jimnoneill/paper-to-field-training huggingface dataset:
Propagation of Human Papillomavirus 16 Using a Novel Adenovirus and Cre/LoxP Mechanism

Problem: Human papillomavirus type 16 (HPV16) infection is a major risk factor for the development of squamous cell cancers of the cervix and of the head and neck. A major barrier to understanding the progression from initial infection to cancer has been the lack of in vitro models that allow infection, replication, and persistence of the viral genome as an episome in differentiated epithelial cells.

Methods: To overcome this barrier, we designed an adenoviral delivery vector that contained a full HPV16 genome flanked by LoxP homologous recombination sites plus a fluorescent reporter that was expressed only after the HPV genome was excised by Cre recombinase.

Results: This system delivered circular HPV16 genomes to cervical epithelial cells and well-differentiated human airway epithelia. Following delivery, the HPV16 genome replicated and persisted as an episome in cervical keratinocytes. These cells developed an immortalized phenotype and a dysplastic epithelial appearance. Moreover, induction of differentiation led to the expression of late genes and production of infectious HPV16 virions.

Conclusion: This work provides a novel means of introducing biologically active HPV genomes into epithelial cells, which are normally difficult to transfect. These methods will allow the study of HPV genome replication and gene expression in the earliest stages of HPV genome establishment and may provide a means with which to study non-oncogenic HPV viral types.

Significance: Understanding the papillomavirus life cycle may aid in developing novel treatments for HPV-related head and neck diseases.

Support: None reported.

Topic: Cervical Cancer and HPV Research
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
<scp>C</scp>hronic impairment of ERK signaling in glutamatergic neurons of the forebrain does not affect spatial memory retention and LTP in the same manner as acute blockade of the ERK pathway

Abstract The ERK/MAPK signaling pathway has been extensively studied in the context of learning and memory. Defects in this pathway underlie genetic diseases associated with intellectual disability, including impaired learning and memory. Numerous studies have investigated the impact of acute ERK/MAPK inhibition on long‐term potentiation and spatial memory. However, genetic knockouts of the ERKs have not been utilized to determine whether developmental perturbations of ERK/MAPK signaling affect LTP and memory formation in postnatal life. In this study, two different ERK2 conditional knockout mice were generated that restrict loss of ERK2 to excitatory neurons in the forebrain, but at different time‐points (embryonically and post‐natally). We found that embryonic loss of ERK2 had minimal effect on spatial memory retention and novel object recognition, while loss of ERK2 post‐natally had more pronounced effects in these behaviors. Loss of ERK2 in both models showed intact LTP compared to control animals, while loss of both ERK1 and ERK2 impaired late phase LTP. These findings indicate that ERK2 is not necessary for LTP and spatial memory retention and provide new insights into the functional deficits associated with the chronic impairment of ERK signaling.

Topic: Genetics and Neurodevelopmental Disorders
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Premature chromosome condensation studies in human leukemia. I. Pretreatment characteristics

Abstract The phenomenon of premature chromosome condensation (PCC) was used to compare the bone marrow proliferation characteristics of 163 patients with various forms of leukemia prior to the initiation of new therapy. The proliferative potential index (PPI, or fraction of G1 cells in late G1 phase) and the fraction of cells in S phase was determined and compared to the type of disease and the bone marrow blast infiltrate for each patient. Previously untreated patients with acute leukemia exhibited an average PPI value three times that of normal bone marrow (37.5% for acute myeloblastic leukemia [AML], acute monomyeloblastic leukemia [AMML], or acute promyelocytic leukemia [APML] and 42% for acute lymphocytic leukemia [ALL] or acute undifferentiated leukemia [AUL]). Untreated chronic myelogenous leukemia (CML) patients showed intermediate PPI values (25.2%), whereas CML patients with controlled disease exhibited nearly normal PPI values (14.6%). On the other hand, blastic-phase CML patients exhibited PPI values closer to that observed in patients with acute leukemia (35.4%). Seven patients with chronic lymphocytic leukemia (CLL) exhibited even higher PPI values. No correlations were observed between PPI values, fraction of cells in S phase, and marrow blast infiltrate. For untreated acute disease patients, PPI values were prognostic for response only at low and high PPI values. These results suggest that the PCC-determined proliferative potential is a biologic reflection of the degree of malignancy within the bone marrow.

Topic: Acute Myeloid Leukemia Research
Subfield: Hematology
Field: Medicine
Domain: Health Sciences
Impacts of organic soil amendments on forage grass production under different soil conditions

Organic amendments can improve grassland productivity. Timothy and tall fescue were sown on a sandy loam and a coarse sand at Særheim, Norway, in September 2016 and on a loamy sand at Skierniewice, Poland, in April 2017, and cut and fertilised according to normal practices for the two regions from 2017 to 2019. At both sites, 0.75 kg DM m-2 of either digested or undigested manure (the latter with or without 2.9 kg biochar m-2) were incorporated prior to sowing. On the coarse sand at Særheim, total seasonal tall fescue yield in 2018 was 46–60% higher in the organic amendment treatments, and total seasonal timothy yield in the digestate treatment was 97% higher, than in the control treatment for the same species with only mineral fertiliser. On the sandy loam at Særheim and the loamy sand at Skierniewice, none of the amendments resulted in significant yield increments. These results indicate a clear effect on soil type on grassland biomass response to organic amendments.

Topic: Turfgrass Adaptation and Management
Subfield: Environmental Chemistry
Field: Environmental Science
Domain: Physical Sciences
<scp>Age‐Related</scp> Parkinsonian Signs in Microdeletion 22q11.2

Abstract Background The recurrent hemizygous 22q11.2 deletion associated with 22q11.2 deletion syndrome has been identified as a genetic risk factor for early‐onset PD. However, little is known about early motor signs in this condition. Objectives We examined the presence, severity and possible factors associated with parkinsonism in adults with 22q11.2 deletion syndrome and without PD. Methods We compared motor signs between 82 adults with 22q11.2 deletion syndrome and 25 healthy controls, using the MDS‐UPDRS part III, and three‐dimensional motion‐tracker technology to quantify components of bradykinesia. Results Median MDS‐UPDRS part III total and bradykinesia subscores were significantly higher in 22q11.2 deletion syndrome (median age: 26 years; range, 17–65) than in controls ( P = 0.000; P = 0.000, respectively). Age was a significant contributor to bradykinesia subscore ( B = 0.06; P = 0.01) and to the electronic bradykinesia component, velocity ( B = –0.02; P = 0.000); psychotic illness did not significantly impact these analyses. In 22q11.2 deletion syndrome, MDS‐UPDRS–defined bradykinesia was present in 18.3%, rigidity in 14.6%, and rest tremor in 12.2%. Conclusions Parkinsonian motor signs appear to be common and age related in 22q11.2 deletion syndrome. Longitudinal studies are needed to investigate possible symptom progression to PD. © 2020 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.

Topic: Congenital heart defects research
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Design of a magneto-optic residual current device using aqueous ferrofluid as the sensing material

The paper presents a design for a Magneto-Optic Residual Current Device (MORCD) using ferrofluid as the sensing material. As the selection of suitable magneto-optic material was seen as the critical phase in the design, a novel Magneto-Optical performance Indicator is proposed and verified using known optical materials. It was experimentally established that the designed MORCD is sufficiently fast and capable of detecting residual current as low as 1.51 mA.

Topic: Photonic and Optical Devices
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Extraction of Radio-Strontium from Nitric Acid Medium Using Di-<i>tert</i>-Butyl Cyclohexano18-Crown-6 (DTBCH18C6) in Toluene–1-Octanol Diluent Mixture

Abstract An alternative extraction system to the SREX solvent using a diluent mixture comprising 4,4′(5′)di-tert-butylcyclohexano-18-crown-6 (DTBCH18C6) in 80% toluene–20% 1-octanol was developed and evaluated for Sr(II) extraction from pressurized heavy water reactor simulated high level waste (PHWR-SHLW). The acid uptake (5.7%) by the present solvent was significantly lower as compared to that by the SREX solvent (21%) which used 100% 1-octanol as the diluent. The extracted species conformed to the ion-pair [Sr(DTBCH18C6)(H2O)x]2+·2[(NO3)(H2O)y]−. Studies on Sr(II) extraction as a function of nitric acid concentration indicated more favorable extraction and stripping with the present solvent as compared to the SREX solvent. Loading studies with 0.025 M DTBCH18C6 in the diluent mixture, carried out using the Sr carrier, indicated a decrease in DSr from 3.1 with 10 ppm Sr carrier to 1.62 with 100 ppm Sr carrier. Other important physical parameters relevant for the extraction processes such as phase separation time (dispersion number), viscosity, and density were also measured. The radiation stability and reusability of the solvent was also investigated. In sharp contrast to the SREX solvent, with increasing absorbed dose the proposed solvent showed an increase in Sr extraction and an increased acid uptake. Keywords: crown etherdiluent effecthigh level wasteradio strontiumsolvent extraction Notes Note. a Studies with 3 M HNO3; b Studies with SHLW. Note. a Values in parentheses correspond to SHLW as the feed. b The values were not measurable. † Part of this work has been presented at NRC-7, Budapest, Hungary

Topic: Radioactive element chemistry and processing
Subfield: Inorganic Chemistry
Field: Chemistry
Domain: Physical Sciences
What Is a Novel?

The question ‘What is a novel?’ has received scant attention in the philosophical literature. Meanwhile, this question is important. In the light of this, in this paper, I would like to address it, suggesting a potential answer. I begin by defining what I call ‘novel in the restricted sense’ – the concept that covers all novels except the so-called nonfiction novels, graphic novels, and novels in verse. Then, drawing upon Jerrold Levinson’s approach to defining ‘art’, I provide a definition of the concept that covers nonfiction novels, graphic novels, and novels in verse. Finally, with the help of this definition and the definition of ‘novel in the restricted sense’, I formulate a definition of ‘novel’ simpliciter and defend it against potential objections.

Topic: Ethics, Aesthetics, and Art
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Improved Saturation Determination in Thin-Bed Environments Using 2D Parametric Inversion

The analysis of deep-reading electromagnetic measurements is critical to the evaluation of hydrocarbon reserves. However, in thin bed formations, poor tool vertical resolution and corresponding low sensitivity to hydrocarbon presence make interpretation in the virgin zone difficult. A priori knowledge such as the formation geometry or auxiliary petrophysical information is necessary to overcome these difficulties.This paper presents a prototype code developed by Schlumberger S-RPC in collaboration with AGIP. Using this code, wireline or LWD, laterolog and induction measurements can be more correctly analyzed in thinly bedded environments (2-D geometry, fluid invaded layers perpendicular to the borehole).This code has been implemented in a software framework that provides a common environment specifically designed for electrical tool interpretation. Processing modules have a common interface and share common functionalities. Their organization reflects an implicit processing methodology, with progressive refinements that provides the interpreter with a robust and simple to use product, to better quantify reserves.A preliminary step is to determine the formation geometry, which is carried out by detecting bed boundaries and representing the formation as a vertical sequence of layers. Petrophysical analysis can be invoked to characterize certain formation properties such as shale volume and porosity. These steps are performed prior to resistivity log measurement analysis and serve as a form of a priori knowledge.Once the formation is described as a sequence of layers, wireline logging or logging while drilling (LWD) tool response can be computed using fast 2D simulators. The estimation of resistivity and the subsequent estimation of saturation will correspond to the minimization of a cost function, defined as the weighted squared difference between the measurement and the simulated response. Confidence outputs can be related to the local shape of the cost function at the end of the processing.Two important advantages of the new code must be emphasized: (1) the possibility to choose among several petrophysical models to better describe the environment and determine directly parameters such as hydrocarbon saturation, and (2) the possibility to group together beds which are too thin or too close to each other to be analyzed independently, into a so called single optimization interval described by a reduced set of parameters.This paper presents results obtained on selected benchmarks extracted from real data and compares them with those obtained through more traditional approaches.

Topic: Geophysical and Geoelectrical Methods
Subfield: Geophysics
Field: Earth and Planetary Sciences
Domain: Physical Sciences
Transduction of Primitive Human Marrow and Cord Blood-Derived Hematopoietic Progenitor Cells With Adeno-Associated Virus Vectors

We evaluated the capacity of adeno-associated virus (AAV) vectors to transduce primitive human myeloid progenitor cells derived from marrow and cord blood in long-term cultures and long-term culture-initiating cell (LTC-IC) assays. Single-colony analyses showed that AAV vectors transduced CD34+ and CD34+38− clonogenic cells in long-term culture. Gene transfer was readily observed in LTC-ICs derived from 5-, 8-, and 10-week cultures. Recombinant AAV (rAAV) transduction was observed in every donor analyzed, although a wide range of gene transfer frequencies (5% to 100%) was noted. AAV transduction of LTC-ICs was stable, with week-8 and -10 LTC-ICs showing comparable or better transduction relative to week-5 LTC-ICs. Fluorescence in situ hybridization (FISH) analyses performed to determine the fate of AAV vectors in transduced cells showed that 9% to 28% of CD34+ and CD34+38− cells showed stable vector integration as evidenced by chromosome-associated signals in metaphase spreads. Comparisons of interphase and metaphase FISH suggested that a fraction of cells also contained episomal vector at early time points after transduction. Despite the apparent loss of the episomal forms with continued culture, the number of metaphases containing integrated vector genomes remained stable long term. Transgene transcription and placental alkaline phosphatase (PLAP) expression was observed in CD34+, CD34+38−LTC-ICs in the absence of selective pressure. These results suggest that primitive myeloid progenitors are amenable to genetic modification with AAV vectors.

Topic: Virus-based gene therapy research
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Chylomicron and palmitate metabolism by perfused hearts from diabetic mice

Hydrolysis of triacylglycerols (TG) in circulating chylomicrons by endothelium-bound lipoprotein lipase (LPL) provides a source of fatty acids (FA) for cardiac metabolism. The effect of diabetes on the metabolism of chylomicrons by perfused mouse hearts was investigated with db/db (type 2) and streptozotocin (STZ)-treated (type 1) diabetic mice. Endothelium-bound heparin-releasable LPL activity was unchanged in both type 1 and type 2 diabetic hearts. The metabolism of LPL-derived FA was examined by perfusing hearts with chylomicrons containing radiolabeled TG and by measuring 3 H 2 O accumulation in the perfusate (oxidation) and incorporation of radioactivity into tissue TG (esterification). Rates of LPL-derived FA oxidation and esterification were increased 2.3-fold and 1.7-fold in db/db hearts. Similarly, LPL-derived FA oxidation and esterification were increased 3.4-fold and 2.5-fold, respectively, in perfused hearts from STZ-treated mice. The oxidation and esterification of [ 3 H]palmitate complexed to albumin were also increased in type 1 and type 2 diabetic hearts. Therefore, diabetes may not influence the supply of LPL-derived FA, but total FA utilization (oxidation and esterification) was enhanced.

Topic: Cardiovascular Function and Risk Factors
Subfield: Cardiology and Cardiovascular Medicine
Field: Medicine
Domain: Health Sciences
The effect of coronary arteriography on left veuticle function lowering case of anterior descending branch lesion. Using Continuous Cardio Output Monitoring (CCOM).

当院において平成6年8月から平成7年9月に冠動脈造影を必要とした500例中,前下行枝一枝病変の労作性狭心症30例を対象にcenterline法を用いLVEF(左室駆出率)を算出し,それらを2群(A群;左室機能低下例0.35<EF≦0.59,B群;重症左室機能低下例EF≦0.35)にわけ,肺動脈にCCOM Catheterを挿入・留置し,心拍出量,心拍数,肺動脈圧および体血圧の経時的測定値をもとに冠動脈造影が心機能に及ぼす影響を経時的に比較検討した。A群,B群とも心拍数,肺動脈圧および体血圧には有意な変化は認めなかった。しかし,B群でのみ各冠動脈造影後11%の低下を認め12±2.8秒後に造影前値に回復した。以上の結果により冠動脈造影時間は左室機能にほとんど関係無く行われているが,重症左室機能低下例では明らかな心拍出量の低下を認め,real timeの心機能評価が可能であるCCOM systemの有用性が示された。

Topic: Hemodynamic Monitoring and Therapy
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Market structure and segments for seafood: A stated preference approach

Demand structure and market segmentation for seafood have been investigated intensively. However, most the researches so far applied traditional demand analysis and descriptive segmentation approach by separated models. The traditional demand analysis assuming consumer homogeneity, behavior consistence, and using aggregate data may result biased estimation, while the segmentation based on descriptive approach has results less accessible and actionable. We the first used discrete choice model and stated preference data to simultaneously estimate the demand structure and segments for twelve seafood species in French context. The four-latent segments model have the best fit to the data and demand elasticities estimated are comparable to those in the traditional studies but provide more efficient and actionable guidance for practitioners. Consistence with previous seafood demand study we found that elasticities of high valued fish such as salmon, tuna, cod, sole, and shrimp are price elastic while low valued species like mussels, oyster, and pangasius are inelastic. Moreover, latent class model revealed that 39.5% of the sample are not price sensitive, 29.6% moderate sensitive, 20.3% sensitive, and 10.6% are very sensitive. Similarly, we investigated deeper for particular species and uncovered demand structure of each species. For instance, only 30.9% of consumers are price elastic for salmon, while 39.5% and 29.6% of the sample are inelastic and moderate elastic for this species, respectively. We also regressed the segment membership probabilities on the consumer characteristics to give better segment description and provide efficient guidance for seafood producers and marketers.

Topic: Organic Food and Agriculture
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
IT Governance in Hospitals and Health Systems

Without a governance structure, IT at many hospitals and healthcare systems is a haphazard endeavor that typically results in late, over-budget projects and, ultimately, disparate systems. IT Governance in Hospitals and Health Systems offers a practical "how to" in creating an information technology governance process that ensures the IT projects supporting a hospital or health systems' strategy are completed on-time and on-budget. The authors define and describe IT governance as it is currently practiced in leading healthcare organizations, providing step-by-step guidance of the process to readers can replicate these best practices at their own hospital or health system. The book provides an overview of what IT governance is and why it is important to healthcare organizations. In addition, the book examines keys to IT governance success, as well as common mistakes to avoid; governance processes, workflows and project management; and the important roles that staff, a board of directors and committees play. Special features in the book include case studies from hospitals and health systems that have successfully developed an effective IT governance structure for their organization.

Topic: Big Data and Business Intelligence
Subfield: Management Information Systems
Field: Business, Management and Accounting
Domain: Social Sciences
An Optimal Simulation of Counter Machines: The ACM Case

[SIAM J. on Computing, 14 (1985), 34-40]. This is a companion paper to &amp;quot;P.M.B. Vitanyi, An optimal simulation of counter machines, SIAM Journal on Computing, 14 (1985), 1-33, and the later &amp;quot;J. Seiferas and P.M.B. Vitanyi, Counting is easy, J. Assoc. Comp. Mach. 35 (1988), pp. 985-1000&amp;quot;]. An Augmented Counter Machine (ACM) is a multicounter machine, with initially nonzero counters allowed, and the additional one-step instruction &amp;quot;set counter i to the value of counter j&amp;quot;, for any pair of counters i and j . Each ACM can be real-time simulated by an oblivious one-head tape unit using the information- theoretical storage optimum.

Topic: Error Correcting Code Techniques
Subfield: Computer Networks and Communications
Field: Computer Science
Domain: Physical Sciences
How to Construct a Safety Management System (SMS) That Promotes Safety Culture in Your Organization

Organizations spend considerable resources building robust Safety Management Systems, yet may struggle to develop a strong Safety Culture. The effect can ripple throughout the organization, particularly affecting employee safety, as well as product quality, productivity, engagement, and retention. This paper introduces the four basic components and most critical cultural preconditions of a successful SMS. It then provides recommendations aligned with each of the four basic components to guide management toward creating the kind of work environment that empowers and engages employees at all levels of the organization. Building a strong Safety Culture is simply good business, and the research conducted here culminates in a checklist for safety managers and executives who are committed to creating an environment that promotes a resilient Safety Culture within their organization.

Topic: Occupational Health and Safety Research
Subfield: Radiological and Ultrasound Technology
Field: Health Professions
Domain: Health Sciences