Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Analyses of Four CYP1A1 Missense Mutations Present in Patients with Atypical Femoral Fractures

Osteoporosis is the most common metabolic bone disorder and nitrogen-containing bisphosphonates (BP) are a first line treatment for it. Yet, atypical femoral fractures (AFF), a rare adverse effect, may appear after prolonged BP administration. Given the low incidence of AFF, an underlying genetic cause that increases the susceptibility to these fractures is suspected. Previous studies uncovered rare CYP1A1 mutations in osteoporosis patients who suffered AFF after long-term BP treatment. CYP1A1 is involved in drug metabolism and steroid catabolism, making it an interesting candidate. However, a functional validation for the AFF-associated CYP1A1 mutations was lacking. Here we tested the enzymatic activity of four such CYP1A1 variants, by transfecting them into Saos-2 cells. We also tested the effect of commonly used BPs on the enzymatic activity of the CYP1A1 forms. We demonstrated that the p.Arg98Trp and p.Arg136His CYP1A1 variants have a significant negative effect on enzymatic activity. Moreover, all the BP treatments decreased CYP1A1 activity, although no specific interaction with CYP1A1 variants was found. Our results provide functional support to the hypothesis that an additive effect between CYP1A1 heterozygous mutations p.Arg98Trp and p.Arg136His, other rare mutations and long-term BP exposure might generate susceptibility to AFF.
Activity of meropenem/vaborbactam and comparators against Gram-negative isolates from Eastern and Western European patients hospitalized with pneumonia including ventilator-associated pneumonia (2014–19)

Abstract Objectives Meropenem/vaborbactam has been approved in Europe for the treatment of hospital-acquired bacterial pneumonia, ventilator-associated pneumonia (VAP) and bacteraemia among other indications. Vaborbactam is an inhibitor of class A and C β-lactamases, including Klebsiella pneumoniae carbapenemase (KPC) enzymes, but not class B or D carbapenemases. We analysed the activity of meropenem/vaborbactam and comparators against 6846 Enterobacterales and 3567 Pseudomonas aeruginosa isolates from patients hospitalized with pneumonia (PHP), including VAP. Methods Isolates from PHP were consecutively collected during 2014–19 from 42 European hospitals located in 21 countries and susceptibility tested using the broth microdilution method. Carbapenem-resistant Enterobacterales (CRE) isolates were molecularly characterized to identify their carbapenem-resistance mechanisms. EUCAST (2020) interpretive criteria were used. Results The most common Gram-negative pathogens isolated from PHP were P. aeruginosa (n = 3567), K. pneumoniae (n = 1877) and Escherichia coli (n = 1646). Overall, 98.0% of Enterobacterales and 82.1% of P. aeruginosa were susceptible to meropenem/vaborbactam, with 99.8% of Enterobacterales and 89.7% of P. aeruginosa in Western Europe (WE) and 92.7% of Enterobacterales and 69.1% of P. aeruginosa in Eastern Europe (EE). CRE were more common in EE (15.1%) than WE (2.1%). KPC was the most common carbapenemase in WE, while OXA-48-like was the most common carbapenemase in EE. Meropenem/vaborbactam susceptibility was 63.0% for all CRE (92.2% in WE and 51.5% in EE). Meropenem/vaborbactam inhibited 99.1% of KPC-producing isolates and 40.5% of OXA-48-like-producing isolates. Conclusions These in vitro data demonstrate that meropenem/vaborbactam has potent activity against isolates from PHP, including isolates producing KPC, and may be a useful treatment option for PHP, including VAP.
Prognostic Impact of Immunoglobulin Kappa C (IGKC) in Early Breast Cancer

Simple Summary We examined the relevance of immunoglobulin kappa C (IGKC), an important part of the humoral immune system, in early breast cancer. To our knowledge, our results confirm for the first time previous retrospective findings of a cancer recurrence protective role of IGKC in a large cohort of early breast cancer patients who were treated in the prospective, randomized FinHer clinical trial. We show that an increased amount of IGKC in the tumor is linked to longer distant metastasis-free survival, especially in patients whose breast cancer does not express hormone receptors or human epidermal growth factor receptor-2. This type of breast cancer often has poor prognosis. Since an improved outcome is associated with the presence of tumor-infiltrating IGKC expressing immune cells, this may be a further argument for the use of immunotherapies in these patients. Abstract We studied the prognostic impact of tumor immunoglobulin kappa C (IGKC) mRNA expression as a marker of the humoral immune system in the FinHer trial patient population, where 1010 patients with early breast cancer were randomly allocated to either docetaxel-containing or vinorelbine-containing adjuvant chemotherapy. HER2-positive patients were additionally allocated to either trastuzumab or no trastuzumab. Hormone receptor-positive patients received tamoxifen. IGKC was evaluated in 909 tumors using quantitative real-time polymerase chain reaction, and the influence on distant disease-free survival (DDFS) was examined using univariable and multivariable Cox regression and Kaplan–Meier estimates. Interactions were analyzed using Cox regression. IGKC expression, included as continuous variable, was independently associated with DDFS in a multivariable analysis also including age, molecular subtype, grade, and pT and pN stage (HR 0.930, 95% CI 0.870–0.995, p = 0.034). An independent association with DDFS was also found in a subset analysis of triple-negative breast cancers (TNBC) (HR 0.843, 95% CI 0.724–0.983, p = 0.029), but not in luminal (HR 0.957, 95% CI 0.867–1.056, p = 0.383) or HER2-positive (HR 0.933, 95% CI 0.826–1.055, p = 0.271) cancers. No significant interaction between IGKC and chemotherapy or trastuzumab administration was detected (Pinteraction = 0.855 and 0.684, respectively). These results show that humoral immunity beneficially influences the DDFS of patients with early TNBC.
Cyanovinylation of Aldehydes: Organocatalytic Multicomponent Synthesis of Conjugated Cyanomethyl Vinyl Ethers

A novel organocatalytic multicomponent cyanovinylation of aldehydes was designed for the synthesis of conjugated cyanomethyl vinyl ethers. The reaction was implemented for the synthesis of a 3-substituted 3-(cyanomethoxy)acrylates, using aldehydes as substrates, acetone cyanohydrin as the cyanide anion source, and methyl propiolate as the source of the vinyl component. The multicomponent reaction is catalyzed by N-methyl morpholine (2.5 mol%) to deliver the 3-(cyanomethoxy)acrylates in excellent yields and with preponderance of the E-isomer. The multicomponent reaction manifold is highly tolerant to the structure and composition of the aldehyde (aliphatic, aromatic, heteroaromatics), and it is instrumentally simple (one batch, open atmospheres), economic (2.5 mol% catalyst, stoichiometric reagents), environmentally friendly (no toxic waste), and sustainable (easy scalability).
Efficacy of Modified Treat-and-Extend Regimen of Aflibercept for Macular Edema from Branch Retinal Vein Occlusion: 2-Year Prospective Study Outcomes

This study aimed to evaluate the long-term (24-month) efficacy and safety of a modified treat-and-extend (mTAE) regimen of aflibercept for macular edema (ME) due to branch retinal vein occlusion (BRVO). This was a prospective multicenter intervention study. We evaluated 50 eyes in 50 patients with ME due to BRVO enrolled between October 2016 and September 2017. The patients received intravitreal aflibercept (IVA) injections according to a mTAE regimen for 24 months. This study reports the secondary endpoints of best-corrected visual acuity (BCVA) and central subfield thickness (CST) at 24 months and compares them with previously reported primary endpoints. Compared with baseline BCVA and CST of 0.33 (0.27) and 488 (165) µm (mean (standard deviation)), respectively, BCVA and CST were significantly improved at 12 and 24 months (12 months: 0.059 (0.19) LogMAR and 299 (112) µm; 24 months: 0.034 (0.18) LogMAR and 272 (81) µm, respectively; both p < 0.0001). Over the 24-month period, the mean number of IVA injections and clinic visits was 7.4 (3.3) and 11.1 (2.0), respectively. The mTAE regimen of IVA injections for ME due to BRVO was effective for improving BCVA and reducing CST over 24 months. This regimen shows promise for reducing the number of injections and clinic visits.
Escitalopram Targets Oxidative Stress, Caspase-3, BDNF and MeCP2 in the Hippocampus and Frontal Cortex of a Rat Model of Depression Induced by Chronic Unpredictable Mild Stress

In recent years, escitalopram (ESC) has been suggested to have different mechanisms of action beyond its well known selective serotonin reuptake inhibition. The aim of this study is to investigate the effects of escitalopram on oxidative stress, apoptosis, brain-derived neurotrophic factor (BDNF), Methyl-CpG-binding protein 2 (MeCP2), and oligodendrocytes number in the brain of chronic unpredictable mild stress-induced depressed rats. The animals were randomised in four groups (8 in each group): control, stress, stress + ESC 5 and stress + ESC 5/10. ESC was administered for 42 days in a fixed dose (5 mg/kg b.w.) or in an up-titration regimen (21 days ESC 5 mg/kg b.w. then 21 days ESC 10 mg/kg b.w.). Sucrose preference test (SPT) and elevated plus maze (EPM) were also performed. ESC improved the percentage of sucrose preference, locomotion and anxiety. ESC5/10 reduced the oxidative damage in the hippocampus and improved the antioxidant defence in the hippocampus and frontal lobe. ESC5/10 lowered caspase 3 activity in the hippocampus. Escitalopram had a modulatory effect on BDNF and the number of oligodendrocytes in the hippocampus and frontal lobe and also improved the MeCP2 expressions. The results confirm the multiple pathways implicated in the pathogenesis of depression and suggest that escitalopram exerts an antidepressant effect via different intricate mechanisms.
Porphylipoprotein Accumulation and Porphylipoprotein Photodynamic Therapy Effects Involving Cancer Cell-Specific Cytotoxicity

In photodynamic therapy (PDT) for neoplasms, photosensitizers selectively accumulate in cancer tissue. Upon excitation with light of an optimal wavelength, the photosensitizer and surrounding molecules generate reactive oxygen species, resulting in cancer cell-specific cytotoxicity. Porphylipoprotein (PLP) has a porphyrin-based nanostructure. The porphyrin moiety of PLP is quenched because of its structure. When PLP is disrupted, the stacked porphyrins are separated into single molecules and act as photosensitizers. Unless PLP is disrupted, there is no photosensitive disorder in normal tissues. PLP can attenuate the photosensitive disorder compared with other photosensitizers and is ideal for use as a photosensitizer. However, the efficacy of PLP has not yet been evaluated. In this study, the mechanism of cancer cell-specific accumulation of PLP and its cytotoxic effect on cholangiocarcinoma cells were evaluated. The effects were investigated on normal and cancer-like mutant cells. The cytotoxicity effect of PLP PDT in cancer cells was significantly stronger than in normal cells. In addition, reactive oxygen species regulated intracellular PLP accumulation. The cytotoxic effects were also investigated using a cholangiocarcinoma cell line. The cytotoxicity of PLP PDT was significantly higher than that of laserphyrin-based PDT, a conventional type of PDT. PLP PDT could also inhibit tumor growth in vivo.
Antioxidant Activity and Molecular Docking Study of Volatile Constituents from Different Aromatic Lamiaceous Plants Cultivated in Madinah Monawara, Saudi Arabia

A comparative study of volatile constituents, antioxidant activity, and molecular docking was conducted between essential oils from Mentha longifolia L. , Mentha spicata L. , and Origanum majorana L. , widely cultivated in Madinah. The investigation of volatile oils extracted by hydrodistillation was performed using Gas Chromatography-Mass Spectrometry (GC-MS). A total number of 29, 42, and 29 components were identified in M. longifolia, M. spicata, and O. majorana representing, respectively, 95.91, 94.62, and 98.42, of the total oils. Pulegone (38.42%), 1,8-cineole (15.60%), menthone (13.20%), and isopulegone (9.81%) were the dominant compounds in M. longifolia oil; carvone (35.14%), limonene (27.11%), germacrene D (4.73%), and β-caryophyllene (3.02%) were dominant in M. spicata oil; terpin-4-ol (42.47%), trans-sabinene hydrate (8.52%), γ-terpinene (7.90%), α-terpineol (7.38%), linalool (6.35%), α-terpinene (5.42%), and cis-sabinene hydrate (3.14%) were dominant in O. majorana oil. The antioxidant activity, assessed using DPPH free radical–scavenging and ABTS assays, was found to be the highest in O. majorana volatile oil, followed by M. spicata and M. longifolia, which is consistent with the differences in total phenolic content and volatile constituents identified in investigated oils. In the same context, molecular docking of the main identified volatiles on NADPH oxidase showed a higher binding affinity for cis-verbenyl acetate, followed by β-elemene and linalool, compared to the control (dextromethorphan). These results prove significant antioxidant abilities of the investigated oils, which may be considered for further analyses concerning the control of oxidative stress, as well as for their use as possible antioxidant agents in the pharmaceutical industry.
Rethinking remdesivir for COVID-19: A Bayesian reanalysis of trial findings

Background Following testing in clinical trials, the use of remdesivir for treatment of COVID-19 has been authorized for use in parts of the world, including the USA and Europe. Early authorizations were largely based on results from two clinical trials. A third study published by Wang et al. was underpowered and deemed inconclusive. Although regulators have shown an interest in interpreting the Wang et al. study, under a frequentist framework it is difficult to determine if the non-significant finding was caused by a lack of power or by the absence of an effect. Bayesian hypothesis testing does allow for quantification of evidence in favor of the absence of an effect. Findings Results of our Bayesian reanalysis of the three trials show ambiguous evidence for the primary outcome of clinical improvement and moderate evidence against the secondary outcome of decreased mortality rate. Additional analyses of three studies published after initial marketing approval support these findings. Conclusions We recommend that regulatory bodies take all available evidence into account for endorsement decisions. A Bayesian approach can be beneficial, in particular in case of statistically non-significant results. This is especially pressing when limited clinical efficacy data is available.
FORGE: A Novel Scoring System to Predict the MIB-1 Labeling Index in Intracranial Meningiomas

Simple Summary Meningiomas are predominantly benign intracranial tumors, and surgical therapy represents the treatment of choice. However, the risk of recurrence and scheduling of follow-up intervals are significantly influenced by immunohistochemical items such as the MIB-1 labeling index. To date, it is not possible to integrate this essential information into the pre- or intraoperative surgical decision making. In the present study, we therefore analyzed baseline variables associated with the MIB-1 labeling index. We found four easily identifiable and routinely recorded risk factors for an increased MIB-1 index and developed a simple and quick-to-use score that allows us to estimate the risk of an elevated MIB-1 index prior to the surgical resection. Furthermore, this score seems to predict the progression-free survival in intracranial meningiomas. We believe that this score might us to more reliably guide patients in preoperative surgical strategy planning and postoperative follow-up scheduling. Abstract The MIB-1 index is an essential predictor of progression-free-survival (PFS) in meningioma. To date, the MIB-1 index is not available in preoperative treatment planning. A preoperative score estimating the MIB-1 index in patients with intracranial meningiomas has not been investigated so far. Between 2013 and 2019, 208 patients with tumor morphology data, MIB-1 index data, and plasma fibrinogen and serum C-reactive protein (CRP) data underwent surgery for intracranial WHO grade I and II meningioma. An optimal MIB-1 index cut-off value (≥6/<6) in the prediction of recurrence was determined by ROC curve analysis (AUC: 0.71; 95% CI: 0.55–0.87). A high MIB-1 index (≥6%) was present in 50 cases (24.0%) and was significantly associated with male sex, peritumoral edema, low baseline CRP, and low fibrinogen level in the multivariate analysis. A scoring system (“FORGE”) based on sex, peritumoral edema, preoperative CRP value, and plasma fibrinogen level supports prediction of the MIB-1 index (sensitivity 62%, specificity 79%). The MIB-1 labeling index and the FORGE score are significantly associated with an increased risk of poor PFS time. We suggest a novel score (“FORGE”) to preoperatively estimate the risk of an increased MIB-1 index (≥6%), which might help in surgical decision making and follow-up interval determination and inform future trials investigating inflammatory burden and proliferative activity.
Synoptic Diagnostics of Myeloproliferative Neoplasms: Morphology and Molecular Genetics

Simple Summary The diagnosis of myeloproliferative neoplasms requires assessment of a combination of clinical, morphological, immunophenotypic and genetic features, and this integrated, multimodal approach forms the basis for precise classification. Evaluation includes cell counts and morphology in the peripheral blood, bone marrow aspiration and trephine biopsy, and may encompass flow cytometry for specific questions. Diagnosis nowadays is completed by targeted molecular analysis for the detection of recurrent driver and, optionally, disease-modifying mutations. According to the current World Health Organization classification, all myeloproliferative disorders require assessment of molecular features to support the diagnosis or confirm a molecularly defined entity. This requires a structured molecular analysis workflow tailored for a rapid and cost-effective diagnosis. The review focuses on the morphological and molecular features of Ph-negative myeloproliferative neoplasms and their differential diagnoses, addresses open questions of classification, and emphasizes the enduring role of histopathological assessment in the molecular era. Abstract The diagnosis of a myeloid neoplasm relies on a combination of clinical, morphological, immunophenotypic and genetic features, and an integrated, multimodality approach is needed for precise classification. The basic diagnostics of myeloid neoplasms still rely on cell counts and morphology of peripheral blood and bone marrow aspirate, flow cytometry, cytogenetics and bone marrow trephine biopsy, but particularly in the setting of Ph− myeloproliferative neoplasms (MPN), the trephine biopsy has a crucial role. Nowadays, molecular studies are of great importance in confirming or refining a diagnosis and providing prognostic information. All myeloid neoplasms of chronic evolution included in this review, nowadays feature the presence or absence of specific genetic markers in their diagnostic criteria according to the current WHO classification, underlining the importance of molecular studies. Crucial differential diagnoses of Ph− MPN are the category of myeloid/lymphoid neoplasms with eosinophilia and gene rearrangement of PDGFRA, PDGFRB or FGFR1, or with PCM1-JAK2, and myelodysplastic/myeloproliferative neoplasms (MDS/MPN). This review focuses on morphological, immunophenotypical and molecular features of BCR-ABL1-negative MPN and their differential diagnoses. Furthermore, areas of difficulties and open questions in their classification are addressed, and the persistent role of morphology in the area of molecular medicine is discussed.
Titin N2A Domain and Its Interactions at the Sarcomere

Titin is a giant protein in the sarcomere that plays an essential role in muscle contraction with actin and myosin filaments. However, its utility goes beyond mechanical functions, extending to versatile and complex roles in sarcomere organization and maintenance, passive force, mechanosensing, and signaling. Titin’s multiple functions are in part attributed to its large size and modular structures that interact with a myriad of protein partners. Among titin’s domains, the N2A element is one of titin’s unique segments that contributes to titin’s functions in compliance, contraction, structural stability, and signaling via protein–protein interactions with actin filament, chaperones, stress-sensing proteins, and proteases. Considering the significance of N2A, this review highlights structural conformations of N2A, its predisposition for protein–protein interactions, and its multiple interacting protein partners that allow the modulation of titin’s biological effects. Lastly, the nature of N2A for interactions with chaperones and proteases is included, presenting it as an important node that impacts titin’s structural and functional integrity.
Assessment of Metal Concentrations and Associations with Pulmonary Function among Children with Asthma in Chicago, Illinois

Individuals living in areas with the potential for elevated metal exposure from industrial sources may have reduced pulmonary function. We evaluated cross-sectional associations of toenail concentrations of 17 metals within a community area of residence and asthma control in 75 children, and pulmonary function measures [forced expiratory volume in one second (FEV1; liters), forced vital capacity (FVC; liters), FEV1 to FVC ratio (FEV1:FVC), and mid-exhalation forced expiratory flow rate (FEF 25–75%; liters/second)], in a subsample of 39 children with diagnosed asthma in Chicago, Illinois. Linear regression models were used to estimate adjusted regression coefficients and standard errors (SE) for the associations between ≥ median versus <median metal exposures and natural log-transformed (ln) pulmonary function test parameters. Toenail levels of cadmium, cobalt, iron, manganese, and vanadium were higher among children residing near an industrial corridor than those in a comparison community. Copper concentrations were inversely associated with lnFEV1 (β = −0.10, SE = 0.04, p = 0.01), lnFEV1:FVC (β = −0.07, SE = 0.03, p = 0.02) and lnFEF 25–75% (β = −0.25, SE = 0.09, p = 0.01); manganese concentrations were inversely associated with lnFEV1 (β = −0.11, SE = 0.04, p = 0.01), lnFEV1:FVC (β = −0.07, SE = 0.03, p = 0.02), and lnFEF 25–75% (β = −0.28, SE = 0.10, p = 0.004), and vanadium concentrations were inversely associated with lnFEV1 (β = −0.08, SE = 0.04, p = 0.05) and lnFVC (β = −0.07, SE = 0.03, p = 0.03). Nickel and copper were associated with uncontrolled asthma (OR = 6.8; 95% CI 2.0, 22.8 and OR = 4.6; 95% CI 1.0, 21.0, respectively). These data suggest that selected metal exposures may be associated with impaired pulmonary function parameters and reduced asthma control among children with preexisting asthma.