Unrepaired base excision repair intermediates in template DNA strands trigger replication fork collapse and PARP inhibitor sensitivity.

DNA single-strand breaks (SSBs) disrupt DNA replication and induce chromosome breakage. However, whether SSBs induce chromosome breakage when present behind replication forks or ahead of replication forks is unclear. To address this question, we exploited an exquisite sensitivity of SSB repair-defective human cells lacking PARP activity or XRCC1 to the thymidine analogue 5-chloro-2'-deoxyuridine (CldU). We show that incubation with CldU in these cells results in chromosome breakage, sister chromatid exchange, and cytotoxicity by a mechanism that depends on the S phase activity of uracil DNA glycosylase (UNG). Importantly, we show that CldU incorporation in one cell cycle is cytotoxic only during the following cell cycle, when it is present in template DNA. In agreement with this, while UNG induces SSBs both in nascent strands behind replication forks and in template strands ahead of replication forks, only the latter trigger fork collapse and chromosome breakage. Finally, we show that BRCA-defective cells are hypersensitive to CldU, either alone and/or in combination with PARP inhibitor, suggesting that CldU may have clinical utility.

The NEOLETRIB trial: neoadjuvant treatment with Letrozole and Ribociclib in ER-positive, HER2-negative breast cancer.

Chemotherapy is used as neoadjuvant therapy for all subgroups of breast cancer, including ER-positive, and HER2-negative cases. However, studies have suggested that using aromatase inhibitors combined with CDK4/6-inhibitors might be an appropriate alternative in selected patients. Thus, the NEOLETRIB trial evaluates the response of ER-positive, HER2-negative luminal A/B breast cancer to the combination of letrozole and ribociclib in the neoadjuvant setting. Comprehensive molecular biology procedures, including sequential single-cell RNA-sequencing of tumor biopsies, are performed during 6 months of treatment with extensive biobanking of blood samples, tumor biopsies and gut microbiome specimens. Our findings will hopefully contribute to an improved selection of patients who may benefit from this drug combination and give new insights into the intra-tumoral changes during this treatment.Trial registration number: NCT05163106 (ClinicalTrials.gov).

[Box: see text].

Predictors of non-home discharge after pancreatoduodenectomy in patients aged 80 years and above.

BACKGROUND: Pancreatic cancer has the highest growth in incidence among patients aged ≥80 years. Discharge destination after hospitalization is increasingly recognized as a marker of return to baseline functional status. Our aim was to identify the preoperative and intraoperative predictors of non-home discharge in those aged 80 or older. METHODS: The ACS-NSQIP pancreas-targeted database was queried to identify patients aged ≥80 years who underwent pancreatoduodenectomy (PD) from 2014 to 2020. Home discharge (HD) versus non-HD cohorts were compared using univariate logistic regression. Multivariable logistic regression was used to identify predictors of non-HD. RESULTS: Non-HD was over twice as likely to occur in patients aged ≥80 years than in those aged 65-79 years (p < 0.01). Comorbidity factors significantly associated with non-HD in patients aged ≥80 years included COPD, hypertension, HF, lower preoperative albumin, but not obesity. Non-comorbidity factors included older age, female gender, ASA III-IV, preoperative dependent functional status, and transfer origin before PD. CONCLUSION: Individuals ≥80 years have possibly delayed or lower rate of return to baseline functional status following PD compared to those aged 65-79 years. Predictors of non-HD can be identified to facilitate preoperative counseling and discharge planning, thus enhancing care workflow efficiency.

A trafficome-wide RNAi screen reveals deployment of early and late secretory host proteins and the entire late endo-/lysosomal vesicle fusion machinery by intracellular Salmonella.

The intracellular lifestyle of Salmonella enterica is characterized by the formation of a replication-permissive membrane-bound niche, the Salmonella-containing vacuole (SCV). As a further consequence of the massive remodeling of the host cell endosomal system, intracellular Salmonella establish a unique network of various Salmonella-induced tubules (SIT). The bacterial repertoire of effector proteins required for the establishment for one type of these SIT, the Salmonella-induced filaments (SIF), is rather well-defined. However, the corresponding host cell proteins are still poorly understood. To identify host factors required for the formation of SIF, we performed a sub-genomic RNAi screen. The analyses comprised high-resolution live cell imaging to score effects on SIF induction, dynamics and morphology. The hits of our functional RNAi screen comprise: i) The late endo-/lysosomal SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex, consisting of STX7, STX8, VTI1B, and VAMP7 or VAMP8, which is, in conjunction with RAB7 and the homotypic fusion and protein sorting (HOPS) tethering complex, a complete vesicle fusion machinery. ii) Novel interactions with the early secretory GTPases RAB1A and RAB1B, providing a potential link to coat protein complex I (COPI) vesicles and reinforcing recently identified ties to the endoplasmic reticulum. iii) New connections to the late secretory pathway and/or the recycling endosome via the GTPases RAB3A, RAB8A, and RAB8B and the SNAREs VAMP2, VAMP3, and VAMP4. iv) An unprecedented involvement of clathrin-coated structures. The resulting set of hits allowed us to characterize completely new host factor interactions, and to strengthen observations from several previous studies.

Measuring subjective clustering of verbal information after moderate-severe traumatic brain injury: a preliminary study.

BACKGROUND: There is no agreed upon measure of subjective clustering for clinical use in patients following moderate-severe traumatic brain injury (TBI). OBJECTIVE: This study investigated whether measures of subjective clustering, subjective organization (SO) and adjusted ratio of clustering (ARC), were appropriate for use in patients following moderate-severe TBI. METHODS: Twenty participants with moderate-severe TBI in the chronic stage of recovery and 20 control participants recalled a list of unrelated words over six trials. The authors assessed if the SO and ARC measures could discriminate the groups' ability to subjectively cluster the words. The authors also examined whether the SO and ARC measures correlated with recall and learning rate, and if combining the measures improved the predictive accuracy. RESULTS: Participants with moderate-severe TBI performed significantly worse on the SO measure, but there were no group differences regarding the ARC measure. The SO measure positively correlated with recall, but not learning rate. The ARC measure did not positively correlate with recall or learning rate, and combining the measures did not enhance the predictive accuracy. CONCLUSIONS: The SO measure is likely an appropriate candidate for clinical use. However, there are problems with the ARC measure that limit its use as a clinical tool.

Experience with pharmacy academic programmes and career aspirations of pharmacy students and young pharmacists-an international cross-sectional study.

OBJECTIVES: This study aims to assess pharmacy students and young pharmacists' motives to pursue pharmacy degrees, their overall experiences and satisfaction with their pharmacy academic programmes, and their career aspirations and future plans. METHODS: Between May-2019 and March-2020, a self-administered online questionnaire was distributed via the International Pharmaceutical Students Federation and the Young Pharmacists Group at the International Pharmaceutical Federation. The questionnaire targeted pharmacy students and young pharmacists worldwide. Data were analysed descriptively and inferentially. RESULTS: In total, 1,423 pharmacy students and young pharmacists participated in the study. Almost 70% (993) of respondents reported that pharmacy was their first choice subject for study. Intentions for studying pharmacy were driven by an interest in healthcare, wanting to help people as well as an interest in science. In general, more than 60% of the participants had a satisfactory education experience. However, dissatisfaction was more prevalent among current pharmacy students in comparison to young pharmacists. Out of 1,423 participants, 1,110 (78%) showed a continuing desire to practice pharmacy. Being female and resident of a middle-income country increased the likelihood of being more satisfied with the academic programme. Having pharmacy as the subject first-choice and being generally satisfied with the academic programmes were positively associated with participants' willingness to practice pharmacy. CONCLUSIONS: Our study revealed that the majority of this extensive sample had pharmacy as their profession of choice and wanted to continue to practice in the future. In addition most of the targeted population indicated satisfaction with their pharmacy academic programmes.

Spectrum: fast density-aware spectral clustering for single and multi-omic data.

MOTIVATION: Clustering patient omic data is integral to developing precision medicine because it allows the identification of disease subtypes. A current major challenge is the integration multi-omic data to identify a shared structure and reduce noise. Cluster analysis is also increasingly applied on single-omic data, for example, in single cell RNA-seq analysis for clustering the transcriptomes of individual cells. This technology has clinical implications. Our motivation was therefore to develop a flexible and effective spectral clustering tool for both single and multi-omic data. RESULTS: We present Spectrum, a new spectral clustering method for complex omic data. Spectrum uses a self-tuning density-aware kernel we developed that enhances the similarity between points that share common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to reduce noise and reveal underlying structures. Spectrum contains a new method for finding the optimal number of clusters (K) involving eigenvector distribution analysis. Spectrum can automatically find K for both Gaussian and non-Gaussian structures. We demonstrate across 21 real expression datasets that Spectrum gives improved runtimes and better clustering results relative to other methods. AVAILABILITY AND IMPLEMENTATION: Spectrum is available as an R software package from CRAN https://cran.r-project.org/web/packages/Spectrum/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cognitive differences between adults with traumatic brain injury and specific learning disorder.

Background: Impaired working memory, attention, and processing speed are common in individuals with traumatic brain injury (TBI) and specific learning disorder (SLD). Yet, there is a paucity of research that has examined cognitive differences between these groups.Objective: The current study examined potential group differences between individuals with TBI and SLD on performance-based tests of working memory, attention, and processing speed. Subsequently, the study examined whether just processing speed tests could discriminate persons with TBI versus SLD.Method: The authors analyzed archival data to assess differences between 39 adult participants with moderate-severe TBI versus 57 adult participants with SLD on the Trail Making Test Part A, Trail Making Test Part B, Digit Span test, and Symbol Search test.Results: 95% confidence intervals revealed that participants with TBI performed significantly worse on the Trail Making Test Part A and Symbol Search test. Logistic regression analysis procedures revealed that Trail Making Test Part A was the most sensitive discriminator.Conclusion: Diagnosis of moderate-severe TBI compared to SLD can be determined by poor performance on measures of visual scanning and processing speed. These findings may be used for diagnostic interpretation and treatment planning by clinicians.

Prognostic significance of metabolic tumour volume and maximum standard uptake value of fluor-18-fluorodeoxyglucose positron emission tomography with computed tomography in nasopharyngeal carcinoma.

AIM OF THE STUDY: To evaluate the prognostic role of markers of fluor-18-fluorodeoxyglucose positron emission tomography with computed tomography (18F-FDG-PET-CT), such as maximum standard uptake value (SUVmax) and metabolic tumour volume (MTV) measured at primary and nodal disease, and their clinical significance in terms of predicting treatment outcomes and survival. MATERIAL AND METHODS: Between January 2017 and January 2020, 20 case records of nasopharyngeal carcinoma patients who underwent 18F-FDG-PET-CT as part of staging workup before radiotherapy and as a part of response evaluation after radiotherapy were retrospectively reviewed. RESULTS: At a median follow-up of 34.7 months, the 2-year progression-free survival (PFS) was 70% and 2-year overall survival (OS) was 79%. Patients with a lower nodal SUVmax (SUVmax-N) had a better 2-year PFS (91% vs. 46%; p = 0.035) and 2-year OS (95% vs. 58%; p = 0.015). A high SUVmax-N of > 10.58 was a negative predictor of OS (95% confidence interval [CI]: 0.93-1; p = 0.003) as well as PFS (95% CI: 0.64-1; p = 0.017). Also, a high MTV > 25.8 cm3 was a negative predictor of PFS (95% CI: 0.58-0.98; p = 0.048). MTV was an independent predictor of PFS and OS on univariate analysis, whereas it was not significant in the Cox regression multivariate analysis. CONCLUSIONS: High values of MTV and SUVmax-N can be considered as independent prognostic factors of OS and PFS in nasopharyngeal cancer patients treated with concurrent chemoradiation, highlighting the need for more intensified treatment.

Production of a NiO/Al primary battery employing powder-based electrodes.

This paper describes the use of aluminum and zinc as anodic materials for a battery employing nickel (II) oxide (NiO) as cathode. Comparison of both materials resulted in the development of a compact, cost effective, and easy to use primary NiO/Al battery employing an alkaline electrolyte. The system features electrodes composed of powder forms of the active materials on modified paper substrates that are contained in a simple multilayer design utilizing thin laminated plastic materials to provide structure and flexibility to the battery as well as a paper separator. Various concentrations of potassium hydroxide (KOH) electrolyte were examined and maximum performance was observed at 6 M KOH. A maximum current density and power density of 1.94 mA/cm2 and 1 mW/cm2 , respectively was achieved. This user-friendly device was able to produce a maximum capacity of 2.33 mAh/g when 2 mA/g was applied. This work demonstrates the viability of a paper-based battery featuring powder electrodes as a possible power source for microelectronic devices.

Correction to: Detection of Fusobacterium nucleatum in stool and colonic tissues from Norwegian colorectal cancer patients.

Two affiliations of author John Christopher Noone were not included in the original article and have been added here. Also, Acknowledgments of the originally published article is not complete. Please see the corrected section below.

Defense Mechanisms, Gender, and Adaptiveness in Emerging Personality Disorders in Adolescent Outpatients.

The present study focused on demographic and personality differences in the use of 30 defense mechanisms in adolescents with personality psychopathology and explored the hierarchical organization of personality traits based on the adaptiveness of defensive functioning. A total of 102 self-referred adolescent outpatients were interviewed and assessed on defense mechanisms and personality traits using the Defense Mechanisms Rating Scales and the Shedler-Westen Assessment Procedure 200 for Adolescents, respectively. Age and gender differences were found throughout the hierarchy. Pearson's correlations revealed a hierarchical organization of emerging personality disorders (PDs) in adolescence. More adaptive defenses were clearly associated with healthier personality style, whereas more pathological personality styles such as those with borderline traits were characterized by more rigid and maladaptive defenses. Dissociation was also associated with maladaptive personality types. Identifying the defenses associated with emerging personality disorders may inform the unconscious function of defense mechanisms in specific PDs. The systematic assessment of defense mechanisms might also help therapists to monitor changes during treatment.

Organization and recall of visual information after traumatic brain injury.

BACKGROUND: Subjective organization (SO) is the ability to structure information to help facilitate storage and retrieval. There is a paucity of research concerning how a person subjectively organizes visual information. OBJECTIVES: This study investigates whether traumatic brain injury (TBI) hinders the ability to subjectively organize and recall visual symbols. The authors use an Association Rule Modeling (ARM) procedure to measure SO and explore whether the complexity of the rules generated from the ARM predicted recall of symbols. METHOD: Twenty-two collegiate athletes with self-reported, repetitive, mild TBI and 22 college students without TBI participated. All participants completed a list learning task that assessed their free recall of unfamiliar symbols. ARM revealed the associative structure among the symbols in the list for each participant. RESULTS: Results showed that collegiate athletes with repetitive, mild TBI develop significantly fewer association rules for visual stimuli compared to college students without TBI. Furthermore, collegiate athletes with TBI produce fewer complex SO rules for the visual stimuli relative to college students without TBI. CONCLUSION: Brain injury diminishes a person's ability to subjectively organize novel visual information. ARM is a sensitive clinical measure of SO for patients with TBI.

Structural Origin of the Large Redox-Linked Reorganization in the 2-Oxoglutarate Dependent Oxygenase, TauD.

2-Oxoglutarate (2OG)-dependent oxygenases catalyze a wide range of chemical transformations via C-H bond activation. Prior studies raised the question of whether substrate hydroxylation by these enzymes occurs via a hydroxyl rebound or alkoxide mechanism and highlighted the need to understand the thermodynamic properties of transient intermediates. A recent spectroelectrochemical investigation of the 2OG-dependent oxygenase, taurine hydroxylase (TauD), revealed a strong link between the redox potential of the Fe(II)/Fe(III) couple and conformational changes of the enzyme. In this study, we show that the redox potential of wild-type TauD varies by 468 mV between the reduction of 2OG-Fe(III)-TauD (-272 mV) and oxidation of 2OG-Fe(II)-TauD (+196 mV). We use active site variants to investigate the structural origin of the redox-linked reorganization and the contributions of the metal-bound residues to the dynamic tuning of the redox potential of TauD. Time-dependent redox titrations show that reorganization occurs as a multistep process. Transient optical absorption and infrared spectroelectrochemistry show that substitution of any metal ligand alters the kinetics and thermodynamics of the reorganization. The H99A variant shows the largest net redox change relative to the wild-type protein, suggesting that redox-coupled protonation of H99 is required for high redox potentials of the metal. The D101Q and H255Q variants also suppress the conformational change, supporting their involvement in the structural rearrangement. Similar redox-linked conformational changes are observed in another 2OG dependent oxygenase, ethylene-forming enzyme, indicating that dynamic structural flexibility and the associated thermodynamic tuning may be a common phenomenon in this family of enzymes.

Fourier Transform Infrared Spectrovoltammetry and Quantitative Modeling of Analytes in Kinetically Constrained Redox Mixtures.

Redox-active analytes that do not support direct electron transfer on the electrode, such as proteins with buried redox centers, pose challenges to characterization of their structural and thermodynamic properties. Investigations of indirect transitions in analytes supported by complex redox mixtures require a careful balance between kinetic limitations and spectral interference from the mediators. Using methylene green and thionine acetate as redox mediators and myoglobin as the analyte, we demonstrate that normal pulse spectrovoltammetry (NPSV) with Fourier transform infrared (FT-IR) detection and subsequent global spectral regression analysis can resolve structural and thermodynamic properties simultaneously with little a priori information. Both the E1/2 and unbiased redox difference FT-IR spectra of the Fe(II)/Fe(III) redox couple of myoglobin in reduction and oxidation NPSV modes were in good agreement with those reported earlier by independent techniques. The thermodynamic and kinetic limitations of mediators/analyte interactions were investigated using comprehensive semiempirical kinetic simulation models. This modeling effort yielded a flexible computational tool capable of quantitatively predicting the redox response in mediated electrochemical studies and defining its limitations, thus greatly expanding the range and precision of the formal mediator/analyte concentration ratio rule.

Detecting and Quantifying Microscale Chemical Reactions in Pharmaceutical Tablets by Stimulated Raman Scattering Microscopy.

It has been estimated that approximately 50% of all marketed drug molecules are manufactured and administered in the form of salts, often with the goal of improving solubility, dissolution rate, and efficacy of the drug. However, salt disproportionation during processing or storage is a common adverse effect in these formulations. Due to the heterogeneous nature of solid drug formulations, it is essential to characterize the drug substances noninvasively at micrometer resolution to understand the molecular mechanism of salt disproportionation. However, there is a lack of such capability with current characterization methods. In this study, we demonstrate that stimulated Raman scattering (SRS) microscopy can be used to provide sensitive and quantitative chemical imaging of the salt disproportionation reaction of pioglitazone hydrochloride (PIO-HCl) at a very low drug loading (1% w/w). Our findings illuminate a water mediated pathway of drug disproportionation and highlight the importance of noninvasive chemical imaging in a mechanistic study of solid-state chemical reactions.

Extracellular traps and PAD4 released by macrophages induce citrullination and auto-antibody production in autoimmune arthritis.

The mechanisms underlying the transition of rheumatoid arthritis (RA) systemic autoimmunity to the joints remain largely unknown. Here, we demonstrate that macrophages in the secondary lymphoid organs (SLOs) and synovial ectopic lymphoid-like structures (ELSs) express peptidylarginine deiminase 4 (PAD4) in murine collagen induced arthritis (CIA) and synovial biopsies from RA patients. Moreover, peptidyl citrulline colocalized with macrophages in SLOs and ELSs, and depletion of macrophages in CIA decreased lymphoid tissue citrullination and serum anti-citrullinated protein/peptide antibody (ACPA) levels. Furthermore, PAD was released from activated murine and RA synovial tissue and fluid (SF) macrophages which functionally deiminated extracellular proteins/peptides in vitro. Additionally, activated murine and SF macrophages displayed macrophage extracellular trap formation (METosis) and release of intracellular citrullinated histones. Moreover, presentation of citrullinated proteins induced ACPA production in vitro. Thus, lymphoid tissue macrophages contribute to self-antigen citrullination and ACPA production, indicating that their selective targeting would potentially ameliorate citrullination-dependent autoimmune disorders.

Detection of Fusobacterium nucleatum in stool and colonic tissues from Norwegian colorectal cancer patients.

Norway has one of the world's highest incidences of colorectal cancer (CRC). Accumulating research suggests that the intestinal microbiota may have an important role in initiation and progression of colorectal cancer. In order to evaluate microbiome-based biomarkers for non-invasive detection of CRC, the levels of Fusobacterium nucleatum and selected Escherichia coli toxin genes in stool and mucosa from a small cohort of Norwegian patients were investigated. The study cohort included 72 patients scheduled for colonoscopy. The patients were divided into three groups upon their examinations: cancer, polyp, and control groups. Levels of F. nucleatum in stool samples were significantly higher in the cancer group compared with the control group and the polyp group. High levels of F. nucleatum in stool reflected detection of F. nucleatum in the tumor tissues of colorectal cancer patients. However, no difference in the levels of E. coli toxin genes in neither stool nor biopsy samples between the patient groups was observed. This study suggests that a quantitative PCR assay targeting F. nucleatum in stool samples has the potential to be included in a larger panel of biomarkers for non-invasive testing for colorectal cancer.

Impact of confrontations by therapists on impairment and utilization of the therapeutic alliance.

OBJECTIVE: Striking the balance between creating challenge through confrontation (drawing attention to discrepancies) to encourage change and offering support through the therapeutic relationship to ensure safety for patients represents a central issue for psychotherapists. The aim of the present study was to assess immediate effects of confrontations by therapists on the therapeutic alliance. METHOD: We rated video recordings of 77 therapies to measure incidences of alliance ruptures/resolution attempts as well as confrontations by therapists. Change in the therapeutic alliance and therapy outcome were measured through questionnaires filled out by patients. RESULTS: Confrontations were significantly associated with ruptures/resolution attempts on the micro level. Changes in the therapeutic alliance moderated the association between confrontations and alliance ruptures on the macro level: The bigger the fraction of a session containing confrontations, the larger the fraction containing ruptures, given a prior positive change in the therapeutic alliance. Therapists' use of confrontation during a resolution attempt was associated with significantly better therapy outcomes than no use of confrontation during or no resolution attempt. CONCLUSIONS: Confrontations by therapists may temporarily impair the therapeutic alliance, but might also lead to better therapy outcomes when used to make an alliance rupture explicit as part of a resolution attempt. Clinical or methodological significance: This study provides quantitative explorations of therapists' fears and hopes regarding the use of confrontations (defined as focus on a discrepancy by the therapist). Results point to associations between confrontations and alliance ruptures, especially in the context of a secure alliance. Furthermore, resolution attempts might profit from initial confrontations regarding the relevant alliance rupture.

Somatic EP300-G211S mutations are associated with overall somatic mutational patterns and breast cancer specific survival in triple-negative breast cancer.

PURPOSE: We have compared the mutational profiles of human breast cancer tumor samples belonging to all major subgroups with special emphasis on triple-negative breast cancer (TNBC). Our major goal was to identify specific mutations that could be potentially used for clinical decision making in TNBC patients. PATIENTS AND METHODS: Primary tumor specimens from 149 Norwegian breast cancer patients were available. We analyzed the tissue samples for somatic mutations in 44 relevant breast cancer genes by targeted next-generation sequencing. As a second confirmatory technique, we performed pyrosequencing on selected samples. RESULTS: We observed a distinct subgroup of TNBC patients, characterized by an almost completely lack of pathogenic somatic mutations. A point mutation in the adenoviral E1A binding protein p300 (EP300-G211S) was significantly correlated to this TNBC subgroup. The EP300-G211S mutation was exclusively found in the TNBC patients and its presence reduced the chance for other pathological somatic mutations in typical breast cancer genes investigated in our gene panel by 94.9% (P < 0.005). Interestingly, the EP300-G211S mutation also predicted a lower risk for relapses and decreased breast cancer-specific mortality during long-term follow-up of the patients. CONCLUSION: Next-generation sequencing revealed specific mutations in EP300 to be associated with the mutational patterns in typical breast cancer genes and long-term outcome of triple-negative breast cancer patients.