Complete Genome Sequence of Finnry, a Subcluster L3 Mycobacteriophage from Charleston, South Carolina.

Subcluster L3 bacteriophage Finnry was isolated from soil collected in Charleston, South Carolina, using Mycobacterium smegmatis mc2155 as a host. The genome of this temperate siphovirus is 75,632 bp long (130 predicted protein-coding genes, 9 tRNAs, and no transfer-messenger RNAs), and BLASTn alignment revealed 99.86% identity with the genome of L3 mycobacteriophage Samty.

A case study: The deployment of a novel in situ fluorimeter for monitoring biological contamination within the urban surface waters of Kolkata, India.

The quality and health of many of our vital freshwater systems are poor. To tackle this with ever increasing pressures from anthropogenic and climatic changes, we must improve water quality monitoring and devise and implement more appropriate water quality parameters. Recent research has highlighted the potential for Peak T fluorescence (tryptophan-like fluorescence, TLF) to monitor microbial activity in aquatic systems. The VLux TPro (Chelsea Technologies Ltd., UK), an in situ real-time fluorimeter, was deployed in different urban freshwater bodies within Kolkata (West Bengal, India) during March 2019. This study is the first to apply this technology in surface waters within a densely populated urban area. Spot-sampling was also undertaken at 13 sampling locations enabling physicochemical analysis, bacterial enumeration and determination of nutrient (nitrate and phosphate) concentrations. This case study has demonstrated the ability of an in situ fluorimeter, VLux TPro, to successfully identify both biological contamination events and potential elevated microbial activity, related to nutrient loading, in complex surface freshwaters, without the need for expensive and time-consuming laboratory analysis.

NOD2 signaling in CD11c + cells is critical for humoral immune responses during oral vaccination and maintaining the gut microbiome.

Nucleotide-binding oligomerization domain containing 2 (NOD2) is a critical regulator of immune responses within the gastrointestinal tract. This innate immune receptor is expressed by several cell types, including both hematopoietic and nonhematopoietic cells within the gastrointestinal tract. Vaccination targeting the gastrointestinal mucosal immune system is especially difficult due to both physical and mechanistic barriers to reaching inductive sites. The use of lactic acid bacteria is appealing due to their ability to persist within harsh conditions, expression of selected adjuvants, and manufacturing advantages. Recombinant Lactobacillus acidophilus (rLA) has shown great promise in activating the mucosal immune response with minimal impacts on the resident microbiome. To better classify the kinetics of mucosal vaccination with rLA, we utilized mice harboring knockouts of NOD2 expression specifically within CD11c + cells. The results presented here show that NOD2 signaling in CD11c + cells is necessary for mounting a humoral immune response against exogenous antigens expressed by rLA. Additionally, disruption of NOD2 signaling in these cells results in an altered bacterial microbiome profile in both control mice and mice receiving L. acidophilus strain NCK1895 and vaccine strain LaOVA.

The accuracy of computed tomography for clavicle non-union evaluation.

BACKGROUND: The primary aim of this study is to determine the accuracy of CT scanning when evaluating non-union of the clavicle. METHODS: A retrospective review was performed of all CT scans undertaken for suspected nonunion of midshaft clavicle fractures over a 10-year period. The influence of scan timing, callus and patient characteristics was evaluated. RESULTS: One hundred eighty-four CT scans were analysed. No patient was incorrectly diagnosed with union (n = 85). Ninety-nine scans were reported as non-union with inadequate bridging callus, 19 of which were united at operation or on repeat CT imaging and represented delayed unions. Atrophic callus was found in 57 patients and all of which had a confirmed non-union (positive predictive value 100%). A hypertrophic callus was found in 42 patients, all of the delayed unions were found in this group (positive predictive value for non-union 55%, p < 0.001). CT compared to radiographs showed greater inter-observer agreement for union (weighted kappa 0.75 vs. 0.50 respectively). Overall, CT is 100% sensitive and 81.7% specific for non-union diagnosis. DISCUSSION: CT has excellent accuracy to determine clavicle union but approximately one in five suspected non-unions went onto unite. Hypertrophic callus finding resulted in a delayed union in approximately half of the cases in our study.

Unusual Near-Horizon Cosmic-Ray-like Events Observed by ANITA-IV.

ANITA's fourth long-duration balloon flight in 2016 detected 29 cosmic-ray (CR)-like events on a background of 0.37_{-0.17}^{+0.27} anthropogenic events. CRs are mainly seen in reflection off the Antarctic ice sheets, creating a phase-inverted waveform polarity. However, four of the below-horizon CR-like events show anomalous noninverted polarity, a p=5.3×10^{-4} chance if due to background. All anomalous events are from locations near the horizon; ANITA-IV observed no steeply upcoming anomalous events similar to the two such events seen in prior flights.

Lung organoids and other preclinical models of pulmonary fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a progressive fatal disease affecting over 100 000 people in Europe with an increasing incidence. Available treatments offer only slowing of disease progression and are poorly tolerated by patients leading to cessation of therapy. Lung transplant remains the only cure. Therefore, alternative treatments are urgently required. The pathology of IPF is complex and poorly understood and thus creates a major obstacle to the discovery of novel treatments. Additionally, preclinical assessment of new treatments currently relies upon animal models where disparities with human lung biology often hamper drug development. At a cellular level, IPF is characterized by persistent and abnormal deposition of extracellular matrix by fibroblasts and alveolar epithelial cell injury which is seen as a key event in initiation of disease progression. In-depth investigation of the role of alveolar epithelial cells in health and disease has been impeded due to difficulties in primary cell isolation and culture ex vivo. Novel strategies employing patient-derived induced pluripotent stem cells engineered to produce type 2 alveolar epithelial cells (iAEC2) cultured as three-dimensional organoids have the potential to overcome these hurdles and inform new effective precision treatments for IPF leading to improved survival and quality of life for patients worldwide.

Intratumoral delivery of tavokinogene telseplasmid yields systemic immune responses in metastatic melanoma patients.

BACKGROUND: Interleukin 12 (IL-12) is a pivotal regulator of innate and adaptive immunity. We conducted a prospective open-label, phase II clinical trial of electroporated plasmid IL-12 in advanced melanoma patients (NCT01502293). PATIENTS AND METHODS: Patients with stage III/IV melanoma were treated intratumorally with plasmid encoding IL-12 (tavokinogene telseplasmid; tavo), 0.5 mg/ml followed by electroporation (six pulses, 1500 V/cm) on days 1, 5, and 8 every 90 days in the main study and additional patients were treated in two alternative schedule exploration cohorts. Correlative analyses for programmed death-ligand 1 (PD-L1), flow cytometry to assess changes in immune cell subsets, and analysis of immune-related gene expression were carried out on pre- and post-treatment samples from study patients, as well as from additional patients treated during exploration of additional dosing schedules beyond the pre-specified protocol dosing schedule. Response was measured by study-specific criteria to maximize detection of latent and potentially transient immune responses in patients with multiple skin lesions and toxicities were graded by the Common Terminology Criteria for Adverse Events version 4.0 (CTCAE v4.0). RESULTS: The objective overall response rate was 35.7% in the main study (29.8% in all cohorts), with a complete response rate of 17.9% (10.6% in all cohorts). The median progression-free survival in the main study was 3.7 months while the median overall survival was not reached at a median follow up of 29.7 months. A total of 46% of patients in all cohorts with uninjected lesions experienced regression of at least one of these lesions and 25% had a net regression of all untreated lesions. Transcriptomic and immunohistochemistry analysis showed that immune activation and co-stimulatory transcripts were up-regulated but there was also increased adaptive immune resistance. CONCLUSIONS: Intratumoral Tavo was well tolerated and led to systemic immune responses in advanced melanoma patients. While tumor regression and increased immune infiltration were observed in treated as well as untreated/distal lesions, adaptive immune resistance limited the response.

Efficacy and safety of immune checkpoint inhibitor immunotherapy in elderly cancer patients.

PURPOSE: There is limited evidence on the efficacy and safety of anti-programmed cell death protein 1 (PD-1)-/anti-programmed death-ligand 1 (PD-L1)-based immunotherapy in the elderly, particularly those aged over 75 years. METHODS/PATIENTS: The clinical response and toxicity profile of anti-PD-1-/anti-PD-L1-based immunotherapy in patients aged over 75 years were assessed in this retrospective observational study conducted in the Medical Oncology Service of a tertiary level hospital. The associations among clinical responses, adverse events, and geriatric syndromes were evaluated. RESULTS: In total, 20 patients aged between 75 and 94 years were evaluated. Pembrolizumab and nivolumab were the most commonly used drugs. A clinical benefit (stable disease, partial response or complete response) was documented in 13 patients (65%). This proportion was 80% in patients aged between 75 and 79 years, and 50% in those aged over 79 years (p = 0.236). The adverse events were similar to those reported in younger patients. At least one clinical adverse event (cAE) and one laboratory adverse event (lAE) was reported in 75% and 55% of patients, respectively. Polypharmacy was observed for all patients and multi-morbidity in 95%. Patients without gait disorders showed more responses to immunotherapy. The number of lAEs was significantly associated with the number of commonly prescribed drugs (slope = 0.218, p = 0.010), the Eastern Cooperative Oncology Group score, and the number of cAEs. CONCLUSIONS: The elderly can obtain benefits from anti-PD-1-/anti-PD-L1-based immunotherapy. The toxicity profile was similar to that reported in younger counterparts.

Inmunoterapia para el tratamiento del cáncer de pulmón / Immunotherapy for the treatment of lung cancer

Tradicionalmente, la quimioterapia (QT) ha sido el tratamiento fundamental del cáncer de pulmón avanzado sin mutaciones accionables. La inmunoterapia (IT) con anticuerpos inhibidores del punto de control inmune (immune checkpoint inhibitors; IPCI) que actúan sobre la célula T ha revolucionado el tratamiento del cáncer de pulmón. Las respuestas a los IPCI pueden ser profundas y duraderas, obteniendo largos supervivientes. Actualmente, están aprobados en cáncer de pulmón no microcítico (CPCNP) dos anticuerpos anti-PD-1 (nivolumab y pembrolizumab) y dos anti-PD-L1 (atezolizumab y durvalumab) en diversas indicaciones; y atezolizumab en primera línea de carcinoma microcítico de pulmón metastásico en combinación con QT. Sin embargo, es necesario buscar biomarcadores para optimizar la eficiencia de los IPCI. En este trabajo se revisan las bases moleculares, la evidencia del uso de IPCI en cáncer de pulmón, los biomarcadores disponibles, los métodos de valoración de respuesta, los eventos adversos inmunorrelacionados y las perspectivas futuras de la IT para el cáncer de pulmón

Traditionally, chemotherapy has been the fundamental treatment of advanced lung cancer without actionable mutations. Immunotherapy with antibodies inhibiting the immune checkpoints (ICI) revolutionized the treatment of lung cancer, releasing the brakes of the adaptive immune response against the tumor. Responses to ICI can be deep and lasting, obtaining long-term survivors. Currently, two anti-PD-1 antibodies (nivolumab and pembrolizumab) and two anti-PD-L1 (atezolizumab and durvalumab) are approved in several indications for non-small-cell lung cancer (NSCLC); and atezolizumab in the first-line of treatment of metastatic small-cell lung carcinoma, in combination with chemotherapy. However, biomarkers are necessary to optimize treatment efficiency. In this work we review the molecular basis and the evidence of the use of ICI in lung cancer, available biomarkers, tumor response assessment methods, immune-related adverse events, and future perspectives of immunotherapy for lung cancer

Observation of an Unusual Upward-Going Cosmic-Ray-like Event in the Third Flight of ANITA.

We report on an upward traveling, radio-detected cosmic-ray-like impulsive event with characteristics closely matching an extensive air shower. This event, observed in the third flight of the Antarctic Impulsive Transient Antenna (ANITA), a NASA-sponsored long-duration balloon payload, is consistent with a similar event reported in a previous flight. These events could be produced by the atmospheric decay of an upward-propagating τ lepton produced by a ν_{τ} interaction, although their relatively steep arrival angles create tension with the standard model neutrino cross section. Each of the two events have a posteriori background estimates of ≲10^{-2} events. If these are generated by τ-lepton decay, then either the charged-current ν_{τ} cross section is suppressed at EeV energies, or the events arise at moments when the peak flux of a transient neutrino source was much larger than the typical expected cosmogenic background neutrinos.

Geriatric oncology in Spain: survey results and analysis of the current situation

Introduction: Geriatric oncology (GO) is a discipline that focuses on the management of elderly patients with cancer. The Spanish Society of Medical Oncology (SEOM) created a Working group dedicated to geriatric oncology in February 2016. Objectives: The main goal of this study was to describe the current situation in Spain regarding the management of elderly cancer patients through an online survey of medical oncologists. Methods: A descriptive survey was sent to several hospitals by means of the SEOM website. A personal e-mail was also sent to SEOM members. Results: Between March 2016 and April 2017, 154 answers were collected. Only 74 centers (48%) had a geriatrics department and a mere 21 (14%) medical oncology departments had a person dedicated to GO. The vast majority (n = 135; 88%) had the perception that the number of elderly patients with cancer seen in clinical practice had increased. Eighteen (12%) oncologists had specific protocols and geriatric scales were used at 55 (31%) centers. Almost all (92%) claimed to apply special management practices using specific tools. There was agreement that GO afforded certain potential advantages. Finally, 99% of the oncologists surveyed believed it and that training in GO had to be improved. Conclusions: From the nationwide survey promoted by the Spanish Geriatric Oncology Working Group on behalf of SEOM, we conclude that there is currently no defined care structure for elderly cancer patients. There is an increasing perception of the need for training in GO. This survey reflects a reality in which specific needs are perceived

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MALDI-TOF MS in Anaerobiospirillum succiniciproducens bacteremia: A report of 4 cases in different hosts.

Anaerobiospirillum succiniciproducens is known as an uncommon cause of diarrhea and bacteremia in humans, usually in immunocompromised hosts. We report four cases of A. succiniciproducens bloodstream infection in different hosts, including a previously healthy man. We describe clinical features, antibiotics susceptibility profile, treatment and outcomes. Strains were identified by 16S rRNA gene sequences which contributed to the extension of our MALDI-TOF MS database.

Geriatric oncology in Spain: survey results and analysis of the current situation.

INTRODUCTION: Geriatric oncology (GO) is a discipline that focuses on the management of elderly patients with cancer. The Spanish Society of Medical Oncology (SEOM) created a Working group dedicated to geriatric oncology in February 2016. OBJECTIVES: The main goal of this study was to describe the current situation in Spain regarding the management of elderly cancer patients through an online survey of medical oncologists. METHODS: A descriptive survey was sent to several hospitals by means of the SEOM website. A personal e-mail was also sent to SEOM members. RESULTS: Between March 2016 and April 2017, 154 answers were collected. Only 74 centers (48%) had a geriatrics department and a mere 21 (14%) medical oncology departments had a person dedicated to GO. The vast majority (n = 135; 88%) had the perception that the number of elderly patients with cancer seen in clinical practice had increased. Eighteen (12%) oncologists had specific protocols and geriatric scales were used at 55 (31%) centers. Almost all (92%) claimed to apply special management practices using specific tools. There was agreement that GO afforded certain potential advantages. Finally, 99% of the oncologists surveyed believed it and that training in GO had to be improved. CONCLUSIONS: From the nationwide survey promoted by the Spanish Geriatric Oncology Working Group on behalf of SEOM, we conclude that there is currently no defined care structure for elderly cancer patients. There is an increasing perception of the need for training in GO. This survey reflects a reality in which specific needs are perceived.

The in situ bacterial production of fluorescent organic matter; an investigation at a species level.

Aquatic dissolved organic matter (DOM) plays an essential role in biogeochemical cycling and transport of organic matter throughout the hydrological continuum. To characterise microbially-derived organic matter (OM) from common environmental microorganisms (Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa), excitation-emission matrix (EEM) fluorescence spectroscopy was employed. This work shows that bacterial organisms can produce fluorescent organic matter (FOM) in situ and, furthermore, that the production of FOM differs at a bacterial species level. This production can be attributed to structural biological compounds, specific functional proteins (e.g. pyoverdine production by P. aeruginosa), and/or metabolic by-products. Bacterial growth curve data demonstrates that the production of FOM is fundamentally related to microbial metabolism. For example, the majority of Peak T fluorescence (> 75%) is shown to be intracellular in origin, as a result of the building of proteins for growth and metabolism. This underpins the use of Peak T as a measure of microbial activity, as opposed to bacterial enumeration as has been previously suggested. This study shows that different bacterial species produce a range of FOM that has historically been attributed to high molecular weight allochthonous material or the degradation of terrestrial FOM. We provide definitive evidence that, in fact, it can be produced by microbes within a model system (autochthonous), providing new insights into the possible origin of allochthonous and autochthonous organic material present in aquatic systems.

A Four-Biomarker Blood Signature Discriminates Systemic Inflammation Due to Viral Infection Versus Other Etiologies.

The innate immune system of humans and other mammals responds to pathogen-associated molecular patterns (PAMPs) that are conserved across broad classes of infectious agents such as bacteria and viruses. We hypothesized that a blood-based transcriptional signature could be discovered indicating a host systemic response to viral infection. Previous work identified host transcriptional signatures to individual viruses including influenza, respiratory syncytial virus and dengue, but the generality of these signatures across all viral infection types has not been established. Based on 44 publicly available datasets and two clinical studies of our own design, we discovered and validated a four-gene expression signature in whole blood, indicative of a general host systemic response to many types of viral infection. The signature's genes are: Interferon Stimulated Gene 15 (ISG15), Interleukin 16 (IL16), 2',5'-Oligoadenylate Synthetase Like (OASL), and Adhesion G Protein Coupled Receptor E5 (ADGRE5). In each of 13 validation datasets encompassing human, macaque, chimpanzee, pig, mouse, rat and all seven Baltimore virus classification groups, the signature provides statistically significant (p < 0.05) discrimination between viral and non-viral conditions. The signature may have clinical utility for differentiating host systemic inflammation (SI) due to viral versus bacterial or non-infectious causes.

Immunoscore and Immunoprofiling in cancer: an update from the melanoma and immunotherapy bridge 2015.

The fifth "Melanoma Bridge Meeting" took place in Naples, December 1-5th, 2015. The main topics discussed at this meeting were: Molecular and Immuno advances, Immunotherapies and Combination Therapies, Tumor Microenvironment and Biomarkers and Immunoscore. The natural history of cancer involves interactions between the tumor and the immune system of the host. The immune infiltration at the tumor site may be indicative of host response. Significant correlations were shown between the levels of immune cell infiltration in tumors and patient's clinical outcome. Moreover, incredible progress comes from the discovery of mutation-encoded tumor neoantigens. In fact, as tumors grow, they acquire mutations that are able to influence the response of patients to immune checkpoint inhibitors. It has been demonstrated that sensitivity to PD-1 and CTLA-4 blockade in patients with advanced NSCLC and melanoma was enhanced in tumors enriched for clonal neoantigens. The road ahead is still very long, but the knowledge of the mechanisms of immune escape, the study of tumor neo-antigens as well as of tumor microenvironment and the development of new immunotherapy strategies, will make cancer a more and more treatable disease.

Effectiveness of Rabbit Antithymocyte Globulin in Chronic Lung Allograft Dysfunction.

BACKGROUND: Rabbit antithymocyte globulin (rATG) therapy has been shown to be beneficial in lung transplant recipients as induction therapy for treating acute lung rejection; however, its role in chronic lung rejection has been reported only rarely. We evaluated the effectiveness of rATG therapy in slowing the progression of chronic lung allograft dysfunction (CLAD) syndrome. METHODS: We conducted a retrospective review of 25 lung transplant patients with CLAD who received rATG therapy in the Pulmonary Institute of Rabin Medical Center, Israel, between May 2005 and February 2016. Response to treatment was divided into 2 categories: stabilization, defined as a halting of the decline of forced expiratory volume in 1 second (FEV1) for ≥6 months after rATG therapy, and deterioration, defined as showing a continued decline in FEV1. RESULTS: Of 25 subjects, 8 (32%) were categorized as part of the stabilization group and 17 (68%) were categorized as showing continued deterioration. The stabilization group was older (61 ± 8 vs 44 ± 19 years) and showed longer survival rate after rATG therapy (930 ± 385 vs 414 ± 277 days). The stabilization group also demonstrated a lower mean white blood cell count (7.9 ± 1.8 vs 8.5 ± 2.9 × 10(9) cells/L) and lymphocyte count (0.37 ± 0.1 vs 0.55 ± 0.3 × 10(9) cells/L) during rATG treatment. The stabilization group also demonstrated a higher FEV1 after lung transplantation (91% ± 21% vs 75% ± 15.4%), at the beginning of rATG therapy (51% ± 11% vs 39% ± 9.6%) and at 6 months after rATG therapy follow-up (51% ± 9.1% vs 28% ± 7.6%). CONCLUSIONS: rATG was effective in stabilizing rejection progression in approximately one-third of our patients with CLAD. rATG therapy should be considered early in the course of CLAD. Randomized, controlled studies should be considered to confirm these findings.