Miracle-dz/UniFAR-FTUs huggingface dataset:
The reduced form of the antibody CH2 domain

Among the immunoglobulin domains, the CH2 domain has the lowest thermal stability, which also depends on amino acid sequence and buffer conditions. To further identify factors that influence CH2 folding and stability, we characterized the domain in the reduced form using differential scanning fluorimetry and nuclear magnetic resonance. We show that the CH2 domain can fold, similarly to the disulfide‐bridged form, without forming a disulfide‐bridge, even though the protein contains two Cys residues. Although the reduced form exhibits thermal stability more than 15°C lower than the disulfide‐bridged form, it does not undergo immediate full oxidization. To explain this phenomenon, we compared CH2 oxidization at different conditions and demonstrate a need for significant fluctuation of the folded conformation to enhance CH2 disulfide‐bridge formation. We conclude that, since CH2 can be purified as a folded, semi‐stable, reduced protein that can coexist with the oxidized form, verification of the level of oxidization at each step is critical in CH2 engineering studies.
A Phase Ib Study of Atezolizumab with Radium-223 Dichloride in Men with Metastatic Castration-Resistant Prostate Cancer

Purpose: Men with metastatic castration-resistant prostate cancer (mCRPC) have limited treatment options after progressing on hormonal therapy and chemotherapy. Here, we evaluate the safety and efficacy of atezolizumab (anti–PD-L1) + radium-223 dichloride (radium-223) in men with mCRPC. Patients and Methods: This phase Ib study evaluated atezolizumab + radium-223 in men with mCRPC and bone and lymph node and/or visceral metastases that progressed after androgen pathway inhibitor treatment. Following safety assessment of concurrent dosing, 45 men were randomized 1:1:1 to concurrent or one of two staggered dosing schedules with either agent introduced one cycle before the other. This was followed by a safety–efficacy expansion cohort (randomized 1:1:1). The primary endpoints were safety and objective response rate (ORR) by RECIST 1.1. Secondary endpoints included radiographic progression-free survival (rPFS), PSA responses, and overall survival (OS). Results: As of October 4, 2019, 44 of 45 men were evaluable. All 44 had ≥1 all-cause adverse event (AE); 23 (52.3%) had a grade 3/4 AE. Fifteen (34.1%) grade 3/4 and 3 (6.8%) grade 5 AEs were related to atezolizumab; none were related to radium-223. Confirmed ORR was 6.8% [95% confidence interval (CI), 1.4–18.7], median rPFS was 3.0 months (95% CI, 2.8–4.6), median PSA progression was 3.0 months (95% CI, 2.8–3.3), and median OS was 16.3 months (95% CI, 10.9–22.3). Conclusions: This phase Ib study demonstrated that atezolizumab + radium-223, regardless of administration schedule, had greater toxicity than either drug alone, with no clear evidence of additional clinical benefit for patients with mCRPC and bone and lymph node and/or visceral metastases.
Potential use of serum‐derived bovine immunoglobulin/protein isolate for the management of COVID‐19

COVID‐19 manifests as a mild disease in most people but can progress to severe disease in nearly 20% of individuals. Disease progression is likely driven by a cytokine storm, either directly stimulated by SARS‐CoV‐2 or by increased systemic inflammation in which the gut might play an integral role. SARS‐CoV‐2 replication in the gut may cause increased intestinal permeability, alterations to the fecal microbiome, and increased inflammatory cytokines. Each effect may lead to increased systemic inflammation and the transport of cytokines and inflammatory antigens from the gut to the lung. Few interventions are being studied to treat people with mild disease and prevent the cytokine storm. Serumderived bovine immunoglobulin/protein isolate (SBI) may prevent progression by (1) binding and neutralizing inflammatory antigens, (2) decreasing gut permeability, (3) interfering with ACE2 binding by viral proteins, and (4) improving the fecal microbiome. SBI is therefore a promising intervention to prevent disease progression in COVID‐19 patients.
Endogenous agonist–bound S1PR3 structure reveals determinants of G protein–subtype bias

Active S1PR3 structure reveals the unique ligand-binding mode and signaling selectivity switching mechanism. Sphingosine-1-phosphate (S1P) regulates numerous important physiological functions, including immune response and vascular integrity, via its cognate receptors (S1PR1 to S1PR5); however, it remains unclear how S1P activates S1PRs upon binding. Here, we determined the crystal structure of the active human S1PR3 in complex with its natural agonist S1P at 3.2-Å resolution. S1P exhibits an unbent conformation in the long tunnel, which penetrates through the receptor obliquely. Compared with the inactive S1PR1 structure, four residues surrounding the alkyl tail of S1P (the “quartet core”) exhibit orchestrating rotamer changes that accommodate the moiety, thereby inducing an active conformation. In addition, we reveal that the quartet core determines G protein selectivity of S1PR3. These results offer insight into the structural basis of activation and biased signaling in G protein–coupled receptors and will help the design of biased ligands for optimized therapeutics.
Effect of Various Aminated Single-Walled Carbon Nanotubes on the Epoxy Cross-Linking Reactions

Arc discharge single-walled carbon nanotubes (SWNTs) have been functionalized with terminal primary amines through four experimental approaches that induce either tip/edge or sidewall functionalization. A full characterization of functionalized SWNTs has been carried out through several techniques. The aminated SWNTs have been solvent-free incorporated into a trifunctional high-performance epoxy system, and the mixture has been studied using differential scanning calorimetry (DSC) and isoconversional kinetic calculations. The thermodynamic parameters obtained from DSC and the isoconversional plots reveal that SWNTs aminated through sidewall addition reactions participate in cross-linking processes. Unfunctionalized SWNTs or those aminated on tips and edges do not show any evidence of a covalent anchoring to the matrix. The type and chemical nature of the amine moieties play an important role in the dispersibility and reactivity of SWNTs in the epoxy, but the functionalization degree and metal content do n.
Comparative study on supercapacitive and oxygen evolution reaction applications of hollow nanostructured cobalt sulfides

Due to the diversity of sulfur valence in cobalt-based sulfides, it is difficult to control the crystal phase and composition of the products during synthesis. Herein, a one-pot hydrothermal method is reported to self-assemble the cobalt sulfides (CoS2, Co9S8 and Co3S4) with hollow nanostructures. The whole preparation process is simple and mild, avoiding high temperature calcination. The performances of the three kinds of cobalt sulfide in superior supercapacitors and electrocatalytic oxygen evolution performance applications follow the order of CoS2 > Co9S8 > Co3S4. Further analysis demonstrates that the performance difference in these cobalt sulfides may be attributed to three factors: the presence of S22−, the coordination environment of Co and the presence of continuous network of Co–Co bonds. The distinctive electrochemical performance of CoS2 and Co9S8 may help us to better understand the excellent electrochemical activity of metal polysulfides and metal sulfides after doping or alloying. Therefore, this work may provide a reference in understanding and designing the electrode materials for highly efficient applications in the fields of energy storage and conversion.
Olfactory ganglioneuroblastoma in a dog: case report and literature review

A 7-y-old, intact male Alaskan Malamute was presented with a 3-mo history of stertor and epistaxis. Computed tomography of the skull revealed generalized loss of gas throughout both nasal passages with replacement by a soft tissue mass that traversed the cribriform plate. Histopathology revealed neoplastic neuroblast cells arranged in anastomosing cords, as well as separately located aggregates of ganglion cells. Both neoplastic cell populations demonstrated immunoreactivity to MAP-2, TuJ-1, and synaptophysin. Neuroblastic cells additionally exhibited punctate immunoreactivity to MCK and CK8/18. We document here both the positive neural immunohistochemical markers for this neoplasm, as well as propose possible histomorphologic variants.
Synergistic interaction of N‐3‐Br‐benzyl‐noscapine and docetaxel abrogates oncogenic potential of breast cancer cells

Noscapine, an opium alkaloid, was discovered to bind tubulin, arrest dividing cells at mitosis, and selectively induce apoptosis to cancer cells. N‐3‐Br‐Benzyl‐Noscapine (Br‐Bn‐Nos), one of the derivatives of noscapine, was demonstrated to have improved anticancer potential compared with noscapine. We approached to evaluate the single and combined effect of Br‐Bn‐Nos and docetaxel (DOX) based on molecular modeling and cellular study. The individual predicted free energy of binding (∆Gbind,pred) for Br‐Bn‐Nos and DOX with tubulin was found to be −28.89 and −36.07 kcal/mol based on molecular mechanics generalized Born solvation area (MM‐GBSA) as well as −26.21 and −34.65 kcal/mol based on molecular mechanics Poisson Boltzmann solvation area (MM‐PBSA), respectively. However, the ∆Gbind,pred of Br‐Bn‐Nos was significantly reduced (−33.02 and −30.24 kcal/mol using MM‐GBSA and MM‐PBSA) in the presence of DOX on its binding pocket. Parenthetically, the ∆Gbind,pred of DOX was significantly reduced (−37.17 and −32.80 kcal/mol using MM‐GBSA and MM‐PBSA) in the presence of Br‐Bn‐Nos on its binding pocket. The reduced ∆Gbind,pred in the presence of Br‐Bn‐Nos and DOX together indicated a combination effect of both the ligands. The combined interaction of both the agents onto tubulin dimmer was also determined experimentally using purified tubulin, in which a combination regimen of Br‐Bn‐Nos and DOX reduced the fluorescence intensity of tubulin to a higher value (68%) compared with the single regimen. Further, isobologram analysis revealed the synergistic effect of Br‐Bn‐Nos and DOX in antiproliferative activity using MCF‐7 cell line at 48 hr (sum FIC = 0.49) and at 72 hr (sum FIC = 0.62). The combination dose regimen of Br‐Bn‐Nos and DOX blocks the cell cycle progression at the G2/M phase and induces apoptosis to cancer cells more effectively compared with the single regimen. Taken together, our study provides compelling evidence that the anticancer potential of noscapine derivatives may be substantially improved when it is used in a combined application with DOX for breast cancer.
Impact of Ligands and Metals on the Formation of Metallacyclic Intermediates and a Nontraditional Mechanism for Group VI Alkyne Metathesis Catalysts

The intermediacy of metallacyclobutadienes as part of a [2 + 2]/retro-[2 + 2] cycloaddition-based mechanism is a well-established paradigm in alkyne metathesis with alternative species viewed as off-cycle decomposition products that interfere with efficient product formation. Recent work has shown that the exclusive intermediate isolated from a siloxide podand-supported molybdenum-based catalyst was not the expected metallacyclobutadiene but instead a dynamic metallatetrahedrane. Despite their paucity in the chemical literature, theoretical work has shown these species to be thermodynamically more stable as well as having modest barriers for cycloaddition. Consequentially, we report the synthesis of a library of group VI alkylidynes as well as the roles metal identity, ligand flexibility, secondary coordination sphere, and substrate identity all have on isolable intermediates. Furthermore, we report the disparities in catalyst competency as a function of ligand sterics and metal choice. Dispersion-corrected DFT calculations are used to shed light on the mechanism and role of ligand and metal on the intermediacy of metallacyclobutadiene and metallatetrahedrane as well as their implications to alkyne metathesis.
Lack of efficacy of hydroxychloroquine and azithromycin in patients hospitalized for COVID-19 pneumonia: A retrospective study

Background Hydroxychloroquine combined with azithromycin (HCQ/AZI) has initially been used against coronavirus disease-2019 (COVID-19). In this retrospective study, we assessed the clinical effects of HCQ/AZI, with a 28-days follow-up. Methods In a registry-study which included patients hospitalized for COVID-19 between March 15 and April 2, 2020, we compared patients who received HCQ/AZI to those who did not, regarding a composite outcome of mortality and mechanical ventilation with a 28-days follow-up. QT was monitored for patients treated with HCQ/AZI. Were excluded patients in intensive care units, palliative care and ventilated within 24 hours of admission. Three analyses were performed to adjust for selection bias: propensity score matching, multivariable survival, and inverse probability score weighting (IPSW) analyses. Results Overall, 203 patients were included: 60 patients treated by HCQ/AZI and 143 control patients. During the 28-days follow-up, 32 (16.3%) patients presented the primary outcome and 23 (12.3%) patients died. Propensity-score matching identified 52 unique pairs of patients with similar characteristics. In the matched cohort (n = 104), HCQ/AZI was not associated with the primary composite outcome (log-rank p-value = 0.16). In the overall cohort (n = 203), survival and IPSW analyses also found no benefit from HCQ/AZI. In the HCQ/AZI group, 11 (18.3%) patients prolonged QT interval duration, requiring treatment cessation. Conclusions HCQ/AZI combination therapy was not associated with lower in-hospital mortality and mechanical ventilation rate, with a 28-days follow-up. In the HCQ/AZI group, 18.3% of patients presented a prolonged QT interval requiring treatment cessation, however, control group was not monitored for this adverse event, making comparison impossible.
Diversity of dimethylsulfide-degrading methanogens and sulfate-reducing bacteria in anoxic sediments along the Medway Estuary, UK.

Methane is a powerful greenhouse gas but the microbial diversity mediating methylotrophic methanogenesis is not well-characterised. One overlooked route to methane is via the degradation of dimethylsulfide (DMS), an abundant organosulfur compound in the environment. Methanogens and sulfate-reducing bacteria (SRB) can degrade DMS in anoxic sediments depending on sulfate availability. However, we know little about the underlying microbial community and how sulfate availability affects DMS degradation in anoxic sediments. We studied DMS-dependent methane production along the salinity gradient of the Medway Estuary (UK) and characterised, for the first time, the DMS-degrading methanogens and SRB using cultivation-independent tools. DMS metabolism resulted in high methane yield (39%-42% of the theoretical methane yield) in anoxic sediments regardless of their sulfate content. Methanomethylovorans, Methanolobus and Methanococcoides were dominant methanogens in freshwater, brackish and marine incubations, respectively, suggesting niche-partitioning of the methanogens likely driven by DMS amendment and sulfate concentrations. Adding DMS also led to significant changes in SRB composition and abundance in the sediments. Increases in the abundance of Sulfurimonas and SRB suggest cryptic sulfur cycling coupled to DMS degradation. Our study highlights a potentially important pathway to methane production in sediments with contrasting sulfate content and sheds light on the diversity of DMS-degraders. This article is protected by copyright. All rights reserved.
Prediagnostic White Blood Cell DNA Methylation and Risk of Breast Cancer in the Prostate Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Cohort

Background: White blood cell (WBC) DNA may contain methylation patterns that are associated with subsequent breast cancer risk. Using a high-throughput array and samples collected, on average, 1.3 years prior to diagnosis, a case–cohort analysis nested in the prospective Sister Study identified 250 individual CpG sites that were differentially methylated between breast cancer cases and noncases. We examined five of the top 40 CpG sites in a case–control study nested in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Cohort. Methods: We investigated the associations between prediagnostic WBC DNA methylation in 297 breast cancer cases and 297 frequency-matched controls. Two WBC DNA specimens from each participant were used: a proximate sample collected 1 to 2.9 years and a distant sample collected 4.2–7.3 years prior to diagnosis in cases or the comparable timepoints in controls. WBC DNA methylation level was measured using targeted bisulfite amplification sequencing. We used logistic regression to obtain ORs and 95% confidence intervals (CI). Results: A one-unit increase in percent methylation in ERCC1 in proximate WBC DNA was associated with increased breast cancer risk (adjusted OR = 1.29; 95% CI, 1.06–1.57). However, a one-unit increase in percent methylation in ERCC1 in distant WBC DNA was inversely associated with breast cancer risk (adjusted OR = 0.83; 95% CI, 0.69–0.98). None of the other ORs met the threshold for statistical significance. Conclusions: There was no convincing pattern between percent methylation in the five CpG sites and breast cancer risk. Impact: The link between prediagnostic WBC DNA methylation marks and breast cancer, if any, is poorly understood.
Juvenile hormone affects age polyethism, ovarian status, and cuticular hydrocarbon profile in workers of a Polybia occidentalis wasp.

Division of labor is one of the most striking features in the evolution of eusociality. Juvenile hormone (JH) mediates reproductive status and aggression among nestmates in primitively eusocial Hymenoptera (species without morphologically distinct castes). In highly social species it has apparently lost its gonadotropic role and primarily regulates the division of labor in the worker caste. Polybia occidentalis, a Neotropical swarm-founding wasp, is an ideal model to understand how JH levels mirror social context and reproductive opportunities because of the absence of a clear morphological caste dimorphism. In this study, we tested the hypothesis that JH influences division of labor, ovary activation and cuticular hydrocarbon profiles of workers. Our observations confirmed that JH analog (methoprene) and precocene affected the cuticular chemical profile associated with the age polyethism. Also, methoprene and precocene-I influenced differently ovarian activation of treated females (individuals treated with methoprene expressed more activated ovaries while precocene treatment did not have significant effect). These results suggest that different hormonal levels induce a differential expression in the cuticular chemical profiles associated with the workers' age polyethism, which may be essential for keeping the social cohesion among workers throughout their lives in the colony. Furthermore, JH is likely to play a gonadotropic role in P. occidentalis. JH has apparently undergone certain modifications in social Hymenoptera, presenting multifaceted functions in different species.
Cavity in pulmonary mucormycosis: Is it rare?

Sir, We read with interest the article by Saini et al. The authors describe a successfully managed case of pulmonary mucormycosis (PM) in an individual with previously undiagnosed diabetes mellitus. We do not concur with the authors’ comment that cavity is a rare presentation of PM. The imaging findings in PM are influenced by several factors, including the risk factor (neutropenia versus other causes), the timing of imaging and the treatment response. The occurrence of a cavity in PM on imaging is as high as 48% in various studies. Several radiologic findings have been reported in PM, including lobar consolidation, nodules, mass-like consolidation, halo sign, reversed halo sign (RHS), central low attenuation areas, cavities, cavities with intracavitary content and others. While nodules, halo sign and consolidation are early signs of PM, central necrosis, cavitation and crescent sign occur later. The RHS, a widely recognised indicator of invasive PM in immunosuppressed individuals, is neither sensitive nor specific for PM. One explanation for the lack of sensitivity of various radiologic appearances is the serial changes in these patients over time. Case series from neutropenic patients with haematological malignancies suggest that PM may begin as areas of ground-glass opacities and progress to form nodules and consolidation. Some of these patients progressed to develop cavities, while a few others developed multifocal pneumonia. In the series by Hammer et al., a cavity was present in 10% (3/30) of the subjects in the initial computed tomography (CT) study, while, subsequently, eight more patients developed (37%) cavities. Unlike patients with haematological malignancy where early CT is performed, diabetics often remain unevaluated until late in the disease course. Non-specific symptoms, late presentation to medical facilities, lack of clinical suspicion, consideration of alternate diagnosis like tuberculosis, and delayed imaging explain the higher frequency of cavitation in diabetic individuals with PM. Therefore, invasive mould infections, particularly PM, should be considered as an alternate possibility in diabetic subjects with cavities in addition to bacterial abscesses, tuberculosis and others. Declaration of conflicting interests
Non-canonical Wnt Signaling Promotes Myofibroblast Differentiation in Pulmonary Fibrosis.

The Wnt/β-catenin pathway initiates a signaling cascade critical in cell differentiation and normal development of multiple organ systems. The reactivation of this pathway has been documented in experimental and human idiopathic pulmonary fibrosis (IPF), wherein Wnt/β-catenin activation has been implicated in epithelial cell repair. Furthermore the canonical ligand Wnt3a is known to induce myofibroblast differentiation, however the role of non-canonical Wnt ligands remains unclear. This study showed significantly higher levels of Wnt11 expression in cells from both IPF patients and bleomycin-treated mice, as well as in TGFβ treated mouse lung fibroblasts. Moreover Wnt11 induced myofibroblast differentiation as manifested by increased α-smooth muscle actin (α-SMA) expression, which was similar to that induced by canonical Wnt3a/β-catenin signaling. Further investigation revealed that Wnt11 induction of α-SMA, was associated with the activation of JNK/c-Jun signaling and inhibited by a JNK inhibitor. The potential importance of this signaling pathway was supported by in vivo evidence showing significantly increased levels of Wnt11 and activated JNK in lungs of mice with bleomycin induced pulmonary fibrosis. Interestingly, fibroblasts did not express canonical Wnt3a but treatment of these cells with exogenous Wnt3a induced endogenous Wnt11 and Wnt5a resulting in repression of the Wnt3a/β-catenin target gene Axin2. These findings suggested that the non-canonical Wnt induction of myofibroblast differentiation mediated by JNK/c-Jun pathway might play a significant role in pulmonary fibrosis, in addition to, or synergy with canonical Wnt3a/β-catenin signaling. Moreover Wnt3a activation of non-canonical Wnt signaling might trigger a switch from canonical to non-canonical Wnt signaling to induce myofibroblast differentiation.