Miracle-dz/UniFAR-FTUs huggingface dataset:
Outcomes after viral load rebound on first-line antiretroviral therapy in HIV-infected children in the UK/Ireland: an observational cohort study

Background—Approximately one-third of HIV-infected children experience virological failure within two years of initiating antiretroviral therapy (ART). We determined the probability of switch to second-line ART or viral load (VL) re-suppression without switch among children who experienced VL rebound on first-line ART in an observational cohort in the UK/Ireland. Methods—Children with VL rebound (confirmed VL>400c/ml following suppression <400c/ml) on first-line ART were included. Competing risk analysis estimated the probability of: switch to second-line; confirmed re-suppression (two consecutive VL<400c/ml) without switch; and continued VL>400c/ml without switch. Predictors of time to switch were assessed. Findings—Of 900 children starting first-line ART who had VL<400c/ml by one year, 170 (19%) experienced VL rebound by median [IQR] 20·6 months [9·7-40·5]. At rebound, median age was 10·6 years [5·6-13·4], VL 3·6 log10c/ml [3·1-4·2], and CD4% 24 [17-32]. Eighty-nine (52%) switched to second-line ART at median 4·9 months [1·7-13·4] after VL rebound, 53 (31%) resuppressed without switch (61% of those on PI-based and 24% of those on NNRTI-based first-line regimens), while 28 (16%) neither re-suppressed nor switched. At 12 months after rebound, probabilities of switch or re-suppression without switch were 38% (95% CI 30-45) and 27% (95% CI 21-34), respectively. Faster time to switch was associated with higher VL (p<0·0001), later calendar year (p=0·02) at VL rebound, and NNRTIor triple NRTIversus PI-based first-line (p=0·001). Corresponding author: Intira Jeannie Collins MRC Clinical Trials Unit at UCL Aviation House, 125 Kingsway, London WC2B 6NH jeannie.collins@ucl.ac. uk T: +44 20 7670 4767. Authors contributions: Tristan Childs, Trinh Duong, Ali Judd, Di Gibb and Intira Collins were responsible for the study concept and design. Tristan Childs carried out the statistical analyses. Tristan Childs, Delane Shingadia, Ruth Goodall, Ali Judd, Di Gibb and Intira Collins drafted the manuscript. Delane Shingadia, Katja Doerholt, Hermione Lyall, and Di Gibb collected the data. All co-authors participated in discussions about the design of the study, interpretation of the findings, and critically reviewed the manuscript. Conflicts of interest: We declare that we have no conflicts of interest. Europe PMC Funders Group Author Manuscript Lancet HIV. Author manuscript; available in PMC 2015 October 01. Published in final edited form as: Lancet HIV. 2015 April 1; 2(4): e151–e158. doi:10.1016/S2352-3018(15)00021-1. E uope PM C Fuders A uhor M ancripts E uope PM C Fuders A uhor M ancripts Interpretation—One-third of children with VL rebound re-suppressed without switch. The possibility of re-suppression with adherence support should be considered prior to switching.
Technical Advance A Novel Strategy for Human Papillomavirus Detection and Genotyping with SybrGreen and Molecular Beacon Polymerase Chain Reaction

Human papillomaviruses (HPVs) play an important role in the pathogenesis of cervical cancer. For identification of the large number of different HPV types found in (pre)malignant lesions, a robust methodology is needed that combines general HPV detection with HPV genotyping. We have developed for formal-dehyde-fixed samples a strategy that, in a homogenous, real-time fluorescence polymerase chain reaction (PCR)-based assay, accomplishes general HPV detection by SybrGreen reporting of HPV-DNA amplicons, and genotyping of seven prevalent HPV types (HPV-6, -11, -16, -18, -31, -33, -45) by real-time molecular beacon PCR. The false-positive rate of the HPV SybrGreen-PCR was 4%, making it well suited as a prescreening, general HPV detection technology. The type specificity of the seven selected HPV molecular beacons was 100% and double infections were readily identified. The multiplexing capacity of the HPV molecular beacon PCR was analyzed and up to three differently labeled molecular beacons could be used in one PCR reaction without observing cross talk. The inherent quantitation capacities of real-time fluorescence PCR allowed the determination of average HPV copy number per cell. We conclude that the HPV SybrGreen-PCR in combination
Increased synovial expression of nuclear receptors correlates with arthritis protection: a possible novel genetically-regulated homeostatic mechanism

Objective— To use microarray analyses of gene expression to characterize the synovial molecular pathways regulated by the arthritis regulatory locus Cia25, and how it operates to control disease severity and joint damage. Methods— Synovial tissues from DA and DA.ACI(Cia25) rats obtained 21 days post-induction of pristane-induced arthritis were used for RNA extraction and hybridization to Illumina Rat-Ref 12 Beadchips (22,228 genes). A p-value ≤ 0.01 plus a fold-difference ≥ 1.5 were considered significant. Results— IL-1 β (7-fold), IL-6 (67-fold), Ccl2, Cxcl10, Mmp3, Mmp14, and innate immunity genes were expressed in increased levels in DA and in significantly lower levels in congenics. DA.ACI(Cia25) had increased expression of ten nuclear receptors (NR) genes, including those known to interfere with NF κ B activity and cytokine expression, such as Lxr α , Ppar γ , and Rxr γ . DA.ACI(Cia25) also had increased expression of NR targets suggesting increased NR activity. While the Vdr was not differentially expressed, a Vdr expression signature was detected in congenics, along with up-regulation of mediators of vitamin D synthesis. Conclusions— This is the first description of the association between increased synovial levels of NRs and arthritis protection. The expression of NRs was inversely correlated with the expression of key mediators of arthritis suggesting reciprocally opposing effects either via NF κ B or at the genomic level in the synovial tissue. We consider that the NR signature may have an important role in maintaining synovial homeostasis These results suggest that in addition to the increased expression of IL-1 β in DA, there was also increased transcriptional
Role of phosphorylation in Moesin interactions with Phosphatidylinositol-4,5-bis(phosphate)-containing biomimetic membranes: a biophysical study

Moesin, a protein of the ezrin, radixin, moesin (ERM) family, which links the plasma membrane to the cytoskeleton, is involved in multiple physiological and pathological processes, including viral budding and infection. Its interaction with the plasma membrane occurs via a key phosphoinositide, the phosphatidyl(4,5)inositol-bisphosphate (PIP2), and phosphorylation of residue T558, which has been shown to contribute, in cellulo, to a conformationally open protein. We study the impact of a double phosphomimetic mutation of moesin (T235D, T558D), mimicking the phosphorylation state of the protein, on protein/PIP2/microtubule interactions. Analytical ultracentrifugation in the μM range showed moesin in the monomer and dimer forms, with WT moesin containing a slightly larger fraction (~30%) of dimers than DD moesin (10-20%). Only DD moesin was responsive to PIP2 in its micellar form. Quantitative cosedimentation assays using large unilamellar vesicles and quartz crystal microbalance on supported lipid bilayers containing PIP2, reveal a specific cooperative interaction for DD moesin with an ability to bind two PIP2 molecules simultaneously, while WT moesin was able to bind only one. In addition, DD moesin could subsequently interact with microtubules, while WT moesin was unable to do so. Altogether, our results point to an important role of these two phosphorylation sites in the opening of moesin: DD moesin being intrinsically in a more open conformation than WT moesin, this intermolecular interaction being reinforced by its binding to PIP2. We also highlight important differences between moesin and ezrin, which appear to be finely regulated and to exhibit distinct molecular behaviors. Author contribution CP conceived and coordinated the study; all authors contributed to designing the research and analyzing the data; QL carried out LUV and SLB preparation and protein/membrane interactions with the help of HV and MK; QL, FD, HV and ML produced the recombinant proteins; MW and ML worked on the structural representation; ALR and CE carried out AUC experiments and helped in their analysis; CP, QL and MW wrote the paper; all authors read and commented on the manuscript. Conflict of interest. The authors declare that they have no conflicts of interest with the contents of this article. Europe PMC Funders Group Author Manuscript Biophys J. Author manuscript; available in PMC 2018 July 09. Published in final edited form as: Biophys J. 2018 January 09; 114(1): 98–112. doi:10.1016/j.bpj. 2017.10. 041. E uope PM C Fuders A uhor M ancripts E uope PM C Fuders A uhor M ancripts
Exploring the Ability of LARS2 Carboxy-Terminal Domain in Rescuing the MELAS Phenotype

The m.3243A>G mutation within the mitochondrial mt-tRNALeu(UUR) gene is the most prevalent variant linked to mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome. This pathogenic mutation causes severe impairment of mitochondrial protein synthesis due to alterations of the mutated tRNA, such as reduced aminoacylation and a lack of post-transcriptional modification. In transmitochondrial cybrids, overexpression of human mitochondrial leucyl-tRNA synthetase (LARS2) has proven effective in rescuing the phenotype associated with m.3243A>G substitution. The rescuing activity resides in the carboxy-terminal domain (Cterm) of the enzyme; however, the precise molecular mechanisms underlying this process have not been fully elucidated. To deepen our knowledge on the rescuing mechanisms, we demonstrated the interactions of the Cterm with mutated mt-tRNALeu(UUR) and its precursor in MELAS cybrids. Further, the effect of Cterm expression on mitochondrial functions was evaluated. We found that Cterm ameliorates de novo mitochondrial protein synthesis, whilst it has no effect on mt-tRNALeu(UUR) steady-state levels and aminoacylation. Despite the complete recovery of cell viability and the increase in mitochondrial translation, Cterm-overexpressing cybrids were not able to recover bioenergetic competence. These data suggest that, in our MELAS cell model, the beneficial effect of Cterm may be mediated by factors that are independent of the mitochondrial bioenergetics.
Pulmonary Perspective Intersections between Pulmonary Development and Disease

Recent advances in cellular, molecular, and developmental biology have revolutionized our concepts regarding the process of organogenesis that have important implications for our understanding of both lung formation and pulmonary disease pathogenesis. Pulmonary investigators have long debated whether developmental pro- cesses are recapitulated during normal repair of the lung or in the setting of chronic pulmonary diseases. Although the cellular events involved in lung morphogenesis and those causing pulmonary disease are likely to include processes that are distinct, there is increasing evidence that the pathogenesis of many lung disorders involves the same genetic machinery that regulates cell growth, speciﬁcation, and differentiation during normal lung development.
Sensitivity Analysis as an Ingredient of Modeling

We explore the tasks where sensitivity analysis (SA) can be useful and try to assess the relevance of SA within the modeling process. We suggest that SA could considerably assist in the use of models, by providing objective criteria of judgement for different phases of the model-building process: model identification and discrimination; model calibration; model corroboration. We review some new global quantitative SA methods and suggest that these might enlarge the scope for sensitivity analysis in computational and statistical modeling practice. Among the advantages of the new methods are their robustness, model independence and computational convenience. The discussion is based on worked examples.
Long-term Outcomes in Youth with Diabetes Mellitus

In this chapter, I will review the long-term outcomes and their precursors of type 1 diabetes (T1D) starting in youth. I will also contrast the changing incidence of these long-term complications as we have moved from the pre-DCCT to the post-DCCT standard of care and will review the emerging data related to complications in youth with type 2 diabetes (T2D). Finally, I will review the recent understanding related to the effects of diabetes on the brain and cognition.
Zeaxanthin Epoxidase Activity is Down-regulated by Hydrogen Peroxide.

The xanthophyll zeaxanthin (Zx) serves important photoprotective functions in chloroplasts and is particularly involved in the dissipation of excess light energy as heat in the antenna of photosystem II (PSII). Zx accumulates under high light conditions in thylakoid membranes and is reconverted to violaxanthin by zeaxanthin epoxidase (ZEP) in low light or darkness. ZEP activity is completely inhibited under long-lasting high light stress and ZEP protein becomes degraded along with the PSII subunit D1 during photoinhibition of PSII. This ZEP inactivation ensures that high levels of Zx are maintained under harsh high light stress. The mechanism of ZEP inactivation is unknown. Here, we investigated ZEP inactivation by reactive oxygen species (ROS) under in vitro conditions. Our results show that ZEP activity is completely inhibited by hydrogen peroxide (H2O2), whereas inhibition by singlet oxygen or superoxide seems rather unlikely. Due to the limited information about the amount of singlet oxygen and superoxide accumulating under the applied experimental conditions, however, a possible inhibition of ZEP activity by these two ROS cannot be generally excluded. Despite this limitation, our data support the hypothesis that the accumulation of ROS, and in particular H2O2, might be responsible for HL induced inactivation of ZEP under in vivo conditions.
Anemia, Weight Status, and Fatigue Among Farmworkers in California

Anemia affects physical work capacity and may therefore have health and economic impacts for farmworkers, possibly exacerbating the effects of other occupational hazards such as risk of injury. This study contributes new information on the prevalence of anemia and associated factors in this population. Objective This study aimed to determine the prevalence of anemia and overweight/obesity and assess the relationships between hematocrit (Hct) and body mass index (BMI), and between fatigue and Hct, among a sample of farmworkers in California. Methods We estimated the prevalence of anemia (using Hct), overweight/obesity (BMI ≥25 kg/m2), and self-reported fatigue in 587 farmworkers. Multivariable linear and logistic regression models were used to examine the associations between Hct and BMI, and between fatigue and Hct. Results Anemia prevalence was 3.1%, overweight/obesity prevalence was 80.7%, and 78% of workers reported fatigue at work. There was no association between Hct and BMI or between Hct and reported fatigue. Women were more likely than men to have lower Hct and higher BMI. Conclusions A majority of farmworkers in this sample were overweight/obese, but anemia was uncommon. Anemia among more vulnerable subgroups of farmworkers should be explored.
Soft tissue sarcomas in 2 zoo-housed Alaskan moose

Soft tissue sarcomas (STSs) are common well-described cutaneous neoplasms in many domestic species. Few cutaneous neoplasms have been reported in cervids, other than papilloma virus–induced benign cutaneous fibromas (BCFs). Two wild-caught Alaskan moose (Alces alces), housed at different North American zoos, were both presented with lameness and a mass. The gross appearance of each mass varied greatly; case 1 had a distinct, exophytic, ulcerated mass near the right carpal joint similar in appearance to a BCF, and case 2 had a pronounced swelling over the left hip. Based on histologic evaluation, both masses were diagnosed as STS. The clinical presentation of these masses included rapid growth and associated lameness; however, gross appearance was markedly different. Histopathology revealed characteristics typical of STS in other species, including spindle-shaped cells arranged in streaming sheets with ovoid nuclei. STS should be included as a differential diagnosis for moose with a cutaneous or subcutaneous soft tissue mass or swelling.
Vasculopathy and Increased Vascular Congestion in Fatal COVID-19 and Acute Respiratory Distress Syndrome

Rationale The leading cause of death in coronavirus disease 2019 (COVID-19) is severe pneumonia, with many patients developing acute respiratory distress syndrome (ARDS) and diffuse alveolar damage (DAD). Whether DAD in fatal COVID-19 is distinct from other causes of DAD remains unknown. Objective To compare lung parenchymal and vascular alterations between patients with fatal COVID-19 pneumonia and other DAD-causing etiologies using a multidimensional approach. Methods This autopsy cohort consisted of consecutive patients with COVID-19 pneumonia (n = 20) and with respiratory failure and histologic DAD (n = 21; non–COVID-19 viral and nonviral etiologies). Premortem chest computed tomography (CT) scans were evaluated for vascular changes. Postmortem lung tissues were compared using histopathological and computational analyses. Machine-learning-derived morphometric analysis of the microvasculature was performed, with a random forest classifier quantifying vascular congestion (CVasc) in different microscopic compartments. Respiratory mechanics and gas-exchange parameters were evaluated longitudinally in patients with ARDS. Measurements and Main Results In premortem CT, patients with COVID-19 showed more dilated vasculature when all lung segments were evaluated (P = 0.001) compared with controls with DAD. Histopathology revealed vasculopathic changes, including hemangiomatosis-like changes (P = 0.043), thromboemboli (P = 0.0038), pulmonary infarcts (P = 0.047), and perivascular inflammation (P < 0.001). Generalized estimating equations revealed significant regional differences in the lung microarchitecture among all DAD-causing entities. COVID-19 showed a larger overall CVasc range (P = 0.002). Alveolar-septal congestion was associated with a significantly shorter time to death from symptom onset (P = 0.03), length of hospital stay (P = 0.02), and increased ventilatory ratio [an estimate for pulmonary dead space fraction (Vd); p = 0.043] in all cases of ARDS. Conclusions Severe COVID-19 pneumonia is characterized by significant vasculopathy and aberrant alveolar-septal congestion. Our findings also highlight the role that vascular alterations may play in Vd and clinical outcomes in ARDS in general.
Single-cell antigen-specific landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL

A notable number of acute lymphoblastic leukemia (ALL) patients develop CD19-positive relapse within 1 year after receiving chimeric antigen receptor (CAR) T cell therapy. It remains unclear if the long-term response is associated with the characteristics of CAR T cells in infusion products, hindering the identification of biomarkers to predict therapeutic outcomes. Here, we present 101,326 single-cell transcriptomes and surface protein landscape from the infusion products of 12 ALL patients. We observed substantial heterogeneity in the antigen-specific activation states, among which a deficiency of T helper 2 function was associated with CD19-positive relapse compared with durable responders (remission, >54 months). Proteomic data revealed that the frequency of early memory T cells, rather than activation or coinhibitory signatures, could distinguish the relapse. These findings were corroborated by independent functional profiling of 49 patients, and an integrative model was developed to predict the response. Our data unveil the molecular mechanisms that may inform strategies to boost specific T cell function to maintain long-term remission.
Realistic FRP seismic strengthening schemes for interior reinforced concretebeam-column joints

The observation, in recent earthquakes, of brittle collapses of reinforced concrete (RC) structures built before the introduction of detailed seismic design codes (pre-1970’s), underlines the need for significant upgrades to the existing RC building stock. In particular, weak-column/strong-beam mechanisms and shear failures have potentially catastrophic impacts that could be addressed by repair and retrofit solutions. In recent years, retrofits with fibre reinforced polymers (FRP) are becoming increasingly popular due to the benefits of corrosion resistance, high strength-to-weight ratio and reduced labour time. Experimental evidence for the efficiency of such schemes for joint strengthening can be found in the literature. An analysis of all available literature shows that the reduced scale of most tested specimens, as well as the omission of slabs and transverse beams in many studies, may lead to an unrealistic assessment of FRP retrofit schemes. In this study, pre-1970’s full-scale interior beam-column joints with slab and transverse beams are hence tested under realistic conditions in order to propose and assess new and practical FRP retrofit solutions for seismic actions. Three carbon FRP (CFRP) retrofit schemes with selective retrofit objectives are designed using outcomes from the literature and from calibrated finite-element models. The retrofit schemes are composed of a combination of FRP strengthening and selective weakening components to ensure failure of inadequately reinforced RC beam-column joints according to capacity design principles. The objectives of the schemes include the enhancement in lateral capacity and ductility, as well as changing the failure mechanism of the joint. Results from full-scale cyclic tests on the CFRP retrofitted specimens are compared to the behaviour of a deficient specimen and a specimen designed to modern guidelines (EC8), highlighting the successful achievement of the respective retrofit objectives. To evaluate the effect of the realistic set-up, the results are also compared to specimens without slab and transverse beams, highlighting their importance. Finally, new design equations, to be used in conjunction with existing guidelines, are formulated to ease the practical adoption of the proposed retrofit scheme.
Detection and quantification of Epstein–Barr virus, cytomegalovirus, and human herpesvirus‐6 in stomach frozen tissue of chronic gastritis and gastric cancer patients

Human herpes viruses (HHVs) are among the most common infectious agents detected in the gastrointestinal tract that might be involved in oncogenesis and other gastrointestinal disorders. Although the link between the Epstein–Barr virus (EBV) and gastric cancer (GC) has been established, the role of the viruses in various stomach diseases remains unknown. The frequencies and viral copy number of EBV, cytomegalovirus (CMV), and human herpesvirus 6 (HHV‐6) among 50 gastric cancer tumors and 105 chronic gastritis tissues were measured by quantitative real‐time PCR. In the tumor specimens and the adjacent normal tissues EBV was found in 60% and 30.9%, CMV in 14% and 4.7%, and HHV‐6 in 18%, and 14.2%, respectively. The detection rate of EBV and CMV was found to be significantly higher in tumor tissues relative to the adjacent normal tissues. Also, in chronic gastritis, the frequency of EBV, CMV, and HHV‐6 was 19%, 12.3%, and 15.2%, respectively, compared with 16.4%, 1.1%, and 8.2% in their corresponding normal tissues. Here, the CMV frequency was found to be significantly higher in gastritis tissues relative to the adjacent normal tissues. Furthermore, viral load in both gastric cancer and gastritis groups was higher in either tumor or gastritis lesion compared with matched adjacent normal tissue. This study showed a clear association between gastric cancer with both EBV and CMV. Meanwhile, analyses revealed a strong association between the EBV, CMV, and HHV‐6 viral loads with gastritis (P = 0.0026, P < 0.0001, and P = 0.0405, respectively). Our results suggest that these three viruses might contribute to the induction and development the gastritis and gastric cancer.