bluuebunny/crossref_metadata_2025 huggingface dataset:
Dietary supplementation with free methionine or methionine dipeptide improves environment intestinal of broilers challenged with Eimeria spp.
Authors: Khatlab Angélica de Souza , Del Vesco Ana Paula , Rodrigues Oliveira Neto Adhemar , Almeida Fernanda Losi Alves , Gasparino Eliane
Published: November 2019

This study examined the influence of a diet enriched with free methionine (dl-Met) or methionine dipeptide (dl-MMet) on the intestinal health of Eimeria-challenged (EC) and unchallenged (UC) broilers. A non-supplemented, methionine-deficient diet (NS) was used as control. Treatments were arranged in a 2 × 3 factorial completely randomized design with eight replications. Broilers in the EC group were infected with sporulated oocysts of Eimeria spp. (E. acervulina, E. maxima, E. praecox, and E. mitis) at 14 d of age. Performance analysis, light and electron microscopy of the jejunum, analysis of genes related to apoptosis and cell proliferation in the jejunum, and blood tests were performed at 6 days post-inoculation (dpi). EC broilers had poorer performance than UC broilers, regardless of diet (P < 0.001). Broilers fed the dl-Met diet had greater weight gain (P = 0.004) and lower feed conversion ratio (P = 0.019) than broilers fed other diets. Jejunal sections from EC broilers fed the NS diet showed short (P = 0.001) and wide villi (P < 0.001) with increased crypt depth (P < 0.001) and reduced villus / crypt ratio (P = 0.001), jejunal absorptive surface area (P < 0.001), number of neutral goblet cells (Eimeria challenge: P = 0.048; diet P = 0.016), and mucin 2 (MUC2) gene expression (P = 0.018). EC birds fed the dl-MMet diet had higher enterocyte height (P < 0.001). Birds fed the dl-MMet diet had low lamina propria width (P = 0.009). UC broilers fed the dl-Met diet had the highest number of acidic goblet cells (P = 0.005), whereas EC broilers assigned the dl-MMet diet showed the highest number of intraepithelial lymphocytes (P = 0.033). Reduced expression of caspase-3 (CASP3) (P = 0.005), B-cell lymphoma 2 (BCL2) (P < 0.001), mechanistic target of rapamycin (MTOR) (P < 0.001), and ribosomal protein S6 kinase B1 (RPS6KB1) (P < 0.001) genes was observed in EC animals. MTOR expression levels were highest in birds fed the dl-MMet diet (P = 0.004). Plasma activities of aspartate aminotransferase (AST) was influenced by both diet (P = 0.002) and Eimeria challenge (P = 0.005), with EC broilers assigned the NS diet showing the highest levels. EC broilers fed the NS diet had higher creatine kinase (CK) activity (P = 0.049). EC broilers had lower plasma uric acid (P = 0.004) and higher serum mucoproteins level (P < 0.001). These results indicate that methionine dipeptide supplementation is able to mitigate the harmful intestinal effects of Eimeria spp. in broilers.
Effect of suckling intensity of primiparous sows on production performance during current and subsequent parities1
Authors: Guo Ji Yao , Sun Yawang , DeDecker Ashley E , Coffey Max Terry , Kim Sung Woo
Published: November 2019

This study was conducted to evaluate the effects of suckling intensity (litter size and lactation length) to primiparious sows on production performance during current and subsequent parities. Upon farrowing, 115 primiparous sows (farrowing weight: 222.7 ± 20.0 kg) were initially allotted to 4 treatments in a 2 × 2 factorial arrangement with 2 litter sizes: 10 and 13 piglets (LS10 vs. LS13), and 2 lactation lengths: 21 and 27 d (LL21 vs. LL27). Upon weaning, sows were rebred and those farrowed successfully (n = 66) kept 10 piglets and weaned at 21 d in the second parity. Sows were fed ad libitum during lactation in both parities. Feed intake, BW loss, backfat loss, litter size, and litter weight gain during lactation in both parities were determined. Litter weight gain in LS13 was greater (P < 0.05) than that in LS10 (54.4 vs. 47.7 kg) during the first lactation. Sows in LS13 had a greater (P < 0.05) BW loss than sows in LS10 (24.1 vs. 17.4 kg). Body weight loss was not different between LL27 and LL21. Sows in LS13 tended to have a greater (P = 0.075) removal rate than those in LS10 (47.5 vs. 32.2%). Sows in LL27 had a smaller (P < 0.05) removal rate than those in LL21 (28.0 vs. 51.7%). In the second parity, gestation BW gain in LL27 tended to be greater (P = 0.098) than that in LL21 when the previous litter size was 10 piglets (56.1 vs. 33.2 kg). Litter performance and feed intake of sows were not affected by previous litter size, lactation length, and their interaction. The farrowing weight, farrowing body protein and lipid, body weight loss was not different between LS13 and LS10, whereas backfat loss in LS13 was smaller (P < 0.05) than that in LS10 during the second lactation (0.9 vs. 2.4 mm). The predicted body lipid loss in LS13 was also smaller than that in LS10 (2.3 vs. 5.3 kg) during the second lactation. Sows in LL27 had a smaller (P < 0.05) BW loss and body lipid loss during the second lactation than sows in LL21 (4.0 vs. 9.0 kg; 2.3 vs. 4.8 kg). The concentration of milk fat in LL27 was smaller (P < 0.05) than that in LL21 (7.9 vs. 9.1%). In conclusion, increasing suckling intensity to primiparous sows increased litter weight gain but increasing litter size reduced piglet ADG. Sow performance in the second lactation was not negatively affected by increasing suckling intensity of the first lactation. Interestingly, sows with an increased suckling intensity in the first lactation had reduced loss of body reserves in the second lactation.
Evaluation of different inclusion levels of dry live yeast impacts on various rumen parameters and in situ digestibilities of dry matter and neutral detergent fiber in growing and finishing beef cattle
Authors: Cagle Caitlyn M , Batista Luiz Fernando D , Anderson Robin C , Fonseca Mozart A , Cravey Matt D , Julien Christine , Tedeschi Luis O
Published: November 2019

This study evaluated the effects of supplementing dry live yeast (LY; Saccharomyces cerevisiae) on in vitro gas production (IVGP) fermentation dynamics, pH, and CH4 concentration at 48 h, and in situ rumen parameters and digestibility of DM (DMD) and NDF (NDFD) of growing cattle during 3 feeding phases: grower (GRW) for 17 d (38% steamed-flaked corn; SFC), transition (TRANS) for 15 d (55.5% SFC: 1.2 Mcal/kg NEg), and finisher (FIN) for 13 d (73% SFC: 1.23 Mcal/kg NEg). Twenty British-crossbred, ruminally cannulated steers (183 kg ± 44 kg) 6 mo of age were blocked by weight into 5 pens containing Calan gate feeders and received a control (CON) diet (17.2% CP, 35.8% NDF, 86.7% DM) without LY on days −12 to 0. After that, animals were randomly assigned to treatments (TRT), 5 animals per TRT: CON or LY at inclusion rates of 5 g/d (LY1), 10 g/d (LY2), or 15 g/d (LY3) top dressed every morning at 0800 for 45 d. The DMD and NDFD were assessed during 7 separate collection days using in situ nylon bags containing 5 g of GRW, TRANS, or FIN diets, incubated at 1200 for 48 h. Protozoa counts (PC) were determined during 5 collection periods. Data were analyzed as a repeated measure within a randomized complete block design, assuming a random effect of the pen. For GRW, TRT altered the total gas production of the nonfiber carbohydrate (NFC; P = 0.045) and the fractional rate of degradation (kd) of the fiber carbohydrate (FC) pool (P = 0.001) in a cubic pattern (P ≤ 0.05): LY2 had the most gas production and fastest kd. TRT also influenced DMD (P = 0.035) and NDFD (P = 0.012) with LY2 providing the greatest digestibility. For TRANS, TRT tended to affect the NFC kd (P = 0.078) and influenced pH (P = 0.04) and DMD (P < 0.001) in which LY2 yielded the fastest kd, highest pH, and greatest DMD. For FIN, there was an effect of TRT on total gas production (P < 0.001) and kd (P = 0.004) of the NFC pool, FC kd (P = 0.012), in vitro CH4 concentration (P < 0.001), PC (P < 0.001), DMD (P = 0.039), and NDFD (P = 0.008). LY1 had the highest PC and provided the greatest DMD and NDFD. LY2 had the fastest kd of both the NFC and FC pools and had the least CH4 concentration. LY3 had the greatest NFC gas production. No specific dose–response pattern was observed, but 10 g/d provided the most beneficial result for all diets. We concluded that supplementation with LY affected IVGP as well as ruminal parameters and digestibilities.
Penile reconstruction using scrotal flap after usage of monopolar electrocautery in a 2-month-old Syrian child: a case report
Authors: Assaf Ragheb , Albahhah Tamim , Ayoub Kusay , Al-janzir Zaher , Tarzi Mario , Rahmeh Ahmad Rami , Al-Hadid Ibrahim
Published: November 2019

Circumcision is regarded as one of the most common procedures in pediatrics. We present a case of a newborn, who has undergone circumcision using monopolar electrocautery. He admitted to the hospital with glans necrosis and was treated with antibiotics and surgical debridement. Four months later, phalloplasty was performed for the newborn using scrotal flap. The result is satisfactory, and the penis is esthetically acceptable with effective urination. Our case suggests the use of scrotal flap for penile reconstruction due to feasibility of procedure and anatomic privilege. It would also support usage of bipolar electrocautery for circumcision to avoid possible unwanted complications of monopolar electrocautery.
Using machine learning to study the kinematics of cold gas in galaxies
Authors: Dawson James M , Davis Timothy A , Gomez Edward L , Schock Justus , Zabel Nikki , Williams Thomas G
Published: November 2019

Next generation interferometers, such as the Square Kilometre Array, are set to obtain vast quantities of information about the kinematics of cold gas in galaxies. Given the volume of data produced by such facilities astronomers will need fast, reliable, tools to informatively filter and classify incoming data in real time. In this paper, we use machine learning techniques with a hydrodynamical simulation training set to predict the kinematic behaviour of cold gas in galaxies and test these models on both simulated and real interferometric data. Using the power of a convolutional autoencoder we embed kinematic features, unattainable by the human eye or standard tools, into a three-dimensional space and discriminate between disturbed and regularly rotating cold gas structures. Our simple binary classifier predicts the circularity of noiseless, simulated, galaxies with a recall of $85\%$ and performs as expected on observational CO and HI velocity maps, with a heuristic accuracy of $95\%$. The model output exhibits predictable behaviour when varying the level of noise added to the input data and we are able to explain the roles of all dimensions of our mapped space. Our models also allow fast predictions of input galaxies’ position angles with a 1σ uncertainty range of ±17○ to ±23○ (for galaxies with inclinations of 82.5○ to 32.5○, respectively), which may be useful for initial parameterisation in kinematic modelling samplers. Machine learning models, such as the one outlined in this paper, may be adapted for SKA science usage in the near future.
The Coupled Kinematics of Scapulothoracic Upward Rotation
Authors: Lawrence Rebekah L , Braman Jonathan P , Keefe Daniel F , Ludewig Paula M
Published: November 2019

Background

Scapulothoracic upward rotation (UR) is an important shoulder complex motion allowing for a larger functional work space and improved glenohumeral muscle function. However, the kinematic mechanisms producing scapulothoracic UR remain unclear, limiting the understanding of normal and abnormal shoulder movements.

Objective

The objective of this study was to identify the coupling relationships through which sternoclavicular and acromioclavicular joint motions contribute to scapulothoracic UR.

Design

This was a cross-sectional observational study.

Methods

Sixty participants were enrolled in this study; 30 had current shoulder pain, and 30 had no history of shoulder symptoms. Shoulder complex kinematics were quantified using single-plane fluoroscopy and 2D/3D shape matching and were described as finite helical displacements for 30-degree phases of humerothoracic elevation (30 degrees–60 degrees, 60 degrees–90 degrees, and 90 degrees–120 degrees). A coupling function was derived to estimate scapulothoracic UR from its component motions of acromioclavicular UR, sternoclavicular posterior rotation, and sternoclavicular elevation as a function of acromioclavicular internal rotation. The proportional contributions of each of the component motions were also calculated and compared between phases of humerothoracic elevation and groups.

Results

Scapulothoracic UR displacement could be effectively predicted using the derived coupling function. During the 30- to 60-degree humerothoracic elevation phase, acromioclavicular UR accounted for 84.2% of scapulothoracic UR, whereas sternoclavicular posterior rotation and elevation each accounted for < 10%. During later phases, acromioclavicular UR and sternoclavicular posterior rotation each accounted for 32% to 42%, whereas sternoclavicular elevation accounted for < 11%.

Limitations

Error due to the tracking of sternoclavicular posterior rotation may have resulted in an underprediction of its proportional contribution and an overprediction of the proportional contribution of acromioclavicular UR.

Conclusions

Acromioclavicular UR and sternoclavicular posterior rotation are the predominant component motions of scapulothoracic UR. More research is needed to investigate how these coupling relationships are affected by muscle function and influenced by scapular dyskinesis.
Resource environment and hierarchy in universities
Authors: Lind Jonas K
Published: November 2019

This article investigates the influence of changes in the research funding environment on hierarchy in Danish universities. The article concludes that the claims made by some scholars in the field—that external funding of research and the introduction of ‘strong’ research evaluation systems have penetrated or weakened hierarchy in universities—need to be moderated. In some ways, the developments in the resource environment, in tandem with the implementation of a management reform in Danish universities, have worked to underpin hierarchy in universities.
Integrating Neuropsychology Services in a Multidisciplinary Concussion Clinic
Authors: Baker John G. , Willer Barry S. , Leddy John J.
Published: November 2019

Objective:

To describe the integration of neuropsychology services in a multidisciplinary concussion clinic and provide descriptive information on patients, services, and initial health status.

Setting:

A university-based outpatient sports medicine concussion clinic.

Participants:

A consecutive sample of 338 patients ages 8 to 84 years (median 23.5 years, 35% 13-18 years), 49.1% male, seen between 2014 and 2018. Patients' injuries included sports 42%, work 28.4%, and vehicular 12.1% and 48.5% were students.

Design:

Descriptive statistics with group comparisons.

Main Measures:

12-Item Short Form Health Survey (SF-12) T scores (mean = 50, SD = 10) referenced to US population.

Results:

Half of the patients were seen within 24 days of their injury and showed reduced physical functioning (40.2) and average mental (emotional) functioning (48.8). Patients seen after 24 days showed even more reduced physical functioning (33.9) and reduced mental functioning (41.0), bothP< .0001. Average treatment time was also longer, 88.1 (173.9) versus 186.8 (211.1) days,P< .0001. Two-thirds of patients were referred for cervical or vestibular physical therapy at their initial visit.

Conclusion:

Early referral for specialized care, including neuropsychology services, may be beneficial.
Addition of Occupational Therapy to an Interdisciplinary Concussion Clinic Improves Identification of Functional Impairments
Authors: Harris Madison B. , Rafeedie Samia , McArthur David , Babikian Talin , Snyder Aliyah , Polster Douglas , Giza Christopher C.
Published: November 2019

Background:

Concussions, or mild traumatic brain injuries, are prevalent among youth and young adults. These injuries may disrupt a person's daily activities (occupations) including school, physical activity, work, and socialization. Rehabilitation professionals, such as occupational therapists (OTs), are experts in providing individualized intervention to address these temporary life changes during recovery.

Objective:

This article aims to identify the benefit of having an occupational therapy practitioner on an interdisciplinary treatment team when providing intervention to patients with concussion.

Setting:

Concussion clinic at an academic institution.

Participants:

Participants ages 12 to 24 years with a reported history of mild traumatic brain injury or concussion were evaluated by a physician, or by a physician and OT, in an initial evaluation appointment.

Design:

A single researcher (OT) with training in concussion qualitatively compared reported impacted occupational domains as defined in the Occupational Therapy Practice Framework, using both a retrospective and a prospective cohort. The prospective group differed from the retrospective group in that an OT was present, and participated in the initial evaluation.

Results:

The domains of performance patterns (P = .007) and performance skills (P ≤ .001) were identified significantly more often when an occupational therapy practitioner participated in the initial evaluation.

Conclusions:

Rehabilitation professionals, such as OTs, play an important role in identifying impacted domains after a concussion, which can help optimize patient care.
Does Retinal Ganglion Cell Loss Precede Visual Field Loss in Glaucoma?
Authors: Hood Donald C.
Published: November 2019

It is often said that substantial retinal ganglion cells are lost before glaucomatous damage is detected by standard automated perimetry. There are 4 key articles referenced to support this belief. To test the hypothesis that the 4 key articles are incorrectly cited, the publications in the first 6 months of 2019 that reference 1 or more of these 4 articles were examined. In particular, the degree to which the quotes from these 2019 publications accurately reflected the evidence in the 4 key articles was assessed. These quotes are inadequately supported by the data, and in some cases even by the conclusions found in the abstracts of the key articles. This is despite several review articles that have questioned the evidence in these key articles. Further, a case can be made that the evidence in the key articles better supports the opposite conclusion. That is, the data suggest that sensitivity loss can be seen on standard automated perimetry before retinal ganglion cells are missing.
Precepting nurse practitioner students in the graduate nurse education demonstration: A cross-sectional analysis of the preceptor experience
Authors: Todd Barbara A. , Brom Heather , Blunt Elizabeth , Dillon Patricia , Doherty Caroline , Drayton-Brooks Shirlee , Hung Irene , Montgomery Kymberlee , Peoples Lynda , Powell Mary , Vanacore Denise , Whalen Dara , Aiken Linda
Published: November 2019

Background:

The Graduate Nurse Education (GNE) Demonstration seeks to increase the number of advanced practice registered nurses (APRNs) in clinical practice. With the overall increase in APRN programs and, particularly, enrollment in nurse practitioner (NP) programs, there is growing competition among students to secure quality clinical precepting experiences.

Purpose:

This study describes NPs' and physicians' experiences with precepting APRN students within the Greater Philadelphia GNE Consortium.

Methods:

This was a cross-sectional descriptive survey of 1,021 NP and physician preceptors who provided clinical practicum experiences for at least one of the nine Greater Philadelphia GNE Consortium schools.

Results:

Differences between NP and physician precepting experiences regarding the importance of various factors in their decisions to precept were explored. Both NP and physician preceptors provide clinical practicum experiences to APRN students because they enjoy doing so. However, they differ regarding what they find important in their decisions to precept such as having protected time to precept and educational opportunities.

Implications for practice:

As universities work to recruit quality preceptors, they should consider tailoring their approach based on the preceptor's clinical role. In addition, schools located within the same region should consider streamlining administrative processes to form sustaining and productive clinical partnerships.
The Prognostic Value of Early Amplitude-Integrated Electroencephalography Monitoring After Pediatric Cardiac Arrest*
Authors: Bourgoin Pierre , Barrault Victoire , Joram Nicolas , Leclair Visonneau Laurène , Toulgoat Fréderique , Anthoine Emmanuelle , Loron Gauthier , Chenouard Alexis
Published: November 2019

Objectives:

To assess the ability of amplitude-integrated electroencephalography monitoring within 24 hours of the return of spontaneous circulation to prognosticate neurologic outcomes in children following cardiac arrest

Design:

Retrospective review of prospectively recorded data. An amplitude-integrated electroencephalography background score was calculated according to background activity during the first 24 hours after return of spontaneous circulation, a higher score correlating with more impaired background activity. The primary endpoint was the neurologic outcome as defined by the Pediatric Cerebral Performance Category at PICU discharge (Pediatric Cerebral Performance Category 1–3: a good neurologic outcome; Pediatric Cerebral Performance Category 4–6: a poor neurologic outcome).

Setting:

A referral PICU.

Patients:

Thirty children with a median age of 10 months (2–38 mo) and a male/female sex ratio of 1.3 were included.

Interventions:

None.

Measurements and Main Results:

Eighteen patients were assigned to the favorable outcome group and 12 to the unfavorable outcome group. The median time between return of spontaneous circulation and amplitude-integrated electroencephalography initiation was 4 hours (3–9 hr). The amplitude-integrated electroencephalography score within 24 hours after return of spontaneous circulation was significantly higher in the children with poor outcomes compared with those with good outcomes (12 ± 4 vs 25 ± 8; p < 0.001). Background activity during amplitude-integrated electroencephalography monitoring was able to predict poor neurologic outcomes at PICU discharge, with an area under the receiver operating characteristic curve of 0.91 (95% CI, 0.81–1.00).

Conclusions:

Early amplitude-integrated electroencephalography monitoring may help predict poor neurologic outcomes in children within 24 hours following cardiac arrest.
Mindfulness-based Cognitive Therapy for Obsessive-Compulsive Disorder: A Pilot Study
Authors: DIDONNA FABRIZIO , LANFREDI MARIANGELA , XODO ERICA , FERRARI CLARISSA , ROSSI ROBERTA , PEDRINI LAURA
Published: November 2019

Background:

Cognitive-behavioral therapy (CBT) is the first-choice intervention for obsessive-compulsive disorder (OCD); however, a notable proportion of patients either do not respond to treatment or relapse after CBT. Mindfulness-based treatment has been suggested as an alternative or complementary therapeutic strategy for OCD. However, only a few studies have focused on its application in clinical samples.

Objective:

To evaluate the impact of a new treatment, called “Mindfulness-based Cognitive Therapy for OCD.” It is an 11-session manualized group intervention that integrates elements of CBT, mindfulness, compassion-focused therapy, and acceptance and commitment therapy.

Methods:

The program was delivered to 35 patients with a primary diagnosis of OCD.

Results:

Participants demonstrated good adherence to the intervention. There was a significant reduction in mean total score on the Yale-Brown Obsessive-Compulsive Scale (Y-BOCS-TS) (P<0.001; Cohend=−0.72). One third of the participants (n=13) showed at least a 25% reduction on the Y-BOCS-TS, and 40% of the sample (n=14) were assigned to a lower Y-BOCS severity category after treatment. Significant changes were also found in depression (P<0.001;d=−0.80), worry (P<0.001;d=−0.79), alexithymia (P<0.01;d=−0.41), dissociation (P<0.05;d=−0.46), and general psychopathology (P<0.001;d=−0.58). Repeated measures linear mixed models showed that OCD symptom reduction was associated with an increase in mindfulness skills, in particular on the acting with awareness (P=0.006), nonjudging (P=0.001), and nonreactivity (P=0.001) facets.

Conclusions:

Overall, these findings are promising and they suggest that randomized controlled studies be conducted to test the effectiveness of this new treatment program for this challenging and disabling mental disorder.
Borderline Personality Features in Inpatients with Bipolar Disorder: Impact on Course and Machine Learning Model Use to Predict Rapid Readmission
Authors: SALEM HAITHAM , RUIZ ANA , HERNANDEZ SARAH , WAHID KAREEM , CAO FEI , KARNES BRANDI , BEASLEY SARAH , SANCHES MARSAL , ASHTARI ELAHEH , PIGOTT TERESA
Published: November 2019

Background:

Earlier research indicated that nearly 20% of patients diagnosed with either bipolar disorder (BD) or borderline personality disorder (BPD) also met criteria for the other diagnosis. Yet limited data are available concerning the potential impact of co-occurring BPD and/or BPD features on the course or outcome in patients with BD. Therefore, this study examined this comorbidity utilizing the standardized Borderline Personality Questionnaire (BPQ).

Methods:

This study involved 714 adult patients with a primary diagnosis of BD per DSM-IV criteria who were admitted to the psychiatric unit at an academic hospital in Houston, TX between July 2013 and July 2018. All patients completed the BPQ within 72 hours of admission. Statistical analysis was used to detect correlations between severity of BD, length of stay (LOS), and scores on the BPQ. A machine learning model was constructed to predict the parameters affecting patients’ readmission rates within 30 days.

Results:

Analysis revealed that the severity of certain BPD traits at baseline was associated with mood state and outcome measured by LOS. Inpatients with BD who were admitted during acute depressive episodes had significantly higher mean scores on 7 of the 9 BPQ subscales (P<0.05) compared with those admitted during acute manic episodes. Inpatients with BD with greater BPQ scores on 4 of the 9 BPQ subscales had significantly shorter LOS than those with lower BPQ scores (P<0.05). The machine learning model identified 6 variables as predictors for likelihood of 30-day readmission with a high sensitivity (83%), specificity (77%), and area under the receiver operating characteristic curve of 86%.

Conclusions:

Although preliminary, these results suggest that inpatients with BD who have higher levels of BPD features were more likely to have depressive rather than manic symptoms, fewer psychotic symptoms, and a shorter LOS. Moreover, machine learning models may be particularly valuable in identifying patients with BD who are at the highest risk for adverse consequences including rapid readmission.
Toll-like receptor 2 and 9 expression on circulating neutrophils is associated with increased mortality in critically ill patients
Authors: Lenz Max , Draxler Dominik F. , Zhang Chao , Kassem Mona , Kastl Stefan P. , Niessner Alexander , Huber Kurt , Wojta Johann , Heinz Gottfried , Speidl Walter S. , Krychtiuk Konstantin A.
Published: November 2019

Background:

Toll-like receptors (TLRs) play an important role in inflammatory processes in critically ill patients by binding to pathogen-associated molecular patterns and danger-associated molecular patterns (DAMPs). Whether neutrophil or monocyte TLR expression patterns are associated with outcome in critical illness is unknown.

Objectives:

To answer this question, we conducted a prospective, observational study including 215 consecutive patients admitted to a medical ICU at a tertiary care center.

Methods:

Blood was drawn at admission and expression of TLR-2, TLR-4, and TLR-9 on neutrophils and monocytes were analyzed by flow cytometry.

Results:

Median Acute Physiology and Chronic Health Evaluation II (APACHE II) score was 19, and 30-day mortality was 26%. TLR-2 expression on neutrophils was associated with APACHE II, Simplified Acute Physiology Score II, and Sepsis-related Organ Failure Assessment score. TLR-2 (P < 0.001) and TLR-9 (P < 0.05) expression on neutrophils was significantly higher in nonsurvivors. In contrast, neutrophil TLR-4 expression and monocyte TLR expression were not associated with survival. Neutrophil TLR-2 (odds ratio 3.8; 95% confidence interval 1.4–10.2; P < 0.05) and TLR-9 (odds ratio 4.0; 95% confidence interval 2.0–8.1; P < 0.001) expression in the third tertile predicted mortality independent from APACHE II, serum lactate, serum creatinine, and procalcitonin, respectively.

Conclusion:

We provide evidence for prognostic properties of neutrophil TLR-2 and TLR-9 expression regarding 30-day mortality in unselected critically ill patients, independent from baseline clinical characteristics, and laboratory values. These findings suggest that specific TLR-dependent activation of the innate immune system via neutrophils possibly caused by cell damage and release of otherwise intracellular components may play a significant role in the pathophysiology of critical illness.
Stochastic simulation platform for visualization and estimation of transcriptional kinetics
Authors: Gorin Gennady , Wang Mengyu , Golding Ido , Xu Heng
Published: November 2019

We present an implementation of the Gillespie algorithm that simulates the stochastic kinetics of nascent and mature RNA. Our model includes two-state gene regulation, RNA synthesis initiation and stepwise elongation, release to the cytoplasm, and stepwise degradation, a granular description currently tractable only by simulation. To facilitate comparison with experimental data, the algorithm predicts fluorescent probe signals measurable by single-cell RNA imaging. We approach the inverse problem of estimating underlying parameters in a five-dimensional parameter space and suggest optimization heuristics that successfully recover known reaction rates from simulated gene expression turn-on data. The simulation framework includes a graphical user interface, available as a MATLAB app at https://data.caltech.edu/records/1287.
Immunoglobulin gene conversion identification and analysis
Authors: Bonissone Stefano R.
Published: November 2019

Immunoglobulins are highly diverse, diverging from their originating germline genes driven primarily by somatic recombination and hypermutation. However, somatic gene conversion is a strong driver of immunoglobulin diversity in some species, including rabbits and chickens. It is considerably harder to detect by sequence analysis than point mutations, and currently no dedicated tools exist for identifying these events. We presentGECCO, the first dedicated gene conversion identification tool for immunoglobulins based on modified, simultaneous, pairwise alignments to host and donor references. We benchmark our approach on simulated repertoires and findGECCOhas high recall, low false positive rate, and is insensitive to somatic mutations. We apply this new approach to characterize gene conversion events at the repertoire level in hyper-immunized rabbits, to show patterns of donor V gene preferences and donor tract length distributions. The dedicated gene conversion identification method we present allows for the characterization of a new feature of antibody repertoires that has not been possible thus far.GECCOwill benefit future studies to explore the prevalence of immunoglobulin gene conversion in additional species.
Identifying Refugia and Barriers to the Spread of A. graminifolia and D. crumenatum in Puerto Rico
Authors: Foster Evan , Ackerman James D. , Falcón L. Wilfredo
Published: November 2019

Establishment of new populations is contingent on overcoming abiotic and biotic barriers. While this applies to all species, these hurdles are at the forefront of invasion biology where prediction, prevention, eradication, and control strategies depend on an understanding and exploitation of barriers to establishment and spread. Arundina graminifolia and Dendrobium crumenatum are two invasive orchids spreading throughout Puerto Rico. Current records on their distributions across the island are sparse, and their interactions with the surrounding ecosystem are unknown. Through a direct population survey of all known localities, we identified a new, acquired enemy of both orchids: the orchid-specialist weevil, Stethobaris polita. In this study, we used niche modelling to identify suitable habitats for each orchid on the island and map their current distributions and interactions with S. polita, along with their distributions in the most extreme climate scenario in 2050, in order to contextualize projected patterns of establishment on the island. Our findings show that D. crumenatum flourishes in urban environments which also provide refugia from S. polita. In contrast, there is currently no refugia for A. graminifolia from S. polita attack, as it is more sensitive to the same climatic variables as S. polita. Furthermore, projections into the most extreme climate scenario suggests Puerto Rico will be unsuitable for A. graminifolia and S. polita’s survival, and become less suitable for D. crumenatum, by 2050.
TRIM14 is a key regulator of the type I interferon response during Mycobacterium tuberculosis infection
Authors: Hoffpauir Caitlyn T. , Bell Samantha L. , West Kelsi O. , Jing Tao , Torres-Odio Sylvia , Cox Jeffery S. , West A. Phillip , Li Pingwei , Patrick Kristin L. , Watson Robert O.
Published: November 2019

Tripartite motif-containing proteins (TRIMs) play a variety of recently described roles in innate immunity. While many TRIMs regulate type I interferon (IFN) expression following cytosolic nucleic acid sensing of viruses, their contribution to innate immune signaling and gene expression during bacterial infection remains largely unknown. Because Mycobacterium tuberculosis is a potent activator of cGAS-dependent cytosolic DNA sensing, we set out to investigate a role for TRIM proteins in regulating macrophage responses to M. tuberculosis. Here we demonstrate that TRIM14, a non-canonical TRIM that lacks an E3 ligase RING domain, is a critical negative regulator of the type I IFN response in macrophages. We show that TRIM14 physically interacts with both cGAS and TBK1 and that macrophages lacking TRIM14 dramatically hyperinduce interferon stimulated gene (ISG) expression following cytosolic nucleic acid transfection, IFN-β treatment, and M. tuberculosis infection. Consistent with a defect in resolution of the type I IFN response, Trim14 knockout (KO) macrophages have more phospho-Ser754 STAT3 relative to phospho-727 and fail to upregulate the STAT3 target Socs3 (Suppressor of Cytokine Signaling 3), which is required to turn off IFNAR signaling. These data support a model whereby TRIM14 acts as a scaffold between TBK1 and STAT3 to promote phosphorylation of STAT3 at Ser727 and enhance negative regulation of ISG expression. Remarkably, Trim14 KO macrophages hyperinduce antimicrobials like Inos2 and are significantly better than control cells at limiting M. tuberculosis replication. Collectively, these data reveal a previously unappreciated role for TRIM14 in resolving type I IFN responses and controlling M. tuberculosis infection.
Ebselen attenuates mycobacterial virulence through inhibition of ESX-1 secretion
Authors: Osman Morwan M. , Pinckert Malte L. , Peak-Chew Sew , Troll Mark A. , Conrad William H. , Ramakrishnan Lalita
Published: November 2019

The type VII secretion system ESX-1 mediates virulence in Mycobacterium tuberculosis and Mycobacterium marinum. We find that in M. marinum, the synthetic organoselenium compound ebselen inhibits secretion of ESAT-6, a major ESX-1 substrate. We find that ebselen inhibits the in vitro activity of the ESX-1 AAA+ ATPase EccA1, which potentiates ESX-1 substrate secretion and function. Ebselen modifies a cysteine in its N-terminal tetratricopeptide repeat domain that is required for EccA1’s in vitro ATPase activity. Surprisingly, mutational analyses show this this cysteine is not required for ESX-1 secretion or ebselen’s activity, showing that ebselen inhibits ESX-1 secretion independently of inhibiting EccA1 activity in vitro. While the mechanism by which ebselen inhibits ESX-1 secretion remains elusive, we show that it attenuates ESX-1-mediated damage of M. marinum-containing macrophage phagosomes and inhibits intramacrophage growth. Extending our studies to M. tuberculosis, we find that ebselen inhibits ESX-1 secretion and phagosomal membrane damage in this organism. This work provides insight into EccA1 biology. Ebselen is an orally active drug in clinical trials for other conditions and this work suggests its potential in tuberculosis therapy.
Low-disturbance Farming Regenerates Healthy Deep Soil towards Sustainable Agriculture
Authors: Deng Fangbo , Wang Hongjun , Xie Hongtu , Bao Xuelian , He Hongbo , Zhang Xudong , Liang Chao
Published: November 2019

Intensive conventional farming has degraded farmland topsoil and seriously threaten food and environment security globally. Although low-disturbance practices have been widely adapted to restore soil health, whether this measure in a long run can potentially recover the critical deep soil to meet sustainable intensification of crop production are still unclear. Here we compared soil microbiome, physicochemical parameters along 3-m deep soil profiles, and crop yield in Northeast China subjected to ten years of farming practices at 3 levels of disturbance, including conventional tillage (CT), no-tillage without stover mulching (NTNS), and no-tillage with stover mulching (NTSM). We found that low-disturbance practices (NTNS and NTSM) promoted the ability of the deep soil to retain water, nitrogen and salt-extractable organic, regenerated whole-soil microbial diversity and metabolic function, improved topsoil organic carbon stock and corn yield in the drought year, showed the potential to reduce energy consumption and greenhouse gas emissions, thus regenerating highly efficient, sustainable agriculture.
Motivated for near impossibility: How task type and reward modulate task enjoyment and the striatal activation for extremely difficult task
Authors: Sakaki Michiko , Meliss Stef , Murayama Kou , Yomogida Yukihito , Matsumori Kaosu , Sugiura Ayaka , Matsumoto Madoka , Matsumoto Kenji
Published: November 2019

Economic and decision-making theories suppose that people would disengage from a task with near zero success probability, because this implicates little normative utility values. However, humans are often motivated for an extremely challenging task, even without any extrinsic incentives. The current study aimed to address the nature of this challenge-based motivation and its neural correlates. We found that, when participants played a skill-based task without extrinsic incentives, their task enjoyment increased as the chance of success decreased, even if the task was almost impossible to achieve. However, such challenge-based motivation was not observed when participants were rewarded for the task or the reward was determined in a probabilistic manner. The activation in the ventral striatum/pallidum tracked the pattern of task enjoyment. These results suggest that people are intrinsically motivated to challenge a nearly impossible task, but only when the task requires certain skills and extrinsic rewards are unavailable.
Population structure of chum salmon and selection on the markers collected for stock identification
Authors: Kitada Shuichi , Kishino Hirohisa
Published: November 2019

Genetic stock identification (GSI) is a major management tool of Pacific salmon (Oncorhynchus Spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single nucleotide polymorphisms (SNPs) across the Pacific Rim. Here, we analyzed published data sets for adult chum salmon (Oncorhynchus keta), namely 10 microsatellites, 53 SNPs, and a mitochondrial DNA locus (mtDNA3, control region and NADH-3 combined) from 495 locations in the same distribution range (n = 61,813). TreeMix analysis of the microsatellite loci identified the highest level of genetic drift towards Japanese/Korean populations and suggested two admixture events from Japan/Korea to Russia and the Alaskan Peninsula. The SNPs had been purposively collected from rapidly evolving genes to increase the power of GSI. The highest expected heterozygosity was observed in Japanese/Korean populations for microsatellites, whereas it was highest in Western Alaskan populations for SNPs, reflecting the SNP discovery process. By regressing the SNP population structures on those of the microsatellites, we estimated the selection on the SNP loci according to deviations from the predicted structures. Specifically, we matched the sampling locations of the SNPs with those of the microsatellites according to geographical information and performed regression analyses of SNP allele frequencies on the two coordinates of multi-dimensional scaling (MDS) of matched locations obtained from microsatellite pairwise FST values. The MDS first axis indicated a latitudinal cline in American and Russian populations, whereas the second axis found a differentiation of Japanese/Korean populations. The top five outlier SNPs were mtDNA3 (combined locus of the control region and NADH-3), U502241 (unknown), GnRH373, ras1362, and TCP178, which were consistently identified by principal component analysis. We summarized the functions of the 53 nuclear SNPs and mtDNA3 locus by referring to a gene database system and discussed the functions of the outlier SNPs and fitness of chum salmon.
Lessons from Japan marine stock enhancement and sea ranching programmes over 100 years
Authors: Kitada Shuichi
Published: November 2019

More than 26 billion juveniles of 180 marine species are released annually into the wild in over 20 countries, but the usefulness of this strategy remains unclear. Here, I analyse the effects of stocking by Japanese marine and salmon stock-enhancement programmes and evaluate their efficacy through a Bayesian meta-analysis of new and previously considered cases. The posterior mean recapture rate (± SD) was 8.3 ± 4.7%. Without considering personnel costs and negative impacts on wild populations, the mean economic efficiency was 2.8 ± 6.1, with many cases having values of 1 to 2. On the macro-scale, the proportion of released seeds to total catch was 76 ± 20% for Japanese scallop, 28 ± 10% for abalone, 20 ± 5% for swimming crab, 13 ± 5% for kuruma prawn, 11 ± 4% for Japanese flounder, and 7 ± 2% for red sea bream; according to these percentages, stocking effects were generally small, and population dynamics were unaffected by releases but dependent on the carrying capacity of the nursery habitat. All cases of Japanese releases, except for Japanese scallop, were probably economically unprofitable. Captive breeding reduces the fitness of hatchery fish in the wild. In addition, long-term releases replace wild genes and may cause fitness decline in the recipient population when the proportion of hatchery fish is very high. Short-term hatchery stocking can be useful, particularly for conservation purposes, but large-scale programmes may harm the sustainability of populations. Nursery habitat recovery and fishing pressure reduction often outperform hatcheries in the long run.
Offset-related brain activity in the ventrolateral prefrontal cortex promotes long-term memory formation of verbal events
Authors: Medvedeva Angela , Saw Rebecca , Sirota Miroslav , Fuggetta Giorgio , Galli Giulia
Published: November 2019

Recent evidence suggests that brain activity following the offset of a stimulus during encoding contributes to long-term memory formation, however the exact mechanisms underlying offset-related encoding are still unclear. Here we used repetitive transcranial magnetic stimulation (rTMS) to investigate offset-related activity in the left ventrolateral prefrontal cortex (VLPFC). rTMS was administered at different points in time around stimulus offset while male and female participants encoded visually-presented words (first rTMS experiment) or pairs of words (second rTMS experiment) and the analyses focused on the effects of the stimulation on subsequent memory performance. The results show that rTMS administered at the offset of the stimuli, but not during online encoding, disrupted subsequent memory performance. In the first experiment we show that rTMS specifically disrupted encoding mechanisms initiated by the offset of the stimuli rather than general, post-stimulus processes. In the second experiment, we show a robust decline in associative memory performance when rTMS was delivered at the offset of the word pairs, suggesting that offset-related encoding may contribute to the binding of information into an episodic memory trace. A meta-analysis conducted on the two studies and on a previously published dataset confirmed that the involvement of the left VLPFC in memory formation is initiated by the offset of the stimulus. The offset of the stimulus may represent an event boundary that promotes the reinstatement of the previously experienced event and episodic binding.

SIGNIFICANCE STATEMENT

How well an event is encoded predicts how well it is remembered, and verbal encoding is an important part of everyday memory that, if disrupted, can lead to difficulties and disorders. The timing of encoding processes relative to the presentation of an event is important for successful retrieval, and little is known about the interval immediately after an event’s presentation (post-stimulus offset) which is thought to involve critical encoding processes in the VLPFC and hippocampus. The current studies demonstrate that indeed, verbal encoding processes in the VLPFC that are necessary for memory formation are triggered by the offset of the word, and these processes may involve VLPFC-hippocampal interactions that promote binding of event features into a single, coherent memory trace.
Motor imagery practice during arm-immobilization benefits sensorimotor cortical functions and plasticity-related sleep features
Authors: Debarnot Ursula , Perrault Aurore. A. , Sterpenich Virginie , Legendre Guillaume , Huber Chieko , Guillot Aymeric , Schwartz Sophie
Published: November 2019

Motor imagery (MI) is known to engage motor networks and could compensate for the maladaptive neuroplasticity elicited by immobilization. This hypothesis and associated underlying neural mechanisms remain underexplored. Here, we investigated how MI practice during 11 h of arm-immobilization influences sensorimotor and cortical representations of the hands, as well as sleep. Fourteen participants were first tested after a normal day, followed by two 11-h periods of immobilization, either with concomitant MI treatment or control tasks. Data revealed that MI prevented the consequences of immobilization: (i) alteration of the sensorimotor representation of hands, (ii) decrease of cortical excitability over the primary motor cortex (M1) contralateral to arm-immobilization, and (iii) reduction of sleep spindles over both M1s. Furthermore, (iv) the time spent in REM sleep was significantly longer after MI. These results support that implementing MI during immobilization can limit the deleterious effects of limb disuse, at several levels of sensorimotor functioning.