Liver fibrosis phenotyping and severity scoring by quantitative image analysis of biopsy slides.

BACKGROUND & AIMS: Digital pathology image analysis can phenotype liver fibrosis using histological traits that reflect collagen content, morphometry and architecture. Here, we aimed to calculate fibrosis severity scores to quantify these traits. METHODS: Liver biopsy slides were categorised by Ishak stage and aetiology. We used a digital pathology technique to calculate four fibrosis severity scores: Architecture Composite Score (ACS), Collagen Composite Score (CCS), Morphometric Composite Score (MCS) and Phenotypic Fibrosis Composite Score (PH-FCS). We compared how these scores varied according to disease stage and aetiology. RESULTS: We included 80 patients (40% female, mean age 59.0 years, mean collagen proportionate area 17.1%) with mild (F0-2, n = 28), moderate (F3-4, n = 17) or severe (F5-6, n = 35) fibrosis. All four aetiology independent scores corelated with collagen proportionate area (ACS: rp = .512, CCS: rp = .727, MCS: rp = .777, PFCS: r = .772, p < .01 for all) with significant differences between moderate and severe fibrosis (p < .05). ACS increased primarily between moderate and severe fibrosis (by 95% to 226% depending on underlying aetiology), whereas MCS and CCS accumulation was more varied. We used 28 qFTs that distinguished between autoimmune- and alcohol-related liver disease to generate an MCS that significantly differed between mild and severe fibrosis for these aetiologies (p < .05). CONCLUSIONS: We describe four aetiology-dependent and -independent severity scores that quantify fibrosis architecture, collagen content and fibre morphometry. This approach provides additional insight into how progression of architectural changes and accumulation of collagen may differ depending on underlying disease aetiology.

Prospective Evaluation of Low-Fat Diet Monotherapy in Dogs with Presumptive Protein-Losing Enteropathy.

For dogs with protein-losing enteropathy (PLE) and evidence of lymphangiectasia, the efficacy of low-fat diet as monotherapy or combined with prednisone remains poorly characterized. In this prospective, observational cohort study of 14 dogs with presumptive PLE and ultrasonographic evidence of lymphangiectasia, subjects were placed on various low-fat diets as monotherapy and prednisone was added if response was deemed inadequate. Dogs were assessed and scored at four recheck examinations across a 6 mo study period, including a final recheck ultrasound. Clinical and clinicopathologic variables were collected and dogs were divided into three outcome groups: clinical remission on dietary monotherapy (LOF); clinical remission on dietary therapy plus immunosuppressive prednisone (LOP); and treatment failure (TXF). Eleven of 14 dogs were in clinical remission at the study end date (6 mo after enrollment): 6 LOF dogs and 5 LOP dogs. LOF dogs achieved a significant reduction in Canine Chronic Enteropathy Clinical Activity Index score and a significant increase in serum albumin within 2 wk of beginning dietary monotherapy. Four of 11 dogs in remission also had ultrasonographic evidence of resolution of linear striations. Low-fat diet appears to be an effective monotherapy in some dogs with presumptive PLE and ultrasonographic evidence of lymphangiectasia.

Non-Invasive Ventilation for Community-Acquired Pneumonia: Outcomes and Predictors of Failure from an ICU Cohort.

Background and Objectives: The use of non-invasive ventilation (NIV) for community-acquired pneumonia (CAP) remains controversial. NIV failure in the setting of acute hypoxemic respiratory failure is associated with increased mortality, highlighting the need for careful patient selection. Methods and Methods: This is a retrospective observational cohort study. We included 140 patients with severe CAP, treated with either NIV or invasive mechanical ventilation (IMV) as their primary oxygenation strategy. Results: The median PaO2/FiO2 ratio and SOFA score upon ICU admission were 151 mmHg and 6, respectively. We managed 76% of patients with NIV initially and report an NIV success rate of 59%. Overall, the 28-day mortality was 25%, whilst for patients with NIV success, the mortality was significantly lower at 13%. In the univariate analysis, NIV failure was associated with the SOFA score (OR 1.33), the HACOR score (OR 1.14) and the presence of septic shock (OR 3.99). The SOFA score has an AUC of 0.75 for NIV failure upon ICU admission, whilst HACOR has an AUC of 0.76 after 2 h of NIV. Conclusions: Our results suggest that a SOFA ≤ 4 and an HACOR ≤ 5 are reasonable thresholds to identify patients with severe CAP likely to benefit from NIV.

Homologous recombination repair intermediates promote efficient de novo telomere addition at DNA double-strand breaks.

The healing of broken chromosomes by de novo telomere addition, while a normal developmental process in some organisms, has the potential to cause extensive loss of heterozygosity, genetic disease, or cell death. However, it is unclear how de novo telomere addition (dnTA) is regulated at DNA double-strand breaks (DSBs). Here, using a non-essential minichromosome in fission yeast, we identify roles for the HR factors Rqh1 helicase, in concert with Rad55, in suppressing dnTA at or near a DSB. We find the frequency of dnTA in rqh1Δ rad55Δ cells is reduced following loss of Exo1, Swi5 or Rad51. Strikingly, in the absence of the distal homologous chromosome arm dnTA is further increased, with nearly half of the breaks being healed in rqh1Δ rad55Δ or rqh1Δ exo1Δ cells. These findings provide new insights into the genetic context of highly efficient dnTA within HR intermediates, and how such events are normally suppressed to maintain genome stability.

Perceptions and experiences of medical student first responders: a mixed methods study.

CONTEXT: Medical Student First Responders (MSFRs) are volunteers who respond to emergency calls, managing patients before ambulance staff attend. The MSFR role provides opportunities to manage acutely unwell patients in the prehospital environment, not usually offered as part of formal undergraduate medical education. There are few previous studies describing activities or experiences of MSFRs or exploring the potential educational benefits. We aimed to investigate the activity of MSFRs and explore their experiences, particularly from an educational perspective. METHODS: We used a mixed methods design, combining quantitative analysis of ambulance dispatch data with qualitative semi-structured interviews of MSFRs. Dispatch data were from South Central and East Midlands Ambulance Service NHS Trusts from 1st January to 31st December 2019. Using propensity score matching, we compared incidents attended by MSFRs with those attended by other Community First Responders (CFRs) and ambulance staff. We interviewed MSFRs from five English (UK) medical schools in those regions about their experiences and perceptions and undertook thematic analysis supported by NVivo 12. RESULTS: We included 1,939 patients (median age 58.0 years, 51% female) attended by MSFRs. Incidents attended were more urgent category calls (category 1 n = 299, 14.9% and category 2 n = 1,504, 77.6%), most commonly for chest pain (n = 275, 14.2%) and shortness of breath (n = 273, 14.1%). MSFRs were less likely to attend patients of white ethnicity compared to CFRs and ambulance staff, and more likely to attend incidents in areas of higher socioeconomic deprivation (IMD - index of multiple deprivation) (p < 0.05). Interviewees (n = 16) consistently described positive experiences which improved their clinical and communication skills. CONCLUSION: MSFRs' attendance at serious medical emergencies provide a range of reported educational experiences and benefits. Further studies are needed to explore whether MSFR work confers demonstrable improvements in educational or clinical performance.

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1.

Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI-FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5' flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5' flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.

Archaeogenomic evidence from the southwestern US points to a pre-Hispanic scarlet macaw breeding colony.

Hundreds of scarlet macaw (Ara macao cyanoptera) skeletons have been recovered from archaeological contexts in the southwestern United States and northwestern Mexico (SW/NW). The location of these skeletons, >1,000 km outside their Neotropical endemic range, has suggested a far-reaching pre-Hispanic acquisition network. Clear evidence for scarlet macaw breeding within this network is only known from the settlement of Paquimé in NW dating between 1250 and 1450 CE. Although some scholars have speculated on the probable existence of earlier breeding centers in the SW/NW region, there has been no supporting evidence. In this study, we performed an ancient DNA analysis of scarlet macaws recovered from archaeological sites in Chaco Canyon and the contemporaneous Mimbres area of New Mexico. All samples were directly radiocarbon dated between 900 and 1200 CE. We reconstructed complete or near-complete mitochondrial genome sequences of 14 scarlet macaws from five different sites. We observed remarkably low genetic diversity in this sample, consistent with breeding of a small founder population translocated outside their natural range. Phylogeographic comparisons of our ancient DNA mitogenomes with mitochondrial sequences from macaws collected during the last 200 years from their endemic Neotropical range identified genetic affinity between the ancient macaws and a single rare haplogroup (Haplo6) observed only among wild macaws in Mexico and northern Guatemala. Our results suggest that people at an undiscovered pre-Hispanic settlement dating between 900 and 1200 CE managed a macaw breeding colony outside their endemic range and distributed these symbolically important birds through the SW.

PCNA ubiquitylation ensures timely completion of unperturbed DNA replication in fission yeast.

PCNA ubiquitylation on lysine 164 is required for DNA damage tolerance. In many organisms PCNA is also ubiquitylated in unchallenged S phase but the significance of this has not been established. Using Schizosaccharomyces pombe, we demonstrate that lysine 164 ubiquitylation of PCNA contributes to efficient DNA replication in the absence of DNA damage. Loss of PCNA ubiquitylation manifests most strongly at late replicating regions and increases the frequency of replication gaps. We show that PCNA ubiquitylation increases the proportion of chromatin associated PCNA and the co-immunoprecipitation of Polymerase δ with PCNA during unperturbed replication and propose that ubiquitylation acts to prolong the chromatin association of these replication proteins to allow the efficient completion of Okazaki fragment synthesis by mediating gap filling.

Copper Nanocubes for CO2 Reduction in Gas Diffusion Electrodes.

Electroreduction of CO2 represents a promising solution for addressing the global challenges in energy and sustainability. This reaction is highly sensitive to the surface structure of electrocatalysts and the local electrochemical environment. We have investigated the effect of Cu nanoparticle shape on the electrocatalysis of CO2 reduction by using gas-diffusion electrodes (GDEs) and flowing alkaline catholytes. Cu nanocubes of ∼70 nm in edge length are synthesized with {100} facets preferentially exposed on the surface. They are demonstrated to possess substantially enhanced catalytic activity and selectivity for CO2 reduction, compared to Cu nanospheres of similar particle sizes. The electrocatalytic performance was further found to be dependent on the concentration of electrolyte (KOH). The Cu nanocubes reach a Faradaic efficiency of 60% and a partial current density of 144 mA/cm2 toward ethylene (C2H4) production, with the catalytic enhancement being attributable to a combination of surface structure and electrolyte alkalinity effects.

Arthroscopic repair of HAGL lesions yields good clinical results, but may not allow return to former level of sport.

PURPOSE: There is a paucity of evidence regarding mid- to long-term clinical outcomes of arthroscopic repair of humeral avulsion of the glenohumeral ligament (HAGL). This study investigated clinical outcomes, return to sport and the frequency of associated shoulder lesions. METHODS: Eighteen patients underwent arthroscopic repair of a HAGL lesion between 2008 and 2015. Clinical outcome was evaluated using the Rowe Score, the Quick DASH Score (Q-DASH), the Oxford Shoulder Instability Score (OSIS), the ASES Score and Range of Motion (ROM). Return to sports and associated shoulder lesions were documented. RESULTS: Sixteen patients agreed to complete the shoulder scores and nine patients were available for clinical examination. Median time to follow-up was 59 months (range 16-104). The median Rowe Score and Q-DASH Score improved significantly from 33 to 85 points and 61 to 7 points, respectively (p = 0.001, p = 0.001). The median OSIS and ASES Score were 20 and 91 points. External rotation was significantly reduced compared to the contralateral side (p = 0.011). One recurrent dislocation was reported. No neurologic or vascular complications after surgery were reported. Five out of the nine patients did not return to sports at the same level. Associated shoulder lesions were found in 89% of the cases. CONCLUSION: Arthroscopic repair of a HAGL lesion is a reliable method to restore shoulder stability with good clinical results. However, limitations in external rotation and a reduction in sporting ability may persist at 59 months follow-up. Concomitant lesions are common. LEVEL OF EVIDENCE: Case series, level IV.

Early procurement of scarlet macaws and the emergence of social complexity in Chaco Canyon, NM.

High-precision accelerator mass spectrometer (AMS) (14)C dates of scarlet macaw (Ara macao) skeletal remains provide the first direct evidence from Chaco Canyon in northwestern New Mexico that these Neotropical birds were procured from Mesoamerica by Pueblo people as early as ∼ A.D. 900-975. Chaco was a prominent prehistoric Pueblo center with a dense concentration of multistoried great houses constructed from the 9th through early 12th centuries. At the best known great house of Pueblo Bonito, unusual burial crypts and significant quantities of exotic and symbolically important materials, including scarlet macaws, turquoise, marine shell, and cacao, suggest societal complexity unprecedented elsewhere in the Puebloan world. Scarlet macaws are known markers of social and political status among the Pueblos. New AMS (14)C-dated scarlet macaw remains from Pueblo Bonito demonstrate that these birds were acquired persistently from Mesoamerica between A.D. 900 and 1150. Most of the macaws date before the hypothesized apogeal Chacoan period (A.D. 1040-1110) to which they are commonly attributed. The 10th century acquisition of these birds is consistent with the hypothesis that more formalized status hierarchies developed with significant connections to Mesoamerica before the post-A.D. 1040 architectural florescence in Chaco Canyon.

Regulation of ribonucleotide reductase by Spd1 involves multiple mechanisms.

The correct levels of deoxyribonucleotide triphosphates and their relative abundance are important to maintain genomic integrity. Ribonucleotide reductase (RNR) regulation is complex and multifaceted. RNR is regulated allosterically by two nucleotide-binding sites, by transcriptional control, and by small inhibitory proteins that associate with the R1 catalytic subunit. In addition, the subcellular localization of the R2 subunit is regulated through the cell cycle and in response to DNA damage. We show that the fission yeast small RNR inhibitor Spd1 is intrinsically disordered and regulates R2 nuclear import, as predicted by its relationship to Saccharomyces cerevisiae Dif1. We demonstrate that Spd1 can interact with both R1 and R2, and show that the major restraint of RNR in vivo by Spd1 is unrelated to R2 subcellular localization. Finally, we identify a new behavior for RNR complexes that potentially provides yet another mechanism to regulate dNTP synthesis via modulation of RNR complex architecture.

Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex.

BACKGROUND: Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence indicates that sleep is necessary for normal brain function and that sleep need is a tightly regulated process. Surprisingly, molecular mechanisms that determine sleep need are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. Several studies have characterized differential gene expression changes following sleep deprivation. Much less is known, however, about changes in gene expression during the compensatory response to sleep deprivation (i.e. recovery sleep). RESULTS: In this study we present a comprehensive analysis of the effects of sleep deprivation and subsequent recovery sleep on gene expression in the mouse cortex. We used a non-traditional analytical method for normalization of genome-wide gene expression data, Removal of Unwanted Variation (RUV). RUV improves detection of differential gene expression following sleep deprivation. We also show that RUV normalization is crucial to the discovery of differentially expressed genes associated with recovery sleep. Our analysis indicates that the majority of transcripts upregulated by sleep deprivation require 6 h of recovery sleep to return to baseline levels, while the majority of downregulated transcripts return to baseline levels within 1-3 h. We also find that transcripts that change rapidly during recovery (i.e. within 3 h) do so on average with a time constant that is similar to the time constant for the discharge of sleep need. CONCLUSIONS: We demonstrate that proper data normalization is essential to identify changes in gene expression that are specifically linked to sleep deprivation and recovery sleep. Our results provide the first evidence that recovery sleep is comprised of two waves of transcriptional regulation that occur at different times and affect functionally distinct classes of genes.

Extracellular signal-regulated kinase (ERK) activity during sleep consolidates cortical plasticity in vivo.

Ocular dominance plasticity (ODP) in the cat primary visual cortex (V1) is induced during waking by monocular deprivation (MD) and consolidated during subsequent sleep. The mechanisms underlying this process are incompletely understood. Extracellular signal-regulated kinase (ERK) is activated in V1 during sleep after MD, but it is unknown whether ERK activation during sleep is necessary for ODP consolidation. We investigated the role of ERK in sleep-dependent ODP consolidation by inhibiting the ERK-activating enzyme MEK in V1 (via U0126) during post-MD sleep. ODP consolidation was then measured with extracellular microelectrode recordings. Western blot analysis was used to confirm the efficacy of U0126 and to examine proteins downstream of ERK. U0126 abolished ODP consolidation and reduced both phosphorylation of eukaryotic initiation factor 4E (eIF4E) and levels of the synaptic marker PSD-95. Furthermore, interfering with ERK-mediated translation by inhibiting MAP kinase-interacting kinase 1 (Mnk1) with CGP57380 mimicked the effects of U0126. These results demonstrate that ODP consolidation requires sleep-dependent activation of the ERK-Mnk1 pathway.

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy.

Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds.

Visual experience and subsequent sleep induce sequential plastic changes in putative inhibitory and excitatory cortical neurons.

Ocular dominance plasticity in the developing primary visual cortex is initiated by monocular deprivation (MD) and consolidated during subsequent sleep. To clarify how visual experience and sleep affect neuronal activity and plasticity, we continuously recorded extragranular visual cortex fast-spiking (FS) interneurons and putative principal (i.e., excitatory) neurons in freely behaving cats across periods of waking MD and post-MD sleep. Consistent with previous reports in mice, MD induces two related changes in FS interneurons: a response shift in favor of the closed eye and depression of firing. Spike-timing-dependent depression of open-eye-biased principal neuron inputs to FS interneurons may mediate these effects. During post-MD nonrapid eye movement sleep, principal neuron firing increases and becomes more phase-locked to slow wave and spindle oscillations. Ocular dominance (OD) shifts in favor of open-eye stimulation--evident only after post-MD sleep--are proportional to MD-induced changes in FS interneuron activity and to subsequent sleep-associated changes in principal neuron activity. OD shifts are greatest in principal neurons that fire 40-300 ms after neighboring FS interneurons during post-MD slow waves. Based on these data, we propose that MD-induced changes in FS interneurons play an instructive role in ocular dominance plasticity, causing disinhibition among open-eye-biased principal neurons, which drive plasticity throughout the visual cortex during subsequent sleep.

Prospective Randomized Clinical and Radiographic Evaluation of a Novel Bioabsorbable Biocomposite Tibial Tuberosity Advancement Cage Implant.

OBJECTIVE: To evaluate the suitability of a novel bioabsorbable biocomposite cage (BC) implant for use in tibial tuberosity advancement (TTA) surgery in dogs with cranial cruciate ligament (CrCL) disease and to compare radiographic osteotomy healing scores and complications between groups that received either a BC or stainless steel cage (SSC). STUDY DESIGN: Prospective randomized clinical study. ANIMALS: Dogs with unilateral CrCL rupture (n=56). METHODS: TTA was performed in 60 consecutive dogs using either a BC (30 dogs) or SSC (30 dogs). Patient parameters, 6 week and 6 month postoperative radiographic osteotomy healing scores, time elapsed to postoperative rechecks, and complications were compared between groups. Osteotomy healing was graded using a 5-point (0-4) scale. Data were analyzed using Wilcoxon Rank Sum tests and χ(2) tests with significance set at P<.05. RESULTS: Fifty-six dogs (30 BC, 26 SSC) had complete medical and radiographic records at 6 months for inclusion in data analysis. Three complications occurred in the BC group (1 major, 2 minor) and 2 occurred in the SSC group (2 minor). There was no statistical difference in patient parameters, 6 week healing scores, or complications between BC and SSC groups. Healing scores at 6 months were significantly higher in the BC group (3.3 ± 0.52) compared to the SSC group (2.9 ± 0.69; P=.04). CONCLUSION: Based on improved BC osteotomy healing scores 6 months after surgery with no significant differences in complications compared to SSC, BC TTA cages are a viable alternative to SSC.

Spd1 accumulation causes genome instability independently of ribonucleotide reductase activity but functions to protect the genome when deoxynucleotide pools are elevated.

Cullin4, Ddb1 and Cdt2 are core subunits of the ubiquitin ligase complex CRL4(Cdt2), which controls genome stability by targeting Spd1 for degradation during DNA replication and repair in fission yeast. Spd1 has an inhibitory effect on ribonucleotide reductase (RNR), the activity of which is required for deoxynucleotide (dNTP) synthesis. The failure to degrade Spd1 in mutants where CRL4(Cdt2) is defective leads to DNA integrity checkpoint activation and dependency. This correlates with a lower dNTP pool. Pools are restored in a spd1-deleted background and this also suppresses checkpoint activation and dependency. We hypothesized that fission yeast with RNR hyperactivity would display a mutator phenotype on their own, but also possibly repress aspects of the phenotype associated with the inability to target Spd1 for degradation. Here, we report that a mutation in the R1 subunit of ribonucleotide reductase cdc22 (cdc22-D57N), which alleviated allosteric feedback inhibition, caused a highly elevated dNTP pool that was further increased by deleting spd1. The Δspd1 cdc22-D57N double mutant had elevated mutation rates and was sensitive to damaging agents that cause DNA strand breaks, demonstrating that Spd1 can protect the genome when dNTP pools are high. In ddb1-deleted cells, cdc22-D57N also potently elevated RNR activity, but failed to allow cell growth independently of the intact checkpoint. Our results provide evidence that excess Spd1 interferes with other functions in addition to its inhibitory effect on ribonucleotide reduction to generate replication stress and genome instability.

The truncated TrkB receptor influences mammalian sleep.

Brain-derived neurotrophic factor (BDNF) is a neurotrophin hypothesized to play an important role in mammalian sleep expression and regulation. In order to investigate the role of the truncated receptor for BDNF, TrkB.T1, in mammalian sleep, we examined sleep architecture and sleep regulation in adult mice constitutively lacking this receptor. We find that TrkB.T1 knockout mice have increased REM sleep time, reduced REM sleep latency, and reduced sleep continuity. These results demonstrate a novel role for the TrkB.T1 receptor in sleep expression and provide new insights into the relationship between BDNF, psychiatric illness, and sleep.