Attentional enhancement predicts individual differences in visual working memory under go/no-go search conditions.

Attention-control processes transfer relevant information to visual working memory (WM) and prevent irrelevant information from consuming WM resources. Although event-related potentials (ERPs) have revealed attention-control processes associated with enhancement of relevant stimuli (targets) and suppression of irrelevant stimuli (distractors), only the suppressive processes have been found to predict WM capacity. We hypothesised a link between target-enhancement processes and WM capacity would be revealed in a task that requires more control than the conventional visual search paradigms used to study target selection. Here, participants searched for a pop-out target on Go trials and withheld responses on an equal number of randomly intermixed No-Go trials, depending on the colour of the stimulus array. Magnitudes of ERP indices associated with target enhancement (the singleton detection positivity, SDP, and N2pc) were positively correlated with individual differences in WM capacity. These relationships vanished when participants searched for the pop-out target on every trial, regardless of stimulus-array colour. Inhibitory processes associated with suppressing distractors (PD) and withholding responses (no-go P3) on No-Go trials did not predict WM capacity. These findings indicate that target-enhancement mechanisms control access to WM in search tasks that require dynamic control and disconfirm the view that the gateway to WM is entirely inhibitory by nature.

Population genomic structure of a widespread, urban-dwelling mammal: The eastern grey squirrel (Sciurus carolinensis).

Urbanization is a persistent and widespread driver of global environmental change, potentially shaping evolutionary processes due to genetic drift and reduced gene flow in cities induced by habitat fragmentation and small population sizes. We tested this prediction for the eastern grey squirrel (Sciurus carolinensis), a common and conspicuous forest-dwelling rodent, by obtaining 44K SNPs using reduced representation sequencing (ddRAD) for 403 individuals sampled across the species' native range in eastern North America. We observed moderate levels of genetic diversity, low levels of inbreeding, and only a modest signal of isolation-by-distance. Clustering and migration analyses show that estimated levels of migration and genetic connectivity were higher than expected across cities and forested areas, specifically within the eastern portion of the species' range dominated by urbanization, and genetic connectivity was less than expected within the western range where the landscape is fragmented by agriculture. Landscape genetic methods revealed greater gene flow among individual squirrels in forested regions, which likely provide abundant food and shelter for squirrels. Although gene flow appears to be higher in areas with more tree cover, only slight discontinuities in gene flow suggest eastern grey squirrels have maintained connected populations across urban areas in all but the most heavily fragmented agricultural landscapes. Our results suggest urbanization shapes biological evolution in wildlife species depending strongly on the composition and habitability of the landscape matrix surrounding urban areas.

A personalized probabilistic approach to ovarian cancer diagnostics.

OBJECTIVE: The identification/development of a machine learning-based classifier that utilizes metabolic profiles of serum samples to accurately identify individuals with ovarian cancer. METHODS: Serum samples collected from 431 ovarian cancer patients and 133 normal women at four geographic locations were analyzed by mass spectrometry. Reliable metabolites were identified using recursive feature elimination coupled with repeated cross-validation and used to develop a consensus classifier able to distinguish cancer from non-cancer. The probabilities assigned to individuals by the model were used to create a clinical tool that assigns a likelihood that an individual patient sample is cancer or normal. RESULTS: Our consensus classification model is able to distinguish cancer from control samples with 93% accuracy. The frequency distribution of individual patient scores was used to develop a clinical tool that assigns a likelihood that an individual patient does or does not have cancer. CONCLUSIONS: An integrative approach using metabolomic profiles and machine learning-based classifiers has been employed to develop a clinical tool that assigns a probability that an individual patient does or does not have ovarian cancer. This personalized/probabilistic approach to cancer diagnostics is more clinically informative and accurate than traditional binary (yes/no) tests and represents a promising new direction in the early detection of ovarian cancer.

Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase.

Homologs of the mutagenic Escherichia coli DNA polymerase V (pol V) are encoded by numerous pathogens and mobile elements. We have used Rum pol (RumA'2B), from the integrative conjugative element (ICE), R391, as a model mobile element-encoded polymerase (MEPol). The highly mutagenic Rum pol is transferred horizontally into a variety of recipient cells, including many pathogens. Moving between species, it is unclear if Rum pol can function on its own or requires activation by host factors. Here, we show that Rum pol biochemical activity requires the formation of a physical mutasomal complex, Rum Mut, containing RumA'2B-RecA-ATP, with RecA being donated by each recipient bacteria. For R391, Rum Mut specific activities in vitro and mutagenesis rates in vivo depend on the phylogenetic distance of host-cell RecA from E. coli RecA. Rum pol is a highly conserved and effective mobile catalyst of rapid evolution, with the potential to generate a broad mutational landscape that could serve to ensure bacterial adaptation in antibiotic-rich environments leading to the establishment of antibiotic resistance.

The efficacy and safety of tranexamic acid utilization in total ankle arthroplasty: a systematic review and meta-analysis.

INTRODUCTION: There is still a lack of information on the role of Tranexamic acid (TXA) in total ankle arthroplasty (TAA). The purpose of this study is to comprehensively review, consolidate, and analyze findings from existing research on the effectiveness and safety of TXA in TAA. MATERIALS AND METHODS: The comprehensive literature review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) using PubMed, Embase, Web of Science, and Cochrane databases, for original, English-language studies investigating the efficacy and safety of TXA in TAA, through February 2023. Evaluated data for the meta-analysis included estimated blood loss (EBL), change in perioperative hemoglobin, need for transfusion, and complications including DVT/PE, and wound complications. RESULTS: A total of nine studies were included in this study. In total, 450 TAA were included, with 244 receiving TXA (54.2%) and 206 not receiving TXA (45.8%). TXA in TAA significantly decreased EBL. A significantly lower rate of wound complications in the TXA group with the relative risk (RR) of 0.51. We classified wound complications into wound infection and delayed wound healing/dehiscence. A significant decrease in the rate of wound infection and a tendency showing a decrease in the rate of delayed wound healing/dehiscence in the TXA group were noted: the RR of 0.29, and 0.63, respectively. TXA did not increase the incidence of DVT/PE following TAA. CONCLUSIONS: In conclusion, the utilization of TXA during TAA demonstrated a statistically significant reduction in EBL and relative risk for wound complications. However, further RCTs with larger sample sizes will be necessary to establish a more robust conclusion regarding the efficacy and safety of TXA in TAA. LEVEL OF EVIDENCE: Level III, systematic review and meta-analysis.

The comparison of postoperative outcomes in Morton's neuroma excision between plantar versus dorsal approach: A systematic review and meta-analysis.

BACKGROUND: Current literature lacks comprehensive information comparing the clinical outcomes of plantar and dorsal approaches for Civinini-Morton syndrome, also known as Morton's neuroma. This systematic review and meta-analysis was conducted to evaluate and compare the clinical outcomes of neurectomy for Morton's neuroma, focusing on the differences between the plantar and dorsal approach. METHODS: Our comprehensive literature review adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and utilized databases including PubMed, Embase, Web of Science, and the Cochrane Library. Data investigated in this study included postoperative sensory loss, scar tenderness, reoperation, histopathology, complications, pain score, patient satisfaction, functional scores, and time to weight bearing. RESULTS: Total eight studies were included in this study. In aggregate, 237 neuromas underwent excision using the plantar approach, while 312 neuromas were treated via the dorsal approach. A significantly higher rate of postoperative reduced sensory was found in the dorsal group: 48.5 % (64/132) Vs. 62.0 % (80/129) with the relative ratio (RR) of 0.79 (95 % CI, 0.64-0.97). A significantly higher rate of postoperative scar tenderness was noted in the plantar group: 16.7 % (32/192) Vs. 6.2 % (14/225) with the RR of 2.27 (95 % CI, 1.28-4.04). Regarding the histopathology, 99.3 % (143/144) and 97.1 % (134/138) accuracy rate was confirmed in the plantar approach and dorsal approach, respectively, with the RR of 1.02 (95 % CI, 0.98-1.07). Overall reoperations and complications were not different between groups at 5.3 % (10/189) and 8.8 % (19/216) in the plantar group versus 6.1 % and 12.0 % (35/291) in dorsal group. CONCLUSIONS: We recommend detailed discussions with patients prior to surgery to weigh the advantages and disadvantages of each approach.

Isolating the Neural Substrates of Visually Guided Attention Orienting in Humans.

The neural processes that enable healthy humans to orient attention to sudden visual events are poorly understood because they are tightly intertwined with purely sensory processes. Here we isolated visually guided orienting activity from sensory activity using event-related potentials (ERPs). By recording ERPs to a lateral stimulus and comparing waveforms obtained under conditions of attention and inattention, we identified an early positive deflection over the ipsilateral visual cortex that was associated with the covert orienting of visual attention to the stimulus. Across five experiments with male and female adult participants, this ipsilateral visual orienting activity (VOA) could be distinguished from purely sensory-evoked activity and from other top-down spatial attention effects. The VOA was linked with behavioral measures of orienting, being significantly larger when the stimulus was detected rapidly than when it was detected more slowly, and its presence was independent of saccadic eye movements toward the targets. The VOA appears to be a specific neural index of the visually guided orienting of attention to a stimulus that appears abruptly in an otherwise uncluttered visual field.SIGNIFICANCE STATEMENT The study of visual attention orienting has been an important impetus for the field of cognitive neuroscience. Seminal reaction-time studies demonstrated that a suddenly appearing visual stimulus attracts attention involuntarily, but the neural processes associated with visually guided attention orienting have been difficult to isolate because they are intertwined with sensory processes that trigger the orienting. Here, we disentangled orienting activity from sensory activity using scalp recordings of event-related electrical activity in the human brain. A specific neural index of visually guided attention orienting was identified. Surprisingly, whereas peripheral sensory stimulation is processed initially and predominantly by the contralateral visual cortex, this electrophysiological index of visual orienting was recorded over the cerebral hemisphere that was ipsilateral to the attention-capturing stimulus.

Standardizing Scoring Conventions for Crohn's Disease Endoscopy: An International RAND/UCLA Appropriateness Study.

BACKGROUND AND AIMS: Endoscopic assessment of disease activity is integral for evaluating treatment response in patients with Crohn's disease (CD). We aimed to define appropriate items for evaluating endoscopic activity and conventions for consistent endoscopic scoring rules in CD. METHODS: A 2-round modified RAND/University of California at Los Angeles Appropriateness Method study was conducted. A panel of 15 gastroenterologists used a 9-point Likert scale to rate the appropriateness of statements pertaining to the Simple Endoscopic Score for CD, Crohn's Disease Endoscopic Index of Severity, and additional items relevant to endoscopy scoring in CD. Each statement was voted as appropriate, uncertain, or inappropriate based on the median panel rating and presence of disagreement. RESULTS: Panelists voted that it is appropriate for all ulcers to contribute to endoscopic scoring in CD, including aphthous ulcers, ulcerations at a surgical anastomosis, and anal canal ulcers (scored in the rectum). Endoscopic healing should reflect an absence of ulcers. Narrowing should be defined as a clear decrease in luminal diameter; stenosis should be defined by an impassable narrowing, and if occurring at the junction of 2 segments, scored in the distal segment. Scarring and inflammatory polyps were considered inappropriate for including in the affected area score. The optimal method for defining ulcer depth remains uncertain. CONCLUSIONS: We outlined scoring conventions for the Simple Endoscopic Score for CD and Crohn's Disease Endoscopic Index of Severity, noting that both scores have limitations. Therefore, we identified priorities for future research and steps for developing and validating a more representative endoscopic index in CD.

Existing Bowel Preparation Quality Scales Are Reliable in the Setting of Centralized Endoscopy Reading.

BACKGROUND: Development of bowel preparation products has been based upon colon cleansing rating by a local endoscopist. It is unclear how bowel preparation scales perform when centrally evaluated. AIMS: To evaluate the reliability of bowel preparation quality scales when assessed by central readers. METHODS: Four central readers evaluated 52 videos in triplicate, 2 weeks apart, during the entire endoscopic procedure (insertion/withdrawal of the colonoscope) and exclusively on colonoscope withdrawal using the Boston Bowel Preparation Scale (BBPS), Chicago Bowel Preparation scale, Harefield Cleansing Scale, Ottawa Bowel Preparation Quality Scale (OBPQS), Aronchick score, a visual analogue scale, and additional items proposed in a modified Research and Development/University of California Los Angeles appropriateness process. Reliability was assessed with intraclass correlation coefficients. RESULTS: Intraclass correlation coefficients (95% confidence interval) for inter-rater reliability of the quality scales ranged from 0.51 to 0.65 (consistent with moderate to substantial inter-rater reliability) during the entire procedure. Corresponding intraclass correlation coefficients for intra-rater reliability ranged from 0.69 to 0.77 (consistent with substantial intra-rater reliability). Reliability was highest in the right colon and lowest in the left colon. No differences were observed in reliability when assessed for the procedure overall (insertion/withdrawal) relative to assessment on withdrawal alone. CONCLUSION: All five bowel preparation quality scales had moderate to substantial inter-rater reliability. Panelists considered the Aronchick score too simplistic for clinical trials and recognized that assessment of residual fluid in the Ottawa Bowel Preparation Quality Scale was not amenable to central assessment.

The Clinical Significance of Genetic Variation in Ovarian Cancer.

Genetic variation is a well-known contributor to the onset and progression of cancer. The goal of this study is to provide a comprehensive examination of the nucleotide and chromosomal variation associated with the onset and progression of serous ovarian cancer. Using a variety of computational and statistical methods, we examine the exome sequence profiles of genetic variants present in the primary tumors of 432 ovarian cancer patient samples to compute: (1) the tumor mutational burden for all genes and (2) the chromosomal copy number alterations associated with the onset/progression of ovarian cancer. Tumor mutational burden is reduced in the late vs. early stages, with the highest levels being associated with loss-of-function mutations in DNA-repair genes. Nucleotide variation and copy number alterations associated with known cancer driver genes are selectively favored over ovarian cancer development. The results indicate that genetic variation is a significant contributor to the onset and progression of ovarian cancer. The measurement of the relative levels of genetic variation associated with individual ovarian cancer patient tumors may be a clinically valuable predictor of potential tumor aggressiveness and resistance to chemotherapy. Tumors found to be associated with high levels of genetic variation may help in the clinical identification of high-risk ovarian cancer patients who could benefit from more frequent monitoring.

Searching for Visual Singletons Without A Feature to Guide Attention.

RT studies have provided evidence for a singleton-detection strategy that is used to search for salient targets when there is no additional featural knowledge that would help guide attention. Despite this behavioral evidence, there have been few ERP studies of singleton detection mode because it was reported early on that the ERP signature of attentional selection (the N2pc) is absent without feature guidance. Recently, however, it was discovered that a small and relatively late N2pc occurs in singleton detection mode along with a previously unreported component called the singleton detection positivity (SDP). Here, we show that both components are influenced by the number of items in the display, as one might expect in a salience-based search mode. Specifically, the N2pc and SDP were larger when the set size was increased to make the singleton "pop out" more easily, when participants responded more quickly regardless of set size, and when RT search slopes were negative (Experiment 1). The latency of the SDP also depended on set size. In Experiment 2, EEG was recorded with a higher density electrode array to better characterize the scalp topography of the components and to estimate their neural sources. Regional sources near the ventral surface of extrastriate cortex in the occipital lobe explained over 96% of N2pc and SDP activities. These results indicate that searching in singleton detection mode selectively modulates processing within perceptual regions of visual cortex.

Diversion of Attention Leads to Conflict between Concurrently Attended Stimuli, Not Delayed Orienting to the Object of Interest.

The control processes that guide attention to a visual-search target can result in the selection of an irrelevant object with similar features (a distractor). Once attention is captured by such a distractor, search for a subsequent target is momentarily impaired if the two stimuli appear at different locations. The textbook explanation for this impairment is based on the notion of an indivisible focus of attention that moves to the distractor, illuminates a nontarget that subsequently appears at that location, and then moves to the target once the nontarget is rejected. Here, we show that such delayed orienting to the target does not underlie the behavioral cost of distraction. Observers identified a color-defined target appearing within the second of two stimulus arrays. The first array contained irrelevant items, including one that shared the target's color. ERPs were examined to test two predictions stemming from the textbook serial-orienting hypothesis. Namely, when the target and distractor appear at different locations, (1) the target should elicit delayed selection activity relative to same-location trials, and (2) the nontarget search item appearing at the distractor location should elicit selection activity that precedes selection activity tied to the target. Here, the posterior contralateral N2 component was used to track selection of each of these search-array items and the previous distractor. The results supported neither prediction above, thereby disconfirming the serial-orienting hypothesis. Overall, the results show that the behavioral costs of distraction are caused by perceptual and postperceptual competition between concurrently attended target and nontarget stimuli.

CroSR391 , an ortholog of the λ Cro repressor, plays a major role in suppressing polVR391 -dependent mutagenesis.

When subcloned into low-copy-number expression vectors, rumAB, encoding polVR391 (RumA'2 B), is best characterized as a potent mutator giving rise to high levels of spontaneous mutagenesis in vivo. This is in dramatic contrast to the poorly mutable phenotype when polVR391 is expressed from the native 88.5 kb R391, suggesting that R391 expresses cis-acting factors that suppress the expression and/or the activity of polVR391 . Indeed, we recently discovered that SetRR391 , an ortholog of λ cI repressor, is a transcriptional repressor of rumAB. Here, we report that CroSR391 , an ortholog of λ Cro, also serves as a potent transcriptional repressor of rumAB. Levels of RumA are dependent upon an interplay between SetRR391 and CroSR391 , with the greatest reduction of RumA protein levels observed in the absence of SetRR391 and the presence of CroSR391 . Under these conditions, CroSR391 completely abolishes the high levels of mutagenesis promoted by polVR391 expressed from low-copy-number plasmids. Furthermore, deletion of croSR391 on the native R391 results in a dramatic increase in mutagenesis, indicating that CroSR391 plays a major role in suppressing polVR391 mutagenesis in vivo. Inactivating mutations in CroSR391 therefore have the distinct possibility of increasing cellular mutagenesis that could lead to the evolution of antibiotic resistance of pathogenic bacteria harboring R391.

Novel Escherichia coli active site dnaE alleles with altered base and sugar selectivity.

The Escherichia coli dnaE gene encodes the α-catalytic subunit (pol IIIα) of DNA polymerase III, the cell's main replicase. Like all high-fidelity DNA polymerases, pol III possesses stringent base and sugar discrimination. The latter is mediated by a so-called "steric gate" residue in the active site of the polymerase that physically clashes with the 2'-OH of an incoming ribonucleotide. Our structural modeling data suggest that H760 is the steric gate residue in E.coli pol IIIα. To understand how H760 and the adjacent S759 residue help maintain genome stability, we generated DNA fragments in which the codons for H760 or S759 were systematically changed to the other nineteen naturally occurring amino acids and attempted to clone them into a plasmid expressing pol III core (α-θ-ε subunits). Of the possible 38 mutants, only nine were successfully sub-cloned: three with substitutions at H760 and 6 with substitutions at S759. Three of the plasmid-encoded alleles, S759C, S759N, and S759T, exhibited mild to moderate mutator activity and were moved onto the chromosome for further characterization. These studies revealed altered phenotypes regarding deoxyribonucleotide base selectivity and ribonucleotide discrimination. We believe that these are the first dnaE mutants with such phenotypes to be reported in the literature.

Assessment and management of allergy history with a novel mRNA vaccine.

Context: Tertiary care hospital provided onsite COVID-19 vaccine roll out as a work benefit for all care team members with medically supervised waiting period at the time of the distribution of the first round of the novel mRNA COVID-19 vaccines. Little was known about the immediate hypersensivity reactions or what might predispose to cross reactivity. Objective: We developed a working protocol to continuously track the vaccines administered, the patient history of allergy and hypersensistivity, the reactions observed and the care plan developed (determination of allergy to mRNA vaccines or normal vaccine response). Continuous process improvement allowed us to change protocols as the CDC developed guidance. Every patient was observed for at least 15 minutes and every reaction was reviewed by a physician supervising the waiting area. We aimed to determine if there were predictors of adverse, immediate reaction to the vaccine and to assess prevalence of risk factors (history of allergy to polyethylene Glycol or polysorbate; allergy to other injectable medication or vaccines; hypersensitivity to multiple substances). Study Design: Cohort study of all employees who received a first mRNA COVID-19 vaccine between December 16 and January 7th. Descriptive statistics were developed with demographic and medical history recorded, reactions noted and treatment given. Setting or Dataset: Tertiary care hospital in urban area. Population Studied: Employees who received an mRNA COVID-19 vaccine. Intervention/Instrument: Clinical records from employee vaccine clinic. Outcome Measures: Record of immediate response, determination of allergy. Results: We served over 7000 individuals with approximately 10% having a history of anaphylactic reaction. We had fewer with history of anaphylaxis to medications or vaccines. We delivered these vaccines safely, and observed three cases of immediate anaphylaxis on first dose of mRNA and over 50 cases of immediate allergic hypersensitivity. We did not see any patterns that predicted these reactions (gender, age or medical history). Expected Outcomes: We used this data to inform our employee health vaccination campaign and to inform the health system as strategies and safety protocols for vaccination of the population were developed.

Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair.

Several functions have been proposed for the Escherichia coli DNA polymerase IV (pol IV). Although much research has focused on a potential role for pol IV in assisting pol III replisomes in the bypass of lesions, pol IV is rarely found at the replication fork in vivo. Pol IV is expressed at increased levels in E. coli cells exposed to exogenous DNA damaging agents, including many commonly used antibiotics. Here we present live-cell single-molecule microscopy measurements indicating that double-strand breaks induced by antibiotics strongly stimulate pol IV activity. Exposure to the antibiotics ciprofloxacin and trimethoprim leads to the formation of double strand breaks in E. coli cells. RecA and pol IV foci increase after treatment and exhibit strong colocalization. The induction of the SOS response, the appearance of RecA foci, the appearance of pol IV foci and RecA-pol IV colocalization are all dependent on RecB function. The positioning of pol IV foci likely reflects a physical interaction with the RecA* nucleoprotein filaments that has been detected previously in vitro. Our observations provide an in vivo substantiation of a direct role for pol IV in double strand break repair in cells treated with double strand break-inducing antibiotics.

Synthesis, Biological Activity and Molecular Docking of Chimeric Peptides Targeting Opioid and NOP Receptors.

Recently, mixed opioid/NOP agonists came to the spotlight for their favorable functional profiles and promising outcomes in clinical trials as novel analgesics. This study reports on two novel chimeric peptides incorporating the fragment Tyr-c[D-Lys-Phe-Phe]Asp-NH2 (RP-170), a cyclic peptide with high affinity for µ and κ opioid receptors (or MOP and KOP, respectively), conjugated with the peptide Ac-RYYRIK-NH2, a known ligand of the nociceptin/orphanin FQ receptor (NOP), yielding RP-170-RYYRIK-NH2 (KW-495) and RP-170-Gly3-RYYRIK-NH2 (KW-496). In vitro, the chimeric KW-496 gained affinity for KOP, hence becoming a dual KOP/MOP agonist, while KW-495 behaved as a mixed MOP/NOP agonist with low nM affinity. Hence, KW-495 was selected for further in vivo experiments. Intrathecal administration of this peptide in mice elicited antinociceptive effects in the hot-plate test; this action was sensitive to both the universal opioid receptor antagonist naloxone and the selective NOP antagonist SB-612111. The rotarod test revealed that KW-495 administration did not alter the mice motor coordination performance. Computational studies have been conducted on the two chimeras to investigate the structural determinants at the basis of the experimental activities, including any role of the Gly3 spacer.

DNA polymerase η contributes to genome-wide lagging strand synthesis.

DNA polymerase η (pol η) is best known for its ability to bypass UV-induced thymine-thymine (T-T) dimers and other bulky DNA lesions, but pol η also has other cellular roles. Here, we present evidence that pol η competes with DNA polymerases α and δ for the synthesis of the lagging strand genome-wide, where it also shows a preference for T-T in the DNA template. Moreover, we found that the C-terminus of pol η, which contains a PCNA-Interacting Protein motif is required for pol η to function in lagging strand synthesis. Finally, we provide evidence that a pol η dependent signature is also found to be lagging strand specific in patients with skin cancer. Taken together, these findings provide insight into the physiological role of DNA synthesis by pol η and have implications for our understanding of how our genome is replicated to avoid mutagenesis, genome instability and cancer.

DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli.

In Escherichia coli, damage to the chromosomal DNA induces the SOS response, setting in motion a series of different DNA repair and damage tolerance pathways. DNA polymerase IV (pol IV) is one of three specialised DNA polymerases called into action during the SOS response to help cells tolerate certain types of DNA damage. The canonical view in the field is that pol IV primarily acts at replisomes that have stalled on the damaged DNA template. However, the results of several studies indicate that pol IV also acts on other substrates, including single-stranded DNA gaps left behind replisomes that re-initiate replication downstream of a lesion, stalled transcription complexes and recombination intermediates. In this study, we use single-molecule time-lapse microscopy to directly visualize fluorescently labelled pol IV in live cells. We treat cells with the DNA-damaging antibiotic ciprofloxacin, Methylmethane sulfonate (MMS) or ultraviolet light and measure changes in pol IV concentrations and cellular locations through time. We observe that only 5-10% of foci induced by DNA damage form close to replisomes, suggesting that pol IV predominantly carries out non-replisomal functions. The minority of foci that do form close to replisomes exhibit a broad distribution of colocalisation distances, consistent with a significant proportion of pol IV molecules carrying out postreplicative TLS in gaps behind the replisome. Interestingly, the proportion of pol IV foci that form close to replisomes drops dramatically in the period 90-180 min after treatment, despite pol IV concentrations remaining relatively constant. In an SOS-constitutive mutant that expresses high levels of pol IV, few foci are observed in the absence of damage, indicating that within cells access of pol IV to DNA is dependent on the presence of damage, as opposed to concentration-driven competition for binding sites.

Leveraging TCGA gene expression data to build predictive models for cancer drug response.

BACKGROUND: Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning models using gene expression data from patients' primary tumor tissues to predict whether a patient will respond positively or negatively to two chemotherapeutics: 5-Fluorouracil and Gemcitabine. RESULTS: We focused on 5-Fluorouracil and Gemcitabine because based on our exclusion criteria, they provide the largest numbers of patients within TCGA. Normalized gene expression data were clustered and used as the input features for the study. We used matching clinical trial data to ascertain the response of these patients via multiple classification methods. Multiple clustering and classification methods were compared for prediction accuracy of drug response. Clara and random forest were found to be the best clustering and classification methods, respectively. The results show our models predict with up to 86% accuracy; despite the study's limitation of sample size. We also found the genes most informative for predicting drug response were enriched in well-known cancer signaling pathways and highlighted their potential significance in chemotherapy prognosis. CONCLUSIONS: Primary tumor gene expression is a good predictor of cancer drug response. Investment in larger datasets containing both patient gene expression and drug response is needed to support future work of machine learning models. Ultimately, such predictive models may aid oncologists with making critical treatment decisions.