bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating mathematical models with experimental data to investigate the within-host dynamics of bacterial infections
Authors: Vlazaki Myrto , Huber John , Restif Olivier 
Published: January 2020

ABSTRACT
Bacterial infections still constitute a major cause of mortality and morbidity worldwide. The unavailability of therapeutics, antimicrobial resistance and the chronicity of infections due to incomplete clearance contribute to this phenomenon. Despite the progress in antimicrobial and vaccine development, knowledge about the effect that therapeutics have on the host–bacteria interactions remains incomplete. Insights into the characteristics of bacterial colonization and migration between tissues and the relationship between replication and host- or therapeutically induced killing can enable efficient design of treatment approaches. Recently, innovative experimental techniques have generated data enabling the qualitative characterization of aspects of bacterial dynamics. Here, we argue that mathematical modeling as an adjunct to experimental data can enrich the biological insight that these data provide. However, due to limited interdisciplinary training, efforts to combine the two remain limited. To promote this dialogue, we provide a categorization of modeling approaches highlighting their relationship to data generated by a range of experimental techniques in the area of in vivo bacterial dynamics. We outline common biological themes explored using mathematical models with case studies across all pathogen classes. Finally, this review advocates multidisciplinary integration to improve our mechanistic understanding of bacterial infections and guide the use of existing or new therapies.
Effects of diet type on nutrient utilization and energy balance in drylot heifers1
Authors: Baber Jessica R , Wickersham Tryon A , Sawyer Jason E , Freetly Harvey C , Brown-Brandl Tami M , Hales Kristin E 
Published: January 2020

Abstract
Feeding cattle in intensified settings allows cow-calf producers to decrease their reliance on grazed forage and utilize alternative feedstuffs. During times of intense management, diet type may alter energy utilization. Fourteen pregnant MARC III heifers (405 ± 44 kg BW) were used in a 180 d experiment to determine effects of diet type on nutrient and energy utilization. Heifers were randomly assigned to one of two treatments, a forage diet (FOR; 2.10 Mcal metabolizable energy [ME]/kg; 95.75% forage) or a concentrate diet (CONC; 2.94 Mcal ME/kg; 71% concentrate), and individually fed to meet maintenance energy requirements (0.135 Mcal ME/kg BW0.75). The CONC diet contained dry-rolled corn, corn stalks (10.16 cm grind size), soybean meal, corn silage (approximately 45% corn grain; stored in a plastic bag), dicalcium phosphate, urea, and a premix pellet; FOR contained alfalfa hay (harvested at mid-bloom), corn silage, dicalcium phosphate, and a premix pellet. Measurements of energy intake and digestibility were measured over a 4-d period on days 116, 172, and 235 of gestation. Using portable headbox calorimeters, measurements of O2, CO2, and CH4 gases were collected over a period of 24 h. Data were analyzed in a completely randomized design with diet as fixed effect. Dry matter and organic matter digestibility were greater for CONC than FOR (P &lt; 0.01). Intake of gross energy (GE) and digestible energy (DE) were greater for FOR (P &lt; 0.01), but by design, ME intake was not different between treatments (P = 0.26). Energy lost as methane (% of GE intake) was not different between treatments (P = 0.49). The ratio of ME to DE was greater for CONC (86.8 vs. 82.8; P = 0.01) than FOR. Heat production relative to ME was not different between treatments (P = 0.85). Maternal tissue energy did not differ and was 1.2 Mcal/d for CONC and 0.9 Mcal/d for FOR (P = 0.73). Greater nitrogen (N) consumption was observed for FOR (192.2 g/d) than CONC (134.0 g/d; P &lt; 0.01), and retained N was greater for FOR than CONC (P &lt; 0.01) on days 116 and 235 of gestation. Neither concentrate-based or forage-based diets affected body condition score (P = 0.26). Heifers fed concentrate-based diets retained more energy in part because they had larger calves, but this energy was not recovered in maternal tissue.
Efficacy of statistical process control procedures to identify deviations in continuously measured physiologic and behavioral variables in beef steers experimentally challenged with Mannheimia haemolytica
Authors: Kayser William C , Carstens Gordon E , Parsons Ira L , Washburn Kevin E , Lawhon Sara D , Pinchak William E , Chevaux Eric , Skidmore Andrew L 
Published: January 2020

AbstractThe objective of this experiment was to determine if statistical process control (SPC) procedures coupled with the remote continuous collection of feeding behavior patterns, accelerometer-based behaviors, and rumen temperature can accurately differentiate between animals experimentally inoculated with Mannheimia haemolytica (MH) or PBS. Thirty-six crossbred steers (BW = 352 ± 23 kg) seronegative for MH were randomly assigned to bronchoselective endoscopic inoculation with MH (n = 18) or PBS (n = 18). Electronic feed bunks were used to measure DMI and feeding behavior traits, accelerometer-based neck collars measured feeding- and activity-behavior traits, and ruminal thermo-boluses measured rumen temperature. Data were collected for 28 d prior to and following inoculation. Steers inoculated with MH exhibited elevated (P &lt; 0.02) levels of neutrophils and rumen temperature indicating that MH challenge effectively stimulated immunologic responses. However, only nine of the MH steers exhibited increased serum haptoglobin concentrations indicative of an acute-phase protein response and one displayed clinical signs of disease. Shewhart charts (SPC procedure) were used for two analyses, and sensitivity was computed using all MH-challenged steers (n = 18), and a subset that included only MH-challenged haptoglobin-responsive steers (n = 9). Specificity was calculated using all PBS steers in both analyses. In the haptoglobin-responsive only analysis, DMI and bunk visit (BV) duration had the greatest accuracy (89%), with accuracies for head-down (HD) duration, BV frequency, time to bunk, and eating rate being less (83%, 69%, 53%, and 61%, respectively). To address the diurnal nature of rumen temperature, data were averaged over 6-h intervals, and quarterly temperature models were evaluated separately. Accuracy for the fourth quarter rumen temperature was higher (78%) than the other quarterly temperature periods (first = 56%, second = 50%, and third = 67%). In general, the accelerometer-based behavior traits were highly specific ranging from 82% for ingestion to 100% for rest, rumination, and standing. However, the sensitivity of these traits was low (0% to 50%), such that the accuracies were moderate compared with feeding behavior and rumen temperature response variables. These results indicate that Shewhart procedures can effectively identify deviations in feeding behavior and rumen temperature patterns to enable subclinical detection of BRD in beef cattle.
Viral Tropism in Human Immunodeficiency Virus Type 1–Infected Children and Adolescents in Thailand
Authors: Arayapong Natt , Pasomsub Ekawat , Kanlayanadonkit Rujikorn , Keatkla Jiraporn , Techasaensiri Chonnamet , Phuphuakrat Angsana , Sungkanuparph Somnuek , Apiwattanakul Nopporn , Chaisavaneeyakorn Sujittra 
Published: January 2020

Abstract

Background
Maraviroc, a C-C chemokine receptor 5 (CCR5) antagonist, has been used as an alternative antiretroviral drug in treatment-experienced adults and children infected by CCR5-tropic human immunodeficiency virus type 1 (HIV-1) isolates. Prior to widespread use of this drug, rates of HIV-1 coreceptor tropism and factors associated with coreceptor tropism had to be determined.

Methods
HIV-1–infected individuals aged &lt;20 years with HIV-1 viral loads &gt;1000 RNA copies/mL who were treatment-experienced or treatment-naive were enrolled. HIV-1 coreceptor tropism was determined using a genotypic test in which V3 sequences were analyzed with GENO2PHENO version 2.5 and a false discovery rate of 5%.

Results
Fifty-two HIV-1–infected patients were recruited. The median age of participants was 14.9 years (interquartile range [IQR], 8.9–16.8 years). The median CD4 cell count was 396.0 cells/µL (IQR, 72.0–630.3 cells/µL). The median HIV-1 viral load was 43 339 RNA copies/mL (IQR, 8874–197 055 copies/mL). Thirty-nine patients (75%) were treatment-experienced. The most prevalent HIV-1 subtype in this population was CRF01_AE (36 patients, 69.2%). Based on analyses of V3 loop sequences, 5 of 13 treatment-naive patients (38.5%) and 11 of 39 treatment-experienced patients (28.2%) were infected by R5 viruses, while 7 of 13 treatment-naive patients (53.8%) and 19 of 39 treatment-experienced patients (48.7%) were infected by X4 viruses. The only factor associated with the presence of X4 viruses was HIV-1 subtype CRF01_AE.

Conclusions
X4-tropic viruses are associated with the CRF01_AE subtype. Hence, testing of HIV tropism should be performed before treatment with CCR5 inhibitors in children in areas where CRF01_AE predominates.
Live-cell imaging of early events following pollen perception in self-incompatible Arabidopsis thaliana
Authors: Rozier Frédérique , Riglet Lucie , Kodera Chie , Bayle Vincent , Durand Eléonore , Schnabel Jonathan , Gaude Thierry , Fobis-Loisy Isabelle 
Published: January 2020

AbstractEarly events occurring at the surface of the female organ are critical for plant reproduction, especially in species with a dry stigma. After landing on the stigmatic papilla cells, the pollen hydrates and germinates a tube, which penetrates the cell wall and grows towards the ovules to convey the male gametes to the embryo sac. In self-incompatible species within the Brassicaceae, these processes are blocked when the stigma encounters an incompatible pollen. Based on the generation of self-incompatible Arabidopsis lines and by setting up a live imaging system, we showed that control of pollen hydration has a central role in pollen selectivity. The faster the pollen pumps water from the papilla during an initial period of 10 min, the faster it germinates. Furthermore, we found that the self-incompatibility barriers act to block the proper hydration of incompatible pollen and, when hydration is promoted by high humidity, an additional control prevents pollen tube penetration into the stigmatic wall. In papilla cells, actin bundles focalize at the contact site with the compatible pollen but not with the incompatible pollen, raising the possibility that stigmatic cells react to the mechanical pressure applied by the invading growing tube.
The non-photochemical quenching protein LHCSR3 prevents oxygen-dependent photoinhibition in Chlamydomonas reinhardtii
Authors: Roach Thomas , Na Chae Sun , Stöggl Wolfgang , Krieger-Liszkay Anja 
Published: January 2020

AbstractNon-photochemical quenching (NPQ) helps dissipate surplus light energy, preventing formation of reactive oxygen species (ROS). In Chlamydomonas reinhardtii, the thylakoid membrane protein LHCSR3 is involved in pH-dependent (qE-type) NPQ, lacking in the npq4 mutant. Preventing PSII repair revealed that npq4 lost PSII activity faster than the wild type (WT) in elevated O2, while no difference between strains was observed in O2-depleted conditions. Low Fv/Fm values remained 1.5 h after moving cells out of high light, and this qH-type quenching was independent of LHCSR3 and not accompanied by losses of maximum PSII activity. Culturing cells in historic O2 atmospheres (30–35%) increased the qE of cells, due to increased LHCSR1 and PsbS levels, and LHCSR3 in the WT, showing that atmospheric O2 tensions regulate qE capacity. Colony growth of npq4 was severely restricted at elevated O2, and npq4 accumulated more reactive electrophile species (RES) than the WT, which could damage PSI. Levels of PsaA (PSI) were lower in npq4 grown at 35% O2, while PsbA (PSII) levels remained stable. We conclude that even at high O2 concentrations, the PSII repair cycle is sufficient to maintain net levels of PSII. However, LHCSR3 has an important function in protecting PSI against O2-mediated damage, such as via RES.
Critical length in long-read resequencing
Authors: De Coster Wouter , Strazisar Mojca , De Rijk Peter 
Published: January 2020

Abstract
Long-read sequencing has substantial advantages for structural variant discovery and phasing of variants compared to short-read technologies, but the required and optimal read length has not been assessed. In this work, we used long reads simulated from human genomes and evaluated structural variant discovery and variant phasing using current best practice bioinformatics methods. We determined that optimal discovery of structural variants from human genomes can be obtained with reads of minimally 20 kb. Haplotyping variants across genes only reaches its optimum from reads of 100 kb. These findings are important for the design of future long-read sequencing projects.
Concussion Clinical Profiles Screening (CP Screen) Tool: Preliminary Evidence to Inform a Multidisciplinary Approach
Authors: Kontos Anthony P , Elbin R J , Trbovich Alicia , Womble Melissa , Said Azkya , Sumrok Vanessa Fazio , French Jonathan , Kegel Nathan , Puskar Alicia , Sherry Natalie , Holland Cyndi , Collins Michael 
Published: January 2020

AbstractBACKGROUNDCurrent concussion symptom inventories emphasize total number or symptoms and severity and overlap with other conditions, such as mental health disorders, which may limit their specificity and clinical utility.OBJECTIVETo develop and test the reliability and validity of a new Concussion Clinical Profiles Screening tool (CP Screen) in both healthy controls and concussed.METHODSCP Screen is a 29-item self-report, clinical profile-based symptom inventory that measures the following 5 concussion clinical profiles: 1) anxiety/mood, 2) cognitive/fatigue, 3) migraine, 4) ocular, and 5) vestibular; and the following 2 modifying factors: 1) sleep and 2) neck. Post-Concussion Symptom Scale (PCSS), vestibular/ocular motor screening (VOMS) tool, and Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) were conducted. CP Screen was administered in community a concussion surveillance program and 2 sports medicine concussion clinics. Responses include 248 athletes, 121 concussed, and 127 controls, enrolled between 2018 and 2019.RESULTSInternal consistency of the CP Screen in the control (Cronbach's alpha = .87) and concussed (Cronbach's alpha = .93) samples was high. Moderate to high correlations among the CP Screen factors and PCSS factors and VOMS items, supporting concurrent validity. ROC curve analysis for identifying concussed from controls was significant (P < .001) for all CP Screen factor and modifier scores with excellent AUCs for migraine (.93), ocular (.88), vestibular (.85), and cognitive (.81) factors, demonstrating predictive validity.CONCLUSIONThe CP Screen demonstrated strong reliability, concurrent validity with commonly used concussion assessment (ie, PCSS, VOMS, and ImPACT), and predictive validity for identifying concussion. The CP Screen extends current symptom inventories by evaluating more specific symptoms that may reflect clinical profiles and inform better clinical care.
Risk of New Fractures in Vertebroplasty for Multiple Myeloma. A Retrospective Study
Authors: Rocha Romero Andrés , Hernández-Porras Berenice Carolina , Plancarte-Sanchez Ricardo , Espinoza-Zamora José Ramiro , Carvajal Gabriel , Ramos Natarén Reyna Guadalupe , De Los Reyes Pacheco Victor Alfonso , Salazar Carrera Ivan Hamiyd 
Published: January 2020

AbstractObjectiveVertebroplasty is a percutaneous minimally invasive procedure indicated for vertebral collapse pain treatment. Among the known complications of the procedure is the augmented risk of new vertebral fractures. There are no specific studies in this patient population describing the risk of new vertebral fractures after vertebroplasty. This study analyzed risk factors associated with new vertebral fractures after vertebroplasty in patients with multiple myeloma.MethodsObservational retrospective study in patients with multiple myeloma. The data collection took place from January 1, 2010, to December 30, 2017, at the National Cancer Institute. Clinical data and procedural variables such as cement volume, cement leaks, fracture level, number of treated vertebrae, pedicular disease, and cement distribution pattern, with two years follow-up, were analyzed with the Wilcoxon test, and a logistic regression model was used to identify risk factors related to new vertebral fractures. A confidence interval of 95% was used for analysis.ResultsAt one-year follow-up, 30% of fractures were reported after vertebroplasty, most of them at low thoracic and lumbar level (50% adjacent level). Vertebroplasty was most commonly performed at the thoracolumbar and lumbar area. We demonstrated a 70.7% median numerical rating scale reduction at one-year follow-up; a significant decrease in opioid consumption occurred only during the first month.ConclusionsPedicle involvement, disc leakage, cement volume, thoracolumbar and lumbar level, and number of treated vertebrae by intervention are important risk factors when performing vertebroplasty. Prospective randomized studies are needed to evaluate these factors in this specific population.
The Role of Government in Firm Outcomes
Authors: Duchin Ran , Gao Zhenyu , Shu Haibing 
Published: January 2020

Abstract
Using a unique setting in China, where the geographic distance between collective firms and local governments is highly persistent because of legal restrictions on land ownership and mobility, we investigate the role of government involvement in small firms. In our analysis of survey responses, we find that weaker government involvement, measured by greater distance from government, is associated with higher firm autonomy and reduced taxes, protectionism, and anticompetitive behavior. In our analysis of firm-level financial data, we find that distant firms have better operating performance, higher growth, and higher entry rates. We find similar results around exogenous government office relocations.
Comparison of the effect of tildipirosin administered alone or in combination with transdermal flunixin on the performance, health, activity, and well-being of transported feedlot calves on arrival at the feedlot
Authors: Martin Miriam , Kleinhenz Michael , Kleinhenz Katie , Reppert Emily , Blasi Dale , Parks Timothy , Baysinger Angela , Hutcheson John , Coetzee Johann 
Published: January 2020

AbstractLong distance transportation can be a significant source of stress to cattle and is associated with increased risk of bovine respiratory disease (BRD). The administration of a nonsteroidal anti-inflammatory drug (NSAID) has been shown to reduce stress following long distance transport. The objective of this study was to compare performance, health, accelerometer activity, and well-being between calves receiving either tildipirosin (Zuprevo 18%; Merck Animal Health, Madison, NJ) alone or in combination with transdermal flunixin (BANAMINE Transdermal Pour-on Solution; Merck Animal Health, Madison, NJ) on arrival at the feedlot. Three hundred eighty-four polled, Continental × English, and English crossbred bulls (n = 199) and steers (n = 185) were enrolled into one of two treatments: 1) tildipirosin administered in the neck as a single dose of 4 mg/kg only (PLBO) 2) tildipirosin in combination with transdermal flunixin applied to the dorsal midline at a dose of 3.3 mg/kg (FTD). Outcomes measured were average daily gain (ADG), dry mater intake (DMI), gain to feed, morbidity, mortality, accelerometer activity data, and a daily visual analog scale (VAS) assessment of well-being. Body weight (BW) was determined by weighing individual animals; ADG was calculated as initial BW—final BW / total days on feed; DMI was calculated as daily pen feed allocation—feed remaining at next feeding / number of calves in the pen; and gain to feed was calculated as pen level ADG / pen level DMI. The VAS used was a 100 mm line anchored at each end by descriptors of “no pain” or “severe pain”. Statistical analysis was performed using JMP 13 computer software using pen as the experimental unit, lot number as a random variable, and treatment as a fixed variable. There was no treatment effect on DMI (P = 0.51). During the first 14 d on feed, FTD calves had a lower ADG of 0.90 kg/d compared with 1.33 kg/d in the PLBO group (P = 0.05). There were no differences observed in morbidity and mortality between groups (P = 0.29). There were no treatment differences from activity data (P = 0.19). The VAS assessment showed a significant time × treatment interaction (P &lt; 0.001). During the first 36 h after treatment administration, the FTD-treated calves had lower VAS scores [6.23 (95% CI: 5.27–7.20) compared with 7.28 (95% CI: 6.32–8.24)] than PLBO (P &lt; 0.05). Results suggest that FTD-treated calves showed less signs of pain the first 36 h postdrug application relative to PLBO calves.
Using Clinical Profiles and Complete Blood Counts to Differentiate Causes of Acute Febrile Illness during the 2009–11 Outbreak of Typhoid and Chikungunya in a Dengue Endemic Area
Authors: Laoprasopwattana Kamolwish , Limpitikul Wannee , Geater Alan 
Published: January 2020

Abstract

Background and aims
After the 2009–11 outbreak of typhoid and chikungunya (CHIK) in Thailand, an effort was made to use complete blood counts and clinical profiles to differentiate these diseases to facilitate earlier specific treatment.

Methods
Patients aged 2–15 years having fever on first visit ≤3 days without localizing signs were enrolled retrospectively. Typhoid fever was confirmed by hemoculture, dengue by nonstructural protein-1 or polymerase chain reaction (PCR), and CHIK by PCR. Febrile children with negative results for these infections were classified as other acute febrile illness (AFI).

Results
Of the 264 cases, 56, 164, 25 and 19 had typhoid fever, dengue viral infection (DVI), CHIK and other AFI, respectively. Arthralgia had sensitivity, specificity, positive predictive value (PPV) and negative predictive value of 0.96, 0.97, 0.80 and 0.99, respectively, to differentiate CHIK from the others. After excluding CHIK by arthralgia, the PPV of the WHO 1997 and 2009 criteria for DVI increased from 0.65 and 0.73 to 0.95 and 0.84, respectively. Children with one of myalgia, headache or leukopenia had sensitivity of 0.84, specificity of 0.76 and PPV of 0.92 to differentiate DVI from typhoid and other AFIs. Patients with one of abdominal pain, diarrhea or body temperature &gt;39.5°C were more likely to have typhoid fever than another AFI with PPV of 0.90.

Conclusion
Using this flow chart can help direct physicians to perform more specific tests to confirm the diagnosis and provide more specific treatment. Nevertheless, clinical follow-up is the most important tool in unknown causes of febrile illness.