendations.