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The microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. In legumes and actinorhizal plants, a portion of essential nitrogen (N) is obtained through symbiosis with nodule-inhabiting, N2-fixing microorganisms. However, a variety of non-nodulating plant species can also thrive in natural, low-N settings. Some of these species may rely on endophytes, microorganisms that live within plants, to fix N2 gas into usable forms. Here we report the first direct evidence of N2 fixation in the early successional wild tree, Populus trichocarpa, a non-leguminous tree, from its native riparian habitat. In order to measure N2 fixation, surface-sterilized cuttings of wild poplar were assayed using both 15N2 incorporation and the commonly used acetylene reduction assay. The 15N label was incorporated at high levels in a subset of cuttings, suggesting a high level of N-fixation. Similarly, acetylene was reduced to ethylene in some samples. The microbiota of the cuttings was highly variable, both in numbers of cultured bacteria and in genetic diversity. Our results indicated that associative N2-fixation occurred within wild poplar and that a non-uniformity in the distribution of endophytic bacteria may explain the variability in N-fixation activity. These results point to the need for molecular studies to decipher the required microbial consortia and conditions for effective endophytic N2-fixation in trees.

Nanoliposomal irinotecan (nal-IRI) was originally developed using an efficient and high-loading capacity system to encapsulate irinotecan within a liposomal carrier, producing a therapeutic agent with improved biodistribution and pharmacokinetic characteristics compared to free drug. Specifically, administration of nal-IRI results in prolonged exposure of SN-38, the active metabolite of irinotecan, within tumors, while at the same time offering the advantage of less systemic toxicity than traditional irinotecan. These favorable properties of nal-IRI, confirmed in a variety of tumor xenograft models, led to its clinical evaluation in a number of disease indications for which camptothecins have proven activity, including in colorectal, gastric, and pancreatic cancers. The culmination of these clinical trials was the NAPOLI-1 (Nanoliposomal irinotecan with fluorouracil and folinic acid in metastatic pancreatic cancer after previous gemcitabine-based therapy) trial, an international Phase III study evaluating nal-IRI both alone and in combination with 5-fluorouracil and leucovorin in patients with metastatic pancreatic adenocarcinoma following progression on gemcitabine-based chemotherapy. Positive results from NAPOLI-1 led to approval of nal-IRI (with 5-fluorouracil/leucovorin) in October 2015 by the US Food and Drug Administration specifically for the treatment of metastatic pancreatic cancer in the second-line setting and beyond, a clinical context in which there had previously been no accepted standard of care. As such, nal-IRI represents an important landmark in cancer drug development, and potentially ushers in a new era where a greater number of patients with advanced pancreatic cancer can be sequenced through multiple lines of therapy translating into meaningful improvements in survival.

Empirical studies, often in the form of controlled experiments, have been widely adopted in software engineering research as a way to evaluate the merits of new software engineering tools. However, controlled experiments involving human participants actually using new tools are still rare, and when they are conducted, some have serious validity concerns. Recent research has also shown that many software engineering researchers view this form of tool evaluation as too risky and too difficult to conduct, as they might ultimately lead to inconclusive or negative results. In this paper, we aim both to help researchers minimize the risks of this form of tool evaluation, and to increase their quality, by offering practical methodological guidance on designing and running controlled experiments with developers. Our guidance fills gaps in the empirical literature by explaining, from a practical perspective, options in the recruitment and selection of human participants, informed consent, experimental procedures, demographic measurements, group assignment, training, the selecting and design of tasks, the measurement of common outcome variables such as success and time on task, and study debriefing. Throughout, we situate this guidance in the results of a new systematic review of the tool evaluations that were published in over 1,700 software engineering papers published from 2001 to 2011.

BACKGROUND:In trigeminal neuralgia type 1 (TN1), neurovascular compression (NVC) is often assumed to be the pain initiating mechanism. NVC can be surgically addressed by microvascular decompression (MVD). However, some patients with TN1 present without NVC (WONVC). OBJECTIVE:To characterize and analyze the clinical spectrum of a TN1 patient population WONVC. METHODS:A retrospective chart review of patients presenting with TN1 between 2007 and 2017 was performed. Patients who were potential candidates for MVD surgery underwent high-resolution imaging with 3-dimensional (3D) reconstruction to address the presence, or absence, of NVC. Demographic data about the populations with NVC (WNVC) and WONVC were collected. RESULTS:Of 242 patients with TN1, 32% did not have NVC. Patients WONVC were on average 10.6 yr younger than those WNVC. TN1 onset in patients WONVC was more frequent below 48.7 yr, and the opposite was found in patients WNVC. Compared to patients WNVC, those WONVC were predominantly female (odds ratio 4.8), on average were 4 yr younger at symptom onset (34.7 yr) and 7.8 yr younger at first clinic visit, and had a 3.7 yr shorter symptom duration. CONCLUSION:Patients presenting with TN1 WONVC were predominantly females in their mid-30s with short symptom duration. In the absence of NVC, this subgroup of TN1 patients has limited surgical options, and potentially a longer condition duration that must be managed medically or surgically. This population WONVC might provide insights into the true pathophysiology of TN1.

Background The MORPHEUS platform comprises multiple open-label, randomized, phase Ib/II trials designed to identify early efficacy and safety signals of treatment combinations across cancers. Atezolizumab (anti-programmed cell death 1 ligand 1 [PD-L1]) was evaluated in combination with PEGylated recombinant human hyaluronidase (PEGPH20). Methods In 2 randomized MORPHEUS trials, eligible patients with advanced, previously treated pancreatic ductal adenocarcinoma (PDAC) or gastric cancer (GC) received atezolizumab plus PEGPH20, or control treatment (mFOLFOX6 or gemcitabine plus nab-paclitaxel [MORPHEUS-PDAC]; ramucirumab plus paclitaxel [MORPHEUS-GC]). Primary endpoints were objective response rates (ORR) per RECIST 1.1 and safety. Results In MORPHEUS-PDAC, ORRs with atezolizumab plus PEGPH20 (n = 66) were 6.1% (95% CI, 1.68%-14.80%) vs. 2.4% (95% CI, 0.06%-12.57%) with chemotherapy (n = 42). In the respective arms, 65.2% and 61.9% had grade 3/4 adverse events (AEs); 4.5% and 2.4% had grade 5 AEs. In MORPHEUS-GC, confirmed ORRs with atezolizumab plus PEGPH20 (n = 13) were 0% (95% CI, 0%-24.7%) vs. 16.7% (95% CI, 2.1%-48.4%) with control (n = 12). Grade 3/4 AEs occurred in 30.8% and 75.0% of patients, respectively; no grade 5 AEs occurred. Conclusion Atezolizumab plus PEGPH20 showed limited clinical activity in patients with PDAC and none in patients with GC. The safety of atezolizumab plus PEGPH20 was consistent with each agent’s known safety profile. (ClinicalTrials.gov Identifier: NCT03193190 and NCT03281369). In this clinical trial, atezolizumab was evaluated in combination with PEGPH20 to assess clinical activity in patients with pancreatic ductal adenocarcinoma or gastric cancer.

SummaryBackgroundStandard chemotherapy remains inadequate in metastatic pancreatic adenocarcinoma. Combining an agonistic CD40 monoclonal antibody with chemotherapy induces T-cell-dependent tumour regression in mice and improves survival. In this study, we aimed to evaluate the safety of combining APX005M (sotigalimab) with gemcitabine plus nab-paclitaxel, with and without nivolumab, in patients with pancreatic adenocarcinoma to establish the recommended phase 2 dose. MethodsThis non-randomised, open-label, multicentre, four-cohort, phase 1b study was done at seven academic hospitals in the USA. Eligible patients were adults aged 18 years and older with untreated metastatic pancreatic adenocarcinoma, Eastern Cooperative Oncology Group performance status score of 0–1, and measurable disease by Response Evaluation Criteria in Solid Tumors version 1.1. All patients were treated with 1000 mg/m 2 intravenous gemcitabine and 125 mg/m 2 intravenous nab-paclitaxel. Patients received 0·1 mg/kg intravenous APX005M in cohorts B1 and C1 and 0·3 mg/kg in cohorts B2 and C2. In cohorts C1 and C2, patients also received 240 mg intravenous nivolumab. Primary endpoints comprised incidence of adverse events in all patients who received at least one dose of any study drug, incidence of dose-limiting toxicities (DLTs) in all patients who had a DLT or received at least two doses of gemcitabine plus nab-paclitaxel and one dose of APX005M during cycle 1, and establishing the recommended phase 2 dose of intravenous APX005M. Objective response rate in the DLT-evaluable population was a key secondary endpoint. This trial (PRINCE, PICI0002) is registered with ClinicalTrials.gov, NCT03214250 and is ongoing. FindingsBetween Aug 22, 2017, and July 10, 2018, of 42 patients screened, 30 patients were enrolled and received at least one dose of any study drug; 24 were DLT-evaluable with median follow-up 17·8 months (IQR 16·0–19·4; cohort B1 22·0 months [21·4–22·7], cohort B2 18·2 months [17·0–18·9], cohort C1 17·9 months [14·3–19·7], cohort C2 15·9 months [12·7–16·1]). Two DLTs, both febrile neutropenia, were observed, occurring in one patient each for cohorts B2 (grade 3) and C1 (grade 4). The most common grade 3–4 treatment-related adverse events were lymphocyte count decreased (20 [67%]; five in B1, seven in B2, four in C1, four in C2), anaemia (11 [37%]; two in B1, four in B2, four in C1, one in C2), and neutrophil count decreased (nine [30%]; three in B1, three in B2, one in C1, two in C2). 14 (47%) of 30 patients (four each in B1, B2, C1; two in C2) had a treatment-related serious adverse event. The most common serious adverse event was pyrexia (six [20%] of 30; one in B2, three in C1, two in C2). There were two chemotherapy-related deaths due to adverse events: one sepsis in B1 and one septic shock in C1. The recommended phase 2 dose of APX005M was 0·3 mg/kg. Responses were observed in 14 (58%) of 24 DLT-evaluable patients (four each in B1, C1, C2; two in B2). InterpretationAPX005M and gemcitabine plus nab-paclitaxel, with or without nivolumab, is tolerable in metastatic pancreatic adenocarcinoma and shows clinical activity. If confirmed in later phase trials, this treatment regimen could replace chemotherapy-only standard of care in this population. FundingParker Institute for Cancer Immunotherapy, Cancer Research Institute, and Bristol Myers Squibb.

Generating a comprehensive description of cortical networks requires a large-scale, systematic approach. To that end, we have begun a pipeline project using multipatch electrophysiology, supplemented with two-photon optogenetics, to characterize connectivity and synaptic signaling between classes of neurons in adult mouse primary visual cortex (V1) and human cortex. We focus on producing results detailed enough for the generation of computational models and enabling comparison with future studies. Here, we report our examination of intralaminar connectivity within each of several classes of excitatory neurons. We find that connections are sparse but present among all excitatory cell classes and layers we sampled, and that most mouse synapses exhibited short-term depression with similar dynamics. Synaptic signaling between a subset of layer 2/3 neurons, however, exhibited facilitation. These results contribute to a body of evidence describing recurrent excitatory connectivity as a conserved feature of cortical microcircuits. The outer sheet of brain tissue, the neocortex, is composed of circuits formed from trillions of connections among billions of neurons, of which there are about one hundred different neuron types. The scale and complexity of cortical circuitry pose experimental challenges, leading to an incomplete understanding of how cortical cell types are connected and the computations that take place at the connections. About half of the cell types in the brain are excitatory, which means they can activate other cells. The cortex consists of several distinct layers of cells, within which excitatory cells cooperate to process the signals they receive from other cortical layers and brain areas. Using recordings of electrical activity arising from the connections between pairs of excitatory neurons, Seeman, Campagnola et al. measured the likelihood and strength of connectivity among related groups of excitatory cell types in slices of cortex taken from human and mouse brains. The initial results confirm previous findings that individual layers of human cortex can have more and stronger excitatory connections than the same layers of mouse cortex. In most layers of mouse cortex, repeatedly activating the excitatory cells leads to progressively weaker responses. However, in the upper layers of mouse cortex, the opposite effect is sometimes seen: more excitatory activity causes the connections to generate stronger responses. By feeding these data into a computer model, Seeman, Campagnola et al. described and compared the activity of the groups of related excitatory cell types. These results are the first of a new, large-scale project where findings can be integrated across experiments to gain a more detailed picture of cortical circuitry and computation. Neuroscientists will be able to use the results to build advanced computer models of cortical circuits. Such models will, for example, generate predictions for how the attributes of excitatory connectivity revealed by Seeman, Campagnola et al. influence how information is processed in the cortex. In so doing, the models will add to our understanding of how the human brain works both in health and in disease.

This report describes the identification of three molecularly distinct subtypes of pancreatic ductal adenocarninoma (PDA). The classical, quasimesenchymal and exocrine subtypes can further stratify tumors with the same genetic alterations, and could be useful to improve prognosis and predict treatment response. Pancreatic ductal adenocarcinoma (PDA) is a lethal disease. Overall survival is typically 6 months from diagnosis 1 . Numerous phase 3 trials of agents effective in other malignancies have failed to benefit unselected PDA populations, although patients do occasionally respond. Studies in other solid tumors have shown that heterogeneity in response is determined, in part, by molecular differences between tumors. Furthermore, treatment outcomes are improved by targeting drugs to tumor subtypes in which they are selectively effective, with breast 2 and lung 3 cancers providing recent examples. Identification of PDA molecular subtypes has been frustrated by a paucity of tumor specimens available for study. We have overcome this problem by combined analysis of transcriptional profiles of primary PDA samples from several studies, along with human and mouse PDA cell lines. We define three PDA subtypes: classical, quasimesenchymal and exocrine-like, and we present evidence for clinical outcome and therapeutic response differences between them. We further define gene signatures for these subtypes that may have utility in stratifying patients for treatment and present preclinical model systems that may be used to identify new subtype specific therapies.

Adjuvant chemotherapy has not improved disease-free survival among patients with resected esophageal or gastroesophageal junction cancer. In this trial, after neoadjuvant chemoradiotherapy and resection, patients with residual disease were randomly assigned to receive nivolumab or placebo. Nivolumab doubled the median disease-free survival from 11.0 to 22.4 months.

Much of software developers' time is spent understanding unfamiliar code. To better understand how developers gain this understanding and how software development environments might be involved, a study was performed in which developers were given an unfamiliar program and asked to work on two debugging tasks and three enhancement tasks for 70 minutes. The study found that developers interleaved three activities. They began by searching for relevant code both manually and using search tools; however, they based their searches on limited and misrepresentative cues in the code, environment, and executing program, often leading to failed searches. When developers found relevant code, they followed its incoming and outgoing dependencies, often returning to it and navigating its other dependencies; while doing so, however, Eclipse's navigational tools caused significant overhead. Developers collected code and other information that they believed would be necessary to edit, duplicate, or otherwise refer to later by encoding it in the interactive state of Eclipse's package explorer, file tabs, and scroll bars. However, developers lost track of relevant code as these interfaces were used for other tasks, and developers were forced to find it again. These issues caused developers to spend, on average, 35 percent of their time performing the mechanics of navigation within and between source files. These observations suggest a new model of program understanding grounded in theories of information foraging and suggest ideas for tools that help developers seek, relate, and collect information in a more effective and explicit manner.