bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomics insights into the responses of Saccharomyces cerevisiae during mixed-culture alcoholic fermentation with Lachancea thermotolerans
Authors: Peng Chuantao , Andersen Birgit , Arshid Samina , Larsen Martin R , Albergaria Helena , Lametsch Rene , Arneborg Nils 
Published: August 2019

ABSTRACT
The response of Saccharomyces cerevisiae to cocultivation with Lachancea thermotolerans during alcoholic fermentations has been investigated using tandem mass tag (TMT)-based proteomics. At two key time-points, S. cerevisiae was sorted from single S. cerevisiae fermentations and from mixed fermentations using flow cytometry sorting. Results showed that the purity of sorted S. cerevisiae was above 96% throughout the whole mixed-culture fermentation, thereby validating our sorting methodology. By comparing protein expression of S. cerevisiae with and without L. thermotolerans, 26 proteins were identified as significantly regulated proteins at the early death phase (T1), and 32 significantly regulated proteins were identified at the late death phase (T2) of L. thermotolerans in mixed cultures. At T1, proteins involved in endocytosis, increasing nutrient availability, cell rescue and resistance to stresses were upregulated, and proteins involved in proline synthesis and apoptosis were downregulated. At T2, proteins involved in protein synthesis and stress responses were up- and downregulated, respectively. These data indicate that S. cerevisiae was stressed by the presence of L. thermotolerans at T1, using both defensive and fighting strategies to keep itself in a dominant position, and that it at T2 was relieved from stress, perhaps increasing its enzymatic machinery to ensure better survival.
Investigating microbial indicators of anthropogenic marine pollution by 16S and 18S High-Throughput Sequencing (HTS) library analysis
Authors: Buccheri Maria Antonietta , Salvo Eliana , Coci Manuela , Quero Grazia M , Zoccarato Luca , Privitera Vittorio , Rappazzo Giancarlo 
Published: August 2019

ABSTRACT
High-Throughput Sequencing technologies are providing unprecedented inventories of microbial communities in aquatic samples, offering an invaluable tool to estimate the impact of anthropogenic pressure on marine communities. In this case study, the Mediterranean touristic site of Aci Castello (Italy) was investigated by High-Throughput Sequencing of 16S and 18S rRNA genes. The sampling area falls within a Marine Protected Area and, notwithstanding, features an untreated urban wastewater discharge. Seawater samples were collected close to the wastewater output (COL) and at a second station about 400 m further off (PAN), before and after a summer increase in population. Prokaryotic communities clustered according to stations, rather than to seasons. While PAN showed a typical, not impacted, marine microbial composition, COL was consistently enriched in Epsilonproteobacteria and Firmicutes. Protist communities showed a peculiar clustering, as COL at springtime stood alone and was dominated by Ciliophora, while the other samples were enriched in Dinophyta. Analysis of alternative, detectable by High-Throughput Sequencing, microbial indicators, including both faecal- and sewage-associated, allowed uncovering the different sources of pollution in coastal and anthropogenically impacted marine ecosystems, underpinning the relevance of High-Throughput Sequencing-based screening as rapid and precise method for water quality management.
Histologic patterns of liver injury induced by anti-PD-1 therapy
Authors: Zhang Dongwei , Hart John , Ding Xianzhong , Zhang Xuchen , Feely Michael , Yassan Lindsay , Alpert Lindsay , Soldevila-Pico Consuelo , Zhang Xuefeng , Liu Xiuli , Lai Jinping 
Published: August 2019

Abstract

Background
Nivolumab and pembrolizumab—two monoclonal antibodies that block human programmed cell death-1 (PD-1)—have been successfully used to treat patients with multiple advanced malignancies. The histologic patterns of hepatic toxicity induced by anti-PD-1 treatment have not been well studied and the aim of this study was to explore them.

Methods
Eight patients with advanced malignancies who were treated with either nivolumab or pembrolizumab were identified from five institutions. These patients had no history of underlying liver disease and a viral hepatitis panel was negative in all patients.

Results
Seven of eight patients exhibited mild to moderate gastrointestinal symptoms such as abdominal pain, fatigue, nausea, vomiting, and jaundice after anti-PD-1 treatment. Significant elevations in liver-chemistry tests were detected in all patients. Six cases (6/8) demonstrated an acute lobular hepatitis pattern of histologic injury. The remaining two cases showed different histologic patterns of injury: steatohepatitis with mild cholestasis (1/8) and pure acute cholestatic injury (1/8). No case showed typical features of autoimmune hepatitis. The liver function recovered in all eight cases after cessation of anti-PD-1 agents and with immunosuppressive therapy.

Conclusions
Our study suggests that screening patients for abnormal liver-function tests prior to anti-PD-1 therapy as well as periodic monitoring of liver-function tests are necessary to prevent severe liver injury. Rather than causing classical autoimmune hepatitis, PD-1 inhibitors appear to produce an immune-mediated nonspecific acute hepatitis. Drug cessation, without steroid therapy, may therefore be sufficient in some patients.
Visual Impairment and Frailty: Examining an Understudied Relationship
Authors: Swenor Bonnielin K , Lee Moon J , Tian Jing , Varadaraj Varshini , Bandeen-Roche Karen 
Published: August 2019

Abstract

Background
Older adults with visual impairments are at increased risk of negative health outcomes. Here, we investigate the association between visual impairment and frailty.

Methods
Cross-sectional and longitudinal relationships between visual impairment (distance visual acuity) and frailty (frailty phenotype criteria) were examined using data from the National Health and Nutrition Examination Survey (NHANES, 1999–2002, ≥60 years) and the Women’s Health and Aging Studies (WHAS III). Imbalance of potential confounders, particularly age, was addressed using propensity score-based adjustment. Multinomial logistic regression determined the odds of prefrailty and frailty at baseline in NHANES and ordinal logistic regression examined the odds of baseline and incident frailty over 3 years in WHAS III after adjustment for confounders and probability weighting (survey weights × inverse propensity scores).

Results
In NHANES (n = 2,639, 9% vision impairment), participants with visual impairment were more likely to be prefrail (odds ratio [OR] = 3.2; 95% confidence interval [CI]: 1.9–5.3) and frail (OR = 3.7; 95% CI: 1.5–9.2) than those without visual impairment. In WHAS III (n = 796, 26% mild, 37% moderate/severe vision impairment), participants with mild and moderate/severe vision impairment were more likely to be frail (OR = 2.0; 95% CI: 1.5–2.5; OR = 5.5; 95% CI: 4.2–7.2, respectively). A one-line worse visual acuity (0.1 logMAR increase) was associated with greater odds of frailty (OR = 1.5; 95% CI: 1.4–1.7). Of those non-frail at baseline (n = 549), moderate/severe visual impairment and one-line worse visual acuity was associated with greater odds of incident frailty (OR = 3.5; 95% CI: 1.4–8.4; OR = 1.3; 95% CI: 1.1–1.5, respectively) over 3 years.

Conclusions
Visual impairment may be an important, yet understudied risk factor for frailty.
Movements of Atlantic halibut in the Gulf of Maine based on geolocation
Authors: Liu Chang , Bank Crista , Kersula Michael , Cowles Geoffrey W , Zemeckis Douglas R , Cadrin Steven X , McGuire Christopher 
Published: August 2019

AbstractAtlantic halibut are a “Species of Concern” in US waters and little is known about their movements and stock structure. Recent stock assessments drew attention to the paucity of information for assessing and managing this stock. To investigate movement patterns and stock structure, halibut were tagged off Massachusetts and Maine within US waters of the Gulf of Maine region using pop-up satellite archival tags and data storage tags. A hidden Markov model (HMM) geolocation method previously developed for other groundfish species was adapted to estimate the movement tracks of the tagged halibut (n = 25) based on the tag-recorded depth and temperature. Total distance travelled based on geolocation ranged from 36 to 1701 km, whereas straight line distance between tagging and end locations ranged from 0.4 to 440.7 km. Estimated movement rates varied between 2.7 and 10 km day−1. Two tagged halibut made long-distance movements to putative spawning habitat in the Northeast Channel off Georges Bank. Thirteen (13) out of 25 geolocated individuals were estimated to have reached Canadian waters. Geolocation results revealed home range, return movement, and seasonal migration movement patterns exhibited by the tagged halibut. The HMM geolocation method could be a useful tool in providing information on halibut movements that can inform stock assessment and management decisions.
Pulmonary carcinosarcoma: analysis from the Surveillance, Epidemiology and End Results database
Authors: Sun Liangdong , Dai Jie , Wang Xujun , Jiang Gening , Gonzalez-Rivas Diego , Song Jiong , Zhang Peng 
Published: August 2019

AbstractOBJECTIVESPulmonary carcinosarcoma (PCS) is a rare neoplasm. This study explored the clinicopathological characteristics and survival outcomes of PCS.METHODSThe Surveillance, Epidemiology and End Results (SEER) database (1988–2014) was queried for PCS. Overall survival (OS) was evaluated by multivariable Cox regression and nomograms were constructed to predict 3-year OS for PCS. Prognostic performance was evaluated using concordance index and area under the curve analysis. In M0 surgically treated patients, interaction assessments were performed using likelihood ratio tests. Subgroup analysis was performed according to patient age. The clinical features of PCSs were further compared to other non-small-cell lung cancers (NSCLCs).RESULTSMultivariable analysis identified age [hazard ratio (HR) 1.03, 95% confidence interval (CI) 1.01–1.04], surgery (HR 0.53, 95% CI 0.36–0.77) and chemotherapy (HR 0.51, 95% CI 0.36–0.73) as significantly associated with OS. The nomogram had a concordance index of 0.747 and an area under the curve of 0.803. The association between age and OS was stronger in those receiving pneumonectomy (P = 0.04 for interactions) compared to those that did not (HR 5.14, 95% CI 1.64–16.07), and was associated with a poorer outcome compared to lobectomy amongst the elderly (age ≥ 70 years). Patients with PCS were more likely to receive surgical treatment and had lower lymphatic metastasis compared to adenocarcinoma, squamous cell carcinoma and large cell carcinoma (all P &lt; 0.05).CONCLUSIONSPCS had unique clinical features compared to common types of NSCLCs in terms of lymphatic invasion and surgical treatment. Pneumonectomy was associated with poorer survival in elderly patients.
The effects on nutrient utilization and stool quality of Beagle dogs fed diets with beet pulp, cellulose, and Miscanthus grass12
Authors: Donadelli Renan A , Aldrich Charles G 
Published: August 2019

Abstract
Dogs can benefit from dietary fibers. Traditionally, cellulose (CE) and beet pulp (BP) have been used by pet food companies as insoluble and soluble fiber sources. Miscanthus grass (MG) is a novel fiber ingredient made from Miscanthus giganteus, a C4 grass produced for its fiber content, but it has not been evaluated for dogs. The objectives of this study were to determine the effects of different fiber sources on nutrient utilization and stool consistency by dogs. Twelve Beagle dogs were fed 3 dietary treatments varying in their fiber sources (BP, CE, MG). Diets were fed for a 14-d period (9 d adaptation), fecal samples were collected (5 d total fecal collection) and scored. Nutrient digestibility was estimated using total fecal collection (TFC). Dogs fed BP diet had softer stools than dogs fed CE and MG (3.15 vs. 3.68 and 3.64, respectively). Wet fecal output was higher for dogs fed CE compared to MG, with dogs fed BP having the lowest values (254.3 g vs. 241.6 g vs. 208.5 g, respectively). Dogs fed CE and MG had lower DM digestibility than dogs fed BP (P < 0.05), dogs fed BP had lower CP digestibility compared with dogs fed MG and CE (81.4% vs. 85.5% and 85.8%, respectively). In conclusion, MG could be used as an alternative fiber source to CE.
First record of cuticle bands in the stomach ossicles of the red king crab Paralithodes camtschaticus (Tilesius, 1815) (Decapoda: Anomura: Lithodidae) from Norway
Authors: Bluhm Bodil A , Kilada Raouf , Ambrose William , Renaud Paul E , Sundet Jan H 
Published: August 2019

Abstract
The red king crab Paralithodes camtschaticus (Tilesius, 1815) is a large predator intentionally introduced to the Barents Sea and adjacent fjords in the 1960s. Its establishment has given rise to both a high-value fishery and destructive effects on seafloor habitats and communities. Given the need for accurate information on age, growth, and longevity that could improve management and mitigation strategies for red king crab, developing and testing new aging methods for this and other crustaceans has been an active field of research. We contribute to this test bed by investigating cuticle bands in gastric mill ossicles of male and female red king crabs. Cuticle bands were detectable in most individuals studied and maximum cuticle band count was 13 for males (N = 62, 38–180 mm carapace length (CL)) and 9 for females (N = 34, size range 80–147 mm CL). There was large variation of size-at-band count and band count-at-size data. The number of cuticle bands generally increased with CL in male red king crabs; low sample size and small size range in females prevented seeing any trend. Exploring calcein staining in a sub-sample of the crabs suggested uptake of the stain, yet without a clearly defined mark, and showed deposition of ossicular material beyond the calcein stain in the subsequent year. We recommend research on the mechanism generating band deposition to shed light on how and when bands are formed as the basis for testing whether the cuticle bands may reflect chronological (specifically annual) age. Specifically, we recommend long-term maintenance of crabs, study of both moults and newly formed ossicle structures, as well as stringent testing of band periodicity with known-age crabs, including all size classes and both sexes.
NUMB enhances Notch signaling by repressing ubiquitination of NOTCH1 intracellular domain
Authors: Luo Zhiyuan , Mu Lili , Zheng Yue , Shen Wenchen , Li Jiali , Xu Lichao , Zhong Bo , Liu Ying , Zhou Yan 
Published: August 2019

Abstract
The release and nuclear translocation of the intracellular domain of Notch receptor (NICD) is the prerequisite for Notch signaling-mediated transcriptional activation. NICD is subjected to various posttranslational modifications including ubiquitination. Here, we surprisingly found that NUMB proteins stabilize the intracellular domain of NOTCH1 receptor (N1ICD) by regulating the ubiquitin–proteasome machinery, which is independent of NUMB’s role in modulating endocytosis. BAP1, a deubiquitinating enzyme (DUB), was further identified as a positive N1ICD regulator, and NUMB facilitates the association between N1ICD and BAP1 to stabilize N1ICD. Intriguingly, BAP1 stabilizes N1ICD independent of its DUB activity but relying on the BRCA1-inhibiting function. BAP1 strengthens Notch signaling and maintains stem-like properties of cortical neural progenitor cells. Thus, NUMB enhances Notch signaling by regulating the ubiquitinating activity of the BAP1–BRCA1 complex.
Clinical Development of Molecular Targeted Therapy in Head and Neck Squamous Cell Carcinoma
Authors: Gougis Paul , Moreau Bachelard Camille , Kamal Maud , Gan Hui K , Borcoman Edith , Torossian Nouritza , Bièche Ivan , Le Tourneau Christophe 
Published: August 2019

AbstractA better understanding of cancer biology has led to the development of molecular targeted therapy, which has dramatically improved the outcome of some cancer patients, especially when a biomarker of efficacy has been used for patients’ selection. In head and neck oncology, cetuximab that targets epidermal growth factor receptor is the only targeted therapy that demonstrated a survival benefit, both in the recurrent and in the locally advanced settings, yet without prior patients’ selection. We herein review the clinical development of targeted therapy in head and neck squamous cell carcinoma in light of the molecular landscape and give insights in on how innovative clinical trial designs may speed up biomarker discovery and deployment of new molecular targeted therapies. Given the recent approval of immune checkpoint inhibitors targeting programmed cell death-1 in head and neck squamous cell carcinoma, it remains to be determined how targeted therapy will be incorporated into a global drug development strategy that will inevitably incorporate immunotherapy.
An urban wildlife habitat experiment: conservation implications of altering management regimes on animals and plants along urban and rural rights-of-way
Authors: Leston Lionel , Koper Nicola 
Published: August 2019

Abstract
Biodiversity along rights-of-way (ROWs) can decline due to local-scale management, including frequent urban mowing and spraying, or with increasing amount of urban infrastructure surrounding those grassy spaces. Distinguishing effects of mowing regime from effects of surrounding urban land are necessary to determine what management strategies effectively conserve wildlife in different landscapes, and to justify changes in management that could increase populations of weeds. We used a manipulative Before/After-Control/Impact (BACI) experiment in 17 transmission line ROWs during 2007–2009, along an urbanization gradient, to disentangle effects of mowing frequency and the amount of urban land (buildings, hard surfaces like concrete, asphalt) surrounding ROWs. In the BACI study, we halted mowing and spraying for 1 year in five urban ROWs, introduced two rounds of mowing per year in three rural ROWs, and compared vegetation and arthropods found within these manipulated ROWs and within three urban and six rural control ROWs. European skipper butterflies Thymelicus lineola, lepidopteran biomass in herbaceous vegetation, milkweeds (Asclepias spp.) and Canada thistle Cirsium arvense increased when mowing and spraying were halted for one year. Conversely, monarch butterflies Danaus plexippus, legume cover and dandelion Taraxacum officinale increased when mowing was introduced to rural ROWs. To increase taller butterfly resource plants while still controlling weeds within urban ROWs, we recommend reducing management frequency within the interior of ROWs while maintaining frequent management along ROW borders that are adjacent to infrastructure.
Mechanical Ventilation: Advanced Modes
Authors: Lowell Amelia A. , Patel Bhavesh M. 
Published: August 2019

Abstract
The primary purpose of mechanical ventilation is to support the physiologic processes of oxygenation and ventilation and to reduce the work of breathing. The present chapter focuses on advanced modes and modalities of therapy for patients receiving mechanical ventilation. The term advanced must be interpreted with caution because the use of many of the newer modes of ventilation is not supported with substantial evidence of superiority to the basic modes of ventilation for patient outcomes. Rather, advanced refers to the engineering controls and the proposed patient benefits.
Cardiogenic Shock
Authors: Ratzlaff Robert A. , Siegel Jason L. 
Published: August 2019

Abstract
Like all forms of shock, cardiogenic shock (CS) is a life-threatening condition of decreased blood circulation that ultimately causes systemic hypoperfusion and end-organ failure. Unlike other forms of shock, however, CS is characterized by failure of the heart itself. This chapter describes CS, including its causes and diagnosis, and provides a brief overview of management.
Acute Perforations of the Gastrointestinal Tract
Authors: Tsamalaidze Levan , Stauffer John A. 
Published: August 2019

Abstract
Acute perforations of the gastrointestinal tract (GI) with subsequent release of gastric or intestinal contents into the peritoneal space have multiple causes and portend a high mortality depending on the cause. The key symptom is a sudden appearance of abdominal pain followed by signs of peritoneal irritation, severe sepsis, or shock. A proper imaging evaluation should lead to surgical intervention and aggressive supportive management.
Drug Dosing in Renal Failure
Authors: Jackson Daniel A. 
Published: August 2019

Abstract
Optimal dosing of medications can be influenced by many factors. These factors are important to consider because the therapeutic effects of drugs are frequently concentration dependent and can even result in toxicity. One factor of great importance is the pharmacokinetics of a medication. Pharmacokinetics is the way in which medications move through the body during absorption, distribution, metabolism, and excretion. This chapter focuses on the excretion of medications as it relates to renal function.
Principles of Renal Replacement Therapies
Authors: Fitzpatrick Peter M. 
Published: August 2019

Abstract
Renal replacement therapy is frequently used in the intensive care unit, primarily for the management of acute kidney injury, but it is also indicated for removal of some toxins and medications. Additionally, patients with dialysis-dependent chronic kidney failure who are admitted to the intensive care unit require their therapy to be continued. This chapter reviews the mechanisms by which renal replacement therapy operates and the types of replacement therapies that are available. Access for renal replacement and anticoagulation are also discussed.
Antibiotics in the Intensive Care Unit
Authors: Aviles David A. Sotello , Hellinger Walter C. 
Published: August 2019

Abstract
Antimicrobial therapy is a critical component in the management of many infections. Antimicrobial therapy should not be initiated before infection with a susceptible pathogen is suspected or confirmed or before appropriate diagnostic specimens, including those for cultures, are collected. Recognizing indications for antibiotic administration and appropriately selecting antimicrobial agents based on clinical and microbiologic findings are required. Distinguishing between empiric prescribing, when infection syndromes and pathogens are suspected, and therapeutic prescribing, when infection syndromes are confirmed and pathogens identified, is critically important.
Dermatologic Emergencies in the Intensive Care Unit
Authors: Hall Matthew R. 
Published: August 2019

Abstract
Rashes are relatively common in hospitalized patients, but only rarely are they life threatening. Emergent skin conditions in these patients are usually sequelae of medication reactions (drug eruptions) or complications from sepsis. Most drug eruptions are benign and resolve if the offending medication is discontinued. However, the drug hypersensitivity syndrome, Stevens-Johnson syndrome (SJS), and toxic epidermal necrolysis (TEN) are urgent conditions that require prompt diagnosis and management. Purpura fulminans can develop in patients with sepsis and disseminated intravascular coagulation.