Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures.

The lack of benchmark data sets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and differential expression analysis workflows. Here, we present a benchmark experiment using two human lung adenocarcinoma cell lines that were each profiled in triplicate together with synthetic, spliced, spike-in RNAs (sequins). Samples were deeply sequenced on both Illumina short-read and Oxford Nanopore Technologies long-read platforms. Alongside the ground-truth available via the sequins, we created in silico mixture samples to allow performance assessment in the absence of true positives or true negatives. Our results show that StringTie2 and bambu outperformed other tools from the six isoform detection tools tested, DESeq2, edgeR and limma-voom were best among the five differential transcript expression tools tested and there was no clear front-runner for performing differential transcript usage analysis between the five tools compared, which suggests further methods development is needed for this application.

Losartan controls immune checkpoint blocker-induced edema and improves survival in glioblastoma mouse models.

Immune checkpoint blockers (ICBs) have failed in all phase III glioblastoma trials. Here, we found that ICBs induce cerebral edema in some patients and mice with glioblastoma. Through single-cell RNA sequencing, intravital imaging, and CD8+ T cell blocking studies in mice, we demonstrated that this edema results from an inflammatory response following antiprogrammed death 1 (PD1) antibody treatment that disrupts the blood-tumor barrier. Used in lieu of immunosuppressive corticosteroids, the angiotensin receptor blocker losartan prevented this ICB-induced edema and reprogrammed the tumor microenvironment, curing 20% of mice which increased to 40% in combination with standard of care treatment. Using a bihemispheric tumor model, we identified a "hot" tumor immune signature prior to losartan+anti-PD1 therapy that predicted long-term survival. Our findings provide the rationale and associated biomarkers to test losartan with ICBs in glioblastoma patients.

Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions.

Actinobacillus pleuropneumoniae is the cause of porcine pleuropneumonia, a severe respiratory tract infection that is responsible for major economic losses to the swine industry. Many host-adapted bacterial pathogens encode systems known as phasevarions (phase-variable regulons). Phasevarions result from variable expression of cytoplasmic DNA methyltransferases. Variable expression results in genome-wide methylation differences within a bacterial population, leading to altered expression of multiple genes via epigenetic mechanisms. Our examination of a diverse population of A. pleuropneumoniae strains determined that Type I and Type III DNA methyltransferases with the hallmarks of phase variation were present in this species. We demonstrate that phase variation is occurring in these methyltransferases, and show associations between particular Type III methyltransferase alleles and serovar. Using Pacific BioSciences Single-Molecule, Real-Time (SMRT) sequencing and Oxford Nanopore sequencing, we demonstrate the presence of the first ever characterised phase-variable, cytosine-specific Type III DNA methyltransferase. Phase variation of distinct Type III DNA methyltransferase in A. pleuropneumoniae results in the regulation of distinct phasevarions, and in multiple phenotypic differences relevant to pathobiology. Our characterisation of these newly described phasevarions in A. pleuropneumoniae will aid in the selection of stably expressed antigens, and direct and inform development of a rationally designed subunit vaccine against this major veterinary pathogen.

Tracking Symptoms of Patients With Lymphedema Before and After Power-Assisted Liposuction Surgery.

PURPOSE: Lymphedema negatively impacts patients from a psychosocial standpoint and consequently affects patient's quality of life. Debulking procedures using power-assisted liposuction (PAL) are currently deemed an effective treatment for fat-dominant lymphedema and improves anthropometric measurements as well as quality of life. However, there have been no studies specifically evaluating changes in symptoms related to lymphedema after PAL. An understanding of how symptoms change after this procedure would be valuable for preoperative counseling and to guide patient expectations. METHODS: A cross-sectional study was performed in patients with extremity lymphedema who underwent PAL from January 2018 to December 2020 at a tertiary care facility. A retrospective chart review and follow-up phone survey were conducted to compare signs and symptoms related to lymphedema before and after PAL. RESULTS: Forty-five patients were included in this study. Of these, 27 patients (60%) underwent upper extremity PAL and 18 patients (40%) underwent lower extremity PAL. The mean follow-up time was 15.5±7.9 months. After PAL, patients with upper extremity lymphedema reported having resolved heaviness (44%), as well as improved achiness (79%) and swelling (78%). In patients with lower extremity lymphedema, they reported having improved all signs and symptoms, particularly swelling (78%), tightness (72%), and achiness (71%). CONCLUSIONS: In patients with fat-dominant lymphedema, PAL positively impacts patient-reported outcomes in a sustained fashion over time. Continuous surveillance of postoperative studies is required to elucidate factors independently associated with the outcomes found in our study. Moreover, further studies using a mixed method approach will help us better understand patient's expectations to achieve informed decision and adequate treatment goals.

Sociodemographic characteristics, lifestyle behaviors, and symptoms associated with fluid overload among non-hospitalized and community-dwelling older adults with heart failure: A population-based approach.

BACKGROUND: Fluid overload is a major complication in patients with heart failure (HF) and the main reason for hospitalization. The purpose of the study was to explore the associations of fluid overload with sociodemographic characteristics, lifestyle behaviors, and symptoms among non-hospitalized and community-dwelling older adults with HF using large population data. METHODS: Descriptive and multivariate analyses were conducted on the Health and Retirement Study 2016. RESULTS: Fluid overload was prevalent in almost half of the sample. Female older adults with HF were more likely to have fluid overload (OR:1.43, p = 0.037) as well as being Black (OR:1.40, p = 0.041). Higher physical activity scores were associated with less likelihood of having fluid overload (OR:0.99, p = 0.025). Symptoms of shortness of breath (OR=2.18, p = 0.001), pain (OR=1.82, p < 0.001), and fatigue (OR=1.45, p = 0.025) were significantly associated with fluid overload. CONCLUSION: Female and Black community-dwelling older adults with HF are at higher risk of fluid overload. Symptoms of shortness of breath, pain, and fatigue are significant manifestations of fluid overload. Effective patient-centered interventions to promote fluid flow via physical activity may help older adults with HF manage fluid overload and alleviate associated symptoms.

A Pilot Qualitative Case Study of Women's Experiences with Fertility Awareness-Based Methods.

This pilot qualitative case study was able to elicit rich data enabling a description of how women went through the journey of achieving pregnancy using fertility awareness-based methods. Findings underscore that women preferred using natural ways to detect ovulation and would recommend other women to do so, but with healthcare providers' guidance. The findings of this case study can serve as a starting point to provide a framework to understand women's experiences of enduring trial and error with multiple fertility awareness-based methods before discovering their effective method. Findings emphasize the importance for healthcare providers to guide women in using fertility awareness-based methods.

Blocking CXCR4 alleviates desmoplasia, increases T-lymphocyte infiltration, and improves immunotherapy in metastatic breast cancer.

Metastatic breast cancers (mBCs) are largely resistant to immune checkpoint blockade, but the mechanisms remain unclear. Primary breast cancers are characterized by a dense fibrotic stroma, which is considered immunosuppressive in multiple malignancies, but the stromal composition of breast cancer metastases and its role in immunosuppression are largely unknown. Here we show that liver and lung metastases of human breast cancers tend to be highly fibrotic, and unlike primary breast tumors, they exclude cytotoxic T lymphocytes (CTLs). Unbiased analysis of the The Cancer Genome Atlas database of human breast tumors revealed a set of genes that are associated with stromal T-lymphocyte exclusion. Among these, we focused on CXCL12 as a relevant target based on its known roles in immunosuppression in other cancer types. We found that the CXCL12 receptor CXCR4 is highly expressed in both human primary tumors and metastases. To gain insight into the role of the CXCL12/CXCR4 axis, we inhibited CXCR4 signaling pharmacologically and found that plerixafor decreases fibrosis, alleviates solid stress, decompresses blood vessels, increases CTL infiltration, and decreases immunosuppression in murine mBC models. By deleting CXCR4 in αSMA+ cells, we confirmed that these immunosuppressive effects are dependent on CXCR4 signaling in αSMA+ cells, which include cancer-associated fibroblasts as well as other cells such as pericytes. Accordingly, CXCR4 inhibition more than doubles the response to immune checkpoint blockers in mice bearing mBCs. These findings demonstrate that CXCL12/CXCR4-mediated desmoplasia in mBC promotes immunosuppression and is a potential target for overcoming therapeutic resistance to immune checkpoint blockade in mBC patients.

Optimal patient protocols in regional acute stroke care.

In acute stroke care two proven reperfusion treatments exist: (1) a blood thinner and (2) an interventional procedure. The interventional procedure can only be given in a stroke centre with specialized facilities. Rapid initiation of either is key to improving the functional outcome (often emphasized by the common phrase in acute stroke care "time=brain"). Delays between the moment the ambulance is called and the initiation of one or both reperfusion treatment(s) should therefore be as short as possible. The speed of the process strongly depends on five factors: patient location, regional patient allocation by emergency medical services (EMS), travel times of EMS, treatment locations, and in-hospital delays. Regional patient allocation by EMS and treatment locations are sub-optimally configured in daily practice. Our aim is to construct a mathematical model for the joint decision of treatment locations and allocation of acute stroke patients in a region, such that the time until treatment is minimized. We describe acute stroke care as a multi-flow two-level hierarchical facility location problem and the model is formulated as a mixed integer linear program. The objective of the model is the minimization of the total time until treatment in a region and it incorporates volume-dependent in-hospital delays. The resulting model is used to gain insight in the performance of practically oriented patient allocation protocols, used by EMS. We observe that the protocol of directly driving to the nearest stroke centre with special facilities (i.e., the mothership protocol) performs closest to optimal, with an average total time delay that is 3.9% above optimal. Driving to the nearest regional stroke centre (i.e., the drip-and-ship protocol) is on average 8.6% worse than optimal. However, drip-and-ship performs better than the mothership protocol in rural areas and when a small fraction of the population (at most 30%) requires the second procedure, assuming sufficient patient volumes per stroke centre. In the experiments, the time until treatment using the optimal model is reduced by at most 18.9 minutes per treated patient. In economical terms, assuming 150 interventional procedures per year, the value of medical intervention in acute stroke can be improved upon up to € 1,800,000 per year.

Exploring expectations and perceptions of different manual therapy techniques in chronic low back pain: a qualitative study.

BACKGROUND: Chronic low back pain (CLBP) prevalence has steadily increased over the last two decades. Manual therapy (MT) is recommended within a multimodal management approach to improve pain and disability although evidence investigating the patients' experience of MT is scarce. OBJECTIVE: To explore expectations and perceptions of MT techniques in people with CLBP. METHODS: A qualitative study embedded sequential to an experimental trial using semi-structured interviews (SSI) explored participants' experiences of thrust, non-thrust and sham technique. Purposive sampling enabled variance in age and CLBP duration. An evidence informed topic guide was used. Data were analysed using thematic analysis (TA). Respondent validation and peer debriefing enhanced trustworthiness. The Consolidating Criteria for Reporting Qualitative Studies (COREQ) reported methodological rigour. FINDINGS: Ten participants (50% male) with a mean age of 29.1 years (Standard Deviation (SD): 7.9, range: 19-43), a mean pain intensity of 4.5 on a Numeric Rating Scale (NRS) 0-10 (SD: 1.5, range: 2-7), a mean Oswestry Disability Score (ODI) of 9 (SD: 4.6, range: 2-17) and a mean Tampa Scale of Kinesiophobia (TSK) score of 38.6 (SD: 4.8, range: 30-45) participated. Four themes were identified: understanding of pain; forming expectations; perception of care; re-evaluation of body awareness and management. Understanding of CLBP is formed by an individuals' pain perception and exchange with social environment. This, combined with communication with physiotherapist influenced expectations regarding the MT technique. CONCLUSION: Expectations for MT were formed by an individual's social environment and previous experience. A treatment technique is perceived as positive if its characteristics are aligned with the individual's understanding of pain and if care is delivered in an informative and reassuring manner.

Current status and future directions of U.S. genomic nursing health care policy.

BACKGROUND: As genomic science moves beyond government-academic collaborations into routine healthcare operations, nursing's holistic philosophy and evidence-based practice approach positions nurses as leaders to advance genomics and precision health care in routine patient care. PURPOSE: To examine the status of and identify gaps for U.S. genomic nursing health care policy and precision health clinical practice implementation. METHODS: We conducted a scoping review and policy priorities analysis to clarify key genomic policy concepts and definitions, and to examine trends and utilization of health care quality benchmarking used in precision health. FINDINGS: Genomic nursing health care policy is an emerging area. Educating and training the nursing workforce to achieve full dissemination and integration of precision health into clinical practice remains an ongoing challenge. Use of health care quality measurement principles and federal benchmarking performance evaluation criteria for precision health implementation are not developed. DISCUSSION: Nine recommendations were formed with calls to action across nursing practice workforce and education, nursing research, and health care policy arenas. CONCLUSIONS: To advance genomic nursing health care policy, it is imperative to develop genomic performance measurement tools for clinicians, purchasers, regulators and policymakers and to adequately prepare the nursing workforce.

The Microbiome and Metabolome of Malignant Fungating Wounds: A Systematic Review of the Literature From 1995 to 2020.

PURPOSE: Malignant fungating wounds (MFWs) afflict up to 14% of patients with advanced cancer. The bacterial community structures of MFW may influence the development and severity of wound symptoms. The purpose of this systematic review was to evaluate existing evidence regarding the relationship between microbiome and symptoms of MFWs. METHODS: A systematic review of the published literature from January 1995 to January 2020 was conducted. An established quality assessment tool was used to assess the quality of the included studies. SEARCH STRATEGY: We searched 4 major electronic databases and retrieved 724 articles; 7 met inclusion criteria. FINDINGS/CONCLUSIONS: Seven studies were included; the overall quality of the included 7 studies was ranked as adequate. Findings from the studies provided an incomplete characterization of the microbiome and metabolome of MFW; none included modern genomic technologies. Twenty different species of aerobes and 14 species of anaerobes were identified, with inconsistent identification of biofilms and multi-drug-resistant bacteria. Symptom occurrence increased with the number of bacteria species (P = .0003) and the presence of at least 1 anaerobe (P = .0006) in malignant wound beds. Cancer wound-derived odor was associated with dimethyl trisulfide and 4 fatty acid volatiles. Periwound and moisture-associated skin damage were associated with higher putrescine levels in exudates. IMPLICATIONS: Understanding the role of microbiota of MFW in developing or amplifying the severity of wound symptoms is the first step toward development of more precise and effective topical interventions.

Complementary low-level laser therapy for breast cancer-related lymphedema: a pilot, double-blind, randomized, placebo-controlled study.

This pilot, double-blind, randomized, placebo-controlled study is aimed at evaluating the effectiveness of low-level laser therapy (LLLT) as a complementary treatment to complete decongestive therapy (CDT) treating lymphedema among breast cancer patients for 12 months post-intervention. Study population was breast cancer patients who were diagnosed and referred to lymphedema clinic for CDT. Participants (n = 22) were randomized and assigned into either an active laser intervention group or an inactive laser placebo-control group. Active LLLT was administered to participants twice a week at the beginning of each CDT session. Outcome measures included lymphedema symptoms, symptom distress, and limb volume by an infrared perometer. Participants in the active and placebo laser groups were comparable in demographic and clinical predictors of lymphedema. In comparison with the placebo group (83.3%), significantly fewer participants in the active laser group (55.6%) reported more than one lymphedema symptom (p = 0.012) at 12 months post-intervention. Significantly, more patients in the active laser group (44.4%) reported less than two impaired limb mobility symptoms in comparison with the placebo group (33.3%) at 12 months post-intervention (p = 0.017). The active laser group had statistically significant improvements in symptom distress of sadness (p = 0.005) from 73 to 11% and self-perception (p = 0.030) from 36 to 0% over time from baseline to 12-months post-intervention. There was no significant reduction in limb volume. Findings of the trial demonstrated significant benefits of complementary LLLT for relieving symptoms and improvement of emotional distress in breast cancer patients with lymphedema.

Microbial community composition and diversity in rice straw digestion bioreactors with and without dairy manure.

Anaerobic digestion (AD) uses a range of substrates to generate biogas, including energy crops such as globally abundant rice straw (RS). Unfortunately, RS is high in lignocellulosic material and has high to C:N ratios (~80:1), which makes it (alone) a comparatively poor substrate for AD. Co-digestion with dairy manure (DM) has been promoted as a method for balancing C:N ratios to improve RS AD whilst also treating another farm waste and co-producing a potentially useful fertiliser. However, past co-digestion studies have not directly compared RS AD microbial communities with and without DM additions, which has made it hard to assess all impacts of DM addition to RS AD processes. Here, four RS:DM ratios were contrasted in identical semi-continuous-fed AD bioreactors, and 100% RS was found to produce the highest specific methane yields (112 mL CH4/g VS/day; VS, volatile solids), which is over double yields achieved in the reactor with the highest DM content (30:70 RS:DM by mass; 48 mL CH4/g VS/day). To underpin these data, microbial communities were sequenced and characterised across the four reactors. Dominant operational taxonomic units (OTUs) in the 100% RS unit were Bacteroidetes/Firmicutes, whereas the 30:70 RS:DM unit was dominated by Proteobacteria/Spirochaetes, suggesting major microbial community shifts occur with DM additions. However, community richness was lowest with 100% RS (despite higher specific yields), suggesting particular OTUs may be more important to yields than microbial diversity. Further, ambient VFA and VS levels were significantly higher when no DM was added, suggesting DM-amended reactors may cope better with higher organic loading rates (OLR). Results show that RS AD without DM addition is feasible, although co-digestion with DM will probably allow higher OLRs, resulting in great RS throughput in farm AD units.

Phase II and Biomarker Study of Cabozantinib in Metastatic Triple-Negative Breast Cancer Patients.

Currently, no targeted therapies are available for metastatic triplenegative breast cancer (mTNBC). We evaluated the safety, efficacy, and biomarkers of response to cabozantinib, a multikinase inhibitor, in patients with mTNBC. We conducted a single arm phase II and biomarker study that enrolled patients with measurable mTNBC. Patients received cabozantinib (60 mg daily) on a 3-week cycle and were restaged after 6 weeks and then every 9 weeks. The primary endpoint was objective response rate. Predefined secondary endpoints included progression-free survival (PFS), toxicity, and tissue and blood circulating cell and protein biomarkers. Of 35 patients who initiated protocol therapy, 3 (9% [95% confidence interval (CI): 2, 26]) achieved a partial response (PR). Nine patients achieved stable disease (SD) for at least 15 weeks, and thus the clinical benefit rate (PR+SD) was 34% [95% CI: 19, 52]. Median PFS was 2.0 months [95% CI: 1.3, 3.3]. The most common toxicities were fatigue, diarrhea, mucositis, and palmar-plantar erythrodysesthesia. There were no grade 4 toxicities, but 12 patients (34%) required dose reduction. Two patients had TNBCs with MET amplification. During cabozantinib therapy, there were significant and durable increases in plasma placental growth factor, vascular endothelial growth factor (VEGF), VEGF-D, stromal cell-derived factor 1a, and carbonic anhydrase IX, and circulating CD3 + cells and CD8 + T lymphocytes, and decreases in plasma soluble VEGF receptor 2 and CD14+ monocytes (all p < .05). Higher baseline concentrations of soluble MET (sMET) associated with longer PFS (p = .03). In conclusion, cabozantinib showed encouraging safety and efficacy signals but did not meet the primary endpoint in pretreated mTNBC. Exploratory analyses of circulating biomarkers showed that cabozantinib induces systemic changes consistent with activation of the immune system and antiangiogenic activity, and that sMET should be further evaluated a potential biomarker of response. IMPLICATIONS FOR PRACTICE: Triple-negative breast cancer (TNBC)-a disease with a dearth of effective therapies-often overexpress MET, which is associated with poor clinical outcomes. However, clinical studies of agents targeting MET and VEGF pathways-alone or in combination-have shown disappointing results. This study of cabozantinib (a dual VEGFR2/MET) in metastatic TNBC, while not meeting its prespecified endpoint, showed that treatment is associated with circulating biomarker changes, and is active in a subset of patients. Furthermore, this study demonstrates that cabozantinib therapy induces a systemic increase in cytotoxic lymphocyte populations and a decrease in immunosuppressive myeloid populations. This supports the testing of combinations of cabozantinib with immunotherapy in future studies in breast cancer patients.

A dynamic ambulance management model for rural areas : Computing redeployment actions for relevant performance measures.

We study the Dynamic Ambulance Management (DAM) problem in which one tries to retain the ability to respond to possible future requests quickly when ambulances become busy. To this end, we need models for relocation actions for idle ambulances that incorporate different performance measures related to response times. We focus on rural regions with a limited number of ambulances. We model the region of interest as an equidistant graph and we take into account the current status of both the system and the ambulances in a state. We do not require ambulances to return to a base station: they are allowed to idle at any node. This brings forth a high degree of complexity of the state space. Therefore, we present a heuristic approach to compute redeployment actions. We construct several scenarios that may occur one time-step later and combine these scenarios with each feasible action to obtain a classification of actions. We show that on most performance indicators, the heuristic policy significantly outperforms the classical compliance table policy often used in practice.

Dynamic ambulance dispatching: is the closest-idle policy always optimal?

We address the problem of ambulance dispatching, in which we must decide which ambulance to send to an incident in real time. In practice, it is commonly believed that the 'closest idle ambulance' rule is near-optimal and it is used throughout most literature. In this paper, we present alternatives to the classical closest idle ambulance rule. Most ambulance providers as well as researchers focus on minimizing the fraction of arrivals later than a certain threshold time, and we show that significant improvements can be obtained by our alternative policies. The first alternative is based on a Markov decision problem (MDP), that models more than just the number of idle vehicles, while remaining computationally tractable for reasonably-sized ambulance fleets. Second, we propose a heuristic for ambulance dispatching that can handle regions with large numbers of ambulances. Our main focus is on minimizing the fraction of arrivals later than a certain threshold time, but we show that with a small adaptation our MDP can also be used to minimize the average response time. We evaluate our policies by simulating a large emergency medical services region in the Netherlands. For this region, we show that our heuristic reduces the fraction of late arrivals by 18 % compared to the 'closest idle' benchmark policy. A drawback is that this heuristic increases the average response time (for this problem instance with 37 %). Therefore, we do not claim that our heuristic is practically preferable over the closest-idle method. However, our result sheds new light on the popular belief that the closest idle dispatch policy is near-optimal when minimizing the fraction of late arrivals.

CXCR4 inhibition in tumor microenvironment facilitates anti-programmed death receptor-1 immunotherapy in sorafenib-treated hepatocellular carcinoma in mice.

UNLABELLED: Sorafenib, a broad tyrosine kinase inhibitor, is the only approved systemic therapy for advanced hepatocellular carcinoma (HCC) but provides limited survival benefits. Recently, immunotherapy has emerged as a promising treatment strategy, but its role remains unclear in HCCs, which are associated with decreased cytotoxic CD8(+) T-lymphocyte infiltration in both murine and human tumors. Moreover, in mouse models after sorafenib treatment intratumoral hypoxia is increased and may fuel evasive resistance. Using orthotopic HCC models, we now show that increased hypoxia after sorafenib treatment promotes immunosuppression, characterized by increased intratumoral expression of the immune checkpoint inhibitor programmed death ligand-1 and accumulation of T-regulatory cells and M2-type macrophages. We also show that the recruitment of immunosuppressive cells is mediated in part by hypoxia-induced up-regulation of stromal cell-derived 1 alpha. Inhibition of the stromal cell-derived 1 alpha receptor (C-X-C receptor type 4 or CXCR4) using AMD3100 prevented the polarization toward an immunosuppressive microenvironment after sorafenib treatment, inhibited tumor growth, reduced lung metastasis, and improved survival. However, the combination of AMD3100 and sorafenib did not significantly change cytotoxic CD8(+) T-lymphocyte infiltration into HCC tumors and did not modify their activation status. In separate experiments, antibody blockade of the programmed death ligand-1 receptor programmed death receptor-1 (PD-1) showed antitumor effects in treatment-naive tumors in orthotopic (grafted and genetically engineered) models of HCC. However, anti-PD-1 antibody treatment had additional antitumor activity only when combined with sorafenib and AMD3100 and not when combined with sorafenib alone. CONCLUSION: Anti-PD-1 treatment can boost antitumor immune responses in HCC models; when used in combination with sorafenib, anti-PD-1 immunotherapy shows efficacy only with concomitant targeting of the hypoxic and immunosuppressive microenvironment with agents such as CXCR4 inhibitors.

Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate.

In anaerobic digesters, temperature fluctuation could lead to process instability and failure. It is still not well understood how digester microbiota as a whole respond to heat shock, and what specific organisms are vulnerable to perturbation or responsible for process recovery after perturbation. To address these questions, a mesophilic benzoate-degrading methanogenic culture enriched from digester was subjected to different levels of heat shock. Three types of methane production profiles after perturbation were observed in comparison to the control: uninhibited, inhibited with later recovery, and inhibited without recovery. These responses were correlated with the microbial community compositions based on the analyses of 16S rRNA and 16S rRNA gene. Specifically, the primary benzoate-degrading syntroph was highly affected by heat shock, and its abundance and activity were both crucial to the restoration of benzoate degradation after heat shock. In contrast, methanogens were stable regardless whether methane production was inhibited. Populations related to 'Candidatus Cloacimonetes' and Firmicutes showed stimulated growth. These observations indicated distinct physiological traits and ecological niches associated with individual microbial groups. The results obtained after exposure to heat shock can be critical to more comprehensive characterization of digester ecology under perturbations. SIGNIFICANCE AND IMPACT OF THE STUDY: Anaerobic digestion is an essential step in municipal wastewater treatment owing to its striking capacity of reducing wasted sludge and recovering energy. However, as an elaborate microbial process, it requires constant temperature control and is sensitive to heat shock. In this study, we explored the microbial response to heat shock of a methanogenic culture enriched from anaerobic digester sludge. Microorganisms that were vulnerable to perturbation or responsible for process recovery after perturbation were identified.