bluuebunny/crossref_metadata_2025 huggingface dataset:
Home Is Where the Internet Is? High-speed Internet’s Impact on Rural Housing Values
Authors: Conley Kelsey L. , Whitacre Brian E.
Published: April 2020

The deployment of faster household Internet speeds enables new opportunities for entertainment, social interaction, and personal development, and many consider such access an essential component of everyday life. However, rural residents face lower availability, slower speeds and limited provider options, putting them at a disadvantage when compared to their urban counterparts. Connected rural households, especially those with higher speeds, may experience a premium on their home value. Data from the National Broadband Map, the Federal Communications Commission, and over 2,700 housing transactions from June 2011 to June 2017 are used to examine the impact of broadband availability on housing values in two rural Oklahoma counties via a hedonic price model. The results find no support for the existence of a broadband premium, and stress that differences across counties are crucial in assessing rural housing prices.
Survey of entity encounter experiences occasioned by inhaled N,N-dimethyltryptamine: Phenomenology, interpretation, and enduring effects
Authors: Davis Alan K , Clifton John M , Weaver Eric G , Hurwitz Ethan S , Johnson Matthew W , Griffiths Roland R
Published: April 2020

Background:

Experiences of having an encounter with seemingly autonomous entities are sometimes reported after inhaling N,N-dimethyltryptamine.

Aim:

The study characterized the subjective phenomena, interpretation, and persisting changes that people attribute to N,N-dimethyltryptamine-occasioned entity encounter experiences.

Methods:

Two thousand, five hundred and sixty-one individuals (mean age 32 years; 77% male) completed an online survey about their single most memorable entity encounter after taking N,N-dimethyltryptamine.

Results:

Respondents reported the primary senses involved in the encounter were visual and extrasensory (e.g. telepathic). The most common descriptive labels for the entity were being, guide, spirit, alien, and helper. Although 41% of respondents reported fear during the encounter, the most prominent emotions both in the respondent and attributed to the entity were love, kindness, and joy. Most respondents endorsed that the entity had the attributes of being conscious, intelligent, and benevolent, existed in some real but different dimension of reality, and continued to exist after the encounter. Respondents endorsed receiving a message (69%) or a prediction about the future (19%) from the experience. More than half of those who identified as atheist before the experience no longer identified as atheist afterwards. The experiences were rated as among the most meaningful, spiritual, and psychologically insightful lifetime experiences, with persisting positive changes in life satisfaction, purpose, and meaning attributed to the experiences.

Conclusion:

N,N-dimethyltryptamine-occasioned entity encounter experiences have many similarities to non-drug entity encounter experiences such as those described in religious, alien abduction, and near-death contexts. Aspects of the experience and its interpretation produced profound and enduring ontological changes in worldview.
Evaluation of Three Commercially Available Materials in Reducing the White Spot Lesions During Fixed Orthodontic Treatment: A Prospective Randomized Controlled Trial
Authors: Bangi Sayeeda Laeque , Mohd. Mujeeb Uddin Mehraj , Konda Prasad , Talapaneni Ashok Kumar , Fatima Asma , Hussain Arshad
Published: April 2020

Objectives: Treating white spot lesions (WSL) to create a sound and esthetically pleasing enamel surface is a question yet to be fully answered. The objective of this randomized controlled trial was to measure and compare the degree of regression of WSL during orthodontic treatment achieved by using three commercially available materials.

Methods: A single-blinded randomized prospective clinical trial, comprising 80 patients categorized into four groups (one control group and three experimental groups, with 20 subjects per group) using block randomization, was conducted. Group A (control group): Colgate strong toothpaste; and experiments groups were Group B: GC tooth mousse, Group C: Phos-Flur mouthwash and Group D: SHY-NM. Subjects were instructed to use the designated dentifrice/mouthwash and photographs were taken at baseline, third and sixth months, and white spot lesions were reassessed in the maxillomandibular anterior teeth.

Results: All the three groups had shown an improvement in WSL. But Group B has shown the greatest difference in mean values of decalcification index (DI) scores.

Conclusion: All three commercially available products showed a regression of WSL over a 6-month duration. GC tooth mousse proved to be the most effective means of treating WSL over other regimens.
Factors Affecting Satisfaction with the Process of Orthodontic Treatment in Young Adults: A Questionnaire Study
Authors: Zadake Sujit Navnath , Kangane Suresh K. , Ambekar Anand S. , Kondle Mahendra , Kalekar Radhika
Published: April 2020

Introduction: Recently, there has been an increase in adults undergoing orthodontic treatment in both the public and the private sector. Satisfaction during and after the orthodontic treatment process has not been widely discussed so far, however, and few research studies have emphasized patient satisfaction with treatment outcome and the factors affecting patient satisfaction.

Aim: To investigate factors affecting patient satisfaction with the process of orthodontic treatment in young adults.

Material and methods: Fifty-eight patients (33 girls and 25 boys with a mean age of 25.05 years, SD 2.83) were included in the survey. All patients were young adults who had completed their orthodontic treatment with fixed appliances and were taken from two centers (a teaching hospital and a private practice). Data was collected using online survey forms and was analyzed using content thematic analysis. Five main factors were identified related to patient satisfaction with the process of orthodontic treatment: communication, faculty (orthodontist), physical surroundings, consultation/appointments, and impact of appliance treatment.

Results: Effective communication was the most prominent factor among all five factors considered, especially detailed explanation given during treatment and making patients feel comfortable under their care. Median values were generally high for satisfaction with treatment results. There was a clear correlation ( p < 0.001) between patient satisfaction and treatment outcome. Age, sex and treatment time did not have any correlation with treatment satisfaction.

Conclusion: In general, young adults were observed to be satisfied with the treatment process, and good communication played a dominant role in this. Though there were many differences in working models between public and private sectors, many similarities were observed when comparing the factors between the two centers.
Effects of Carbonated Drinks on Mechanical Properties of Three Types of Thermoplastic Aligner Materials: An In vitro Study
Authors: I. Leyona Pushpa Femina , B.S. Chandrashekar , A.V Arun , Raju Aravind S. , P.C. Ramesh Kumar , Shetty Balamohan
Published: April 2020

Objectives: The aim was to assess the mechanical properties of the three types of thermoplastic aligner materials before and after in vitro aging with carbonated drinks.

Materials and methods: Twelve samples of thermoplastic aligner materials produced by three different manufacturers

(Leone S.P.A, Florence, Italy; Duran, SCHEU-dental GmbH, Iserlohn, Germany; Essix ACE, Dentsply Raintree Essix, United States) were selected. Samples were thermoformed and later aged in vitro at a constant temperature in artificial saliva along with carbonated drinks (10 min each day) for 2 weeks. The mechanical properties were characterized using universal testing machine such as instron (MultiTest 10-i) and the results were compared with the control groups (before exposure to carbonated drinks).

Results: All the above-mentioned thermoplastic materials tested showed an insignificant ( p > 0.05) decrease in stiffness, yield strength, and elastic modulus after aging. The stiffness of the thermoplastic materials increased with an increase in thickness. The flexure modulus was higher for the thinner materials, whereas it was lower for the thicker materials.

Conclusion: Experimental results indicate that the aligner material will remain stable during and following exposure to carbonated drinks, which suggests that the orthodontic force from thermoplastic appliances does not decrease with clinical usage of carbonated drinks.
Instagram’s Affordances and the Visual Construction of Solidarity after a Mass Shooting
Authors: Pearce Jessica S.
Published: April 2020

Solidarity is a common response after a mass shooting. Social media and social media affordances, such as hashtags, are valuable technological tools after such events. How does social media facilitate the response to mass shootings? In particular, how do platform affordances shape solidarity practices? To this end, I analyzed Instagram images tagged #LafayetteStrong 2 years after a mass shooting in Lafayette, Louisiana. I observed several solidarity-inspired themes including material objects, community events and landmarks, references to support and reflection, and photographs as advertisements. I argue that Instagram affords a mediated form of solidarity, visually documenting ritualized community practices, while also facilitating individualized and subjective interpretations of solidarity. Users exploited Instagram’s affordances for advertisement purposes, capitalizing on a community-centered hashtag. These findings contribute to the sociological literature on mass shootings, the visual construction of solidarity, and the influence of technology.
Assessment of Sotalol and Dofetilide Dosing at a Large Academic Medical Center
Authors: Ting Clara , Malloy Rhynn , Knowles Danielle
Published: April 2020

Background:

Patients initiated on sotalol and dofetilide require inpatient monitoring and dose adjustments due to risks of corrected QT (QTc) prolongation and Torsades de pointes (TdP). Patients may receive higher initial doses than recommended due to close monitoring by specialized practitioners. The objective of this study was to describe prescribing practices of sotalol and dofetilide and to compare safety outcomes between standard and nonstandard dosing strategies.

Methods:

This was a single-center retrospective analysis of adult inpatients who underwent sotalol or dofetilide initiation between June 1, 2015, and August 1, 2018. The end points of this study included the percentage of patients who received standard and nonstandard dosing, incidence of QTc prolongation (≥500 milliseconds or ≥15% from baseline), incidence of TdP, and dose reduction or medication discontinuation.

Results:

A total of 379 patients (195 sotalol and 184 dofetilide) were included in this analysis. There were 110 (56.4%) patients in the sotalol group and 111 (58.4%) patients in the dofetilide group that received nonstandard initial dosing. Nonstandard dosing was associated with a greater incidence of QTc prolongation compared to standard dosing (57.5% vs 43.0%, P = .005). Only one patient in the nonstandard dosing group experienced TdP. Patients initiated on nonstandard dosing required dose reduction or therapy discontinuation (37.6% vs 23.4%, P = .003) more frequently.

Conclusion:

Higher than recommended initial doses of sotalol or dofetilide were associated with higher incidence of QTc prolongation and more frequent therapy modification.
Duodenal Stenosis Due to Carcinoma of the Lower Bile Duct: A Case Report
Authors: Maki Takumi , Irisawa Atsushi , Notohara Kenji , Shibukawa Goro , Sato Ai , Yamabe Akane , Yoshida Yoshitsugu , Yamamoto Shogo , Soeta Nobutoshi , Saito Takuro
Published: April 2020

An 83-year-old man was referred to our hospital for a detailed evaluation for vomiting. Esophagogastroduodenoscopy and abdominal computed tomography showed duodenal stenosis with wall thickness. Biopsy including endoscopic ultrasound-guided fine-needle aspiration of the thickened wall showed inflammation without malignancy. During the clinical course, wall thickening of the distal bile duct appeared. Biopsy under endoscopic retrograde cholangiography showed papillary adenocarcinoma. Surgery revealed that the tumor had widely invaded the duodenal wall from the outside; therefore, only gastrojejunostomy was performed. It was hypothesized that the cholangiocarcinoma had progressed to the serosal side, disseminated in the peritoneum, infiltrated the duodenal serosa, and caused duodenal stenosis.
A lesson from ‘Cologne’ on intersectionality: strengthening feminist arguments against right-wing co-option
Authors: Schuster Julia
Published: April 2020

Analysing feminist responses to the (mainstream) media coverage of the sexual assaults of New Year’s Eve 2015 in Cologne, this article shows how a theoretical concept that is used to frame feminist arguments can influence the strength of those arguments. German-speaking media extensively reported on the large number of sexual assaults against women that happened during that night in Cologne. The dominant narrative in those media reports dwells on the circumstance that the arrested suspects all had a refugee or migrant background, which assisted right-wing politics in re-creating a racist stereotype about male refugees and migrants being a threat to western women. Feminist responses to that media discourse insisted that rape culture was a cross-cultural phenomenon and that media as well as political analyses of the assaults need to take into account an understanding of intersectionality. Based on a content analysis of twenty-five feminist texts about the events of ‘Cologne’, I argue that the application of the concept of intersectionality created contradictions and argumentative voids within the – otherwise strong – feminist arguments because it conflated sexist and racist dynamics, which were both present in the context of ‘Cologne’ but not always intersecting. I further argue that these contradictions unintentionally aided the right-wing co-option of feminist demands concerning ‘Cologne’ and I suggest that the theoretical concept of femonationalism is better equipped to analyse events like ‘Cologne’.
Technical and Anatomical Considerations for Reproducible Inactivation of Large Animal Carcasses by Steam Sterilization
Authors: Schinköthe Jan , Bartram-Sitzius Benjamin , Teifke Jens-Peter , Pfitzner Ute , Reiche Sven
Published: April 2020

Introduction:

The complete inactivation of infectious tissues of large animal carcasses is one of the most challenging tasks in high-containment facilities. Steam sterilization is a method frequently in use to achieve biological inactivation of liquid and solid waste.

Objective:

This study aims to highlight parameters most effective in creating reproducible cycles for steam sterilization of pig and calf carcasses.

Methods:

Two pigs or 1 calf were sterilized by running a liquid cycle (n = 3) at 121°C for at least 120 minutes in a pass-through autoclave. To assess the physical and biological parameters, temperature data loggers and biological indicators (BIs) with spores of Geobacillus stearothermophilus (ATCC 7953) were placed at defined positions within animal carcasses. After completion of each cycle, data loggers were analyzed and BIs were incubated for 7 days at 60°C.

Results:

Initial testing with an undissected pig carcass resulted in suboptimal temperatures at the tissue level with growth on 1 BI. After modifications of the used stainless-steel boxes and by placing the reference probe of the autoclave in the animal carcass, reproducible cycles could be created. A complete inactivation of BIs and a temperature profile of >121°C for at least 20 minutes could be achieved in almost all probed tissues.

Conclusion:

Only minor modifications in carcass preparation and the used sterilization equipment resulted in effective and reproducible cycles to inactivate large animal carcasses by using a steam autoclave.
Progress in the Treatment of Diabetes Mellitus Based on Intestinal Flora Homeostasis and the Advancement of Holistic Analysis Methods
Authors: Bi Ruohong , Gao Jie , Pan Lin , Lai Xianrong
Published: April 2020

Diabetes mellitus (DM) is a complex metabolic disorder characterized by abnormal glucose metabolism, which is accompanied by alterations in energy metabolism, intestinal bacterial metabolism, amino acid metabolism, lipid metabolism, nucleotide metabolism, and others. However, intestinal flora metabolism plays a fundamental role in host metabolism; they are complementary to each other and help maintain homeostasis, thus ensuring the normal operation of the host metabolic system. This suggests that a holistic analysis method would be of great use in the study of the overall metabolism in patients with DM. With this in mind, this review summarizes the mechanism of intestinal flora metabolism regarding the occurrence of DM and assesses the effects of drug treatments on the intestinal flora of patients with diabetes. Based on these results, we combined intestinal flora metabolism with host metabolism to evaluate the necessity and the advantages of holistic metabonomics analyses in the treatment of DM and its complications.
Regulation of PI3k-WNK Pathway by Ethyl Acetate Partition Fraction of Gardenia jasminoides var. radicans Makino in SHR, NRK52e Cells, and IMCD3 Cells
Authors: Fu Yang , Yuan Peipei , Ke Yingying , Cao Yangang , Zhang Qi , Hou Ying , Wei Yaxin , Gao Liyuan , Zheng Xiaoke , feng Weisheng
Published: April 2020

The antihypertensive mechanism was studied of the ethyl acetate fraction of the ethanol extract (EAPF) of Gardenia jasminoides var. radicans Makino (GJRM). GJRM is a fake product of Gardenia jasminoides Ellis ( G. jasminoides), but in China’s Henan province, the production of GJRM is much more than G. jasminoides’s, but its traditional usage is as a dye. Gardenia jasminoides can be used to reduce blood pressure and blood glucose levels. The chemical compositions of GJRM and G. jasminoides are similar, and we previously confirmed that GJRM can also reduce blood pressure. Here, we report that the EAPF of GJRM could activate the phosphoinositide 3-kinases (PI3K) pathway in the kidneys of spontaneously hypertensive rats, thus increasing the content of nitric oxide and bradykinin in sera and decreasing endothelin-1 content. EAPF can also decrease the levels of with-no-lysine kinase 1 (WNK1) expression, WNK4 and oxidative stress-responsive kinase 1 messenger ribonucleic acid (mRNA), and Na-K-2Cl cotransporter and sodium chloride cotransporters mRNA and phosphorylation. To investigate the antihypertensive effects of the EAPF of GJRM, 5 monoterpenoids isolated from EAPF were studied for their effects on NRK52e and IMCD3 cells. These compounds inhibited the PI3K-WNK signaling pathway to varying degrees under hypotonic conditions; 4-methoxyrehmapicrogenin had the best effect.
Application of human lymphoid cells for the evaluation of antivirals against human adenovirus type 19: Zalcitabine has superior activity compared to cidofovir
Authors: Nakagawara Kohsuke , Hayashi Hironori , Kawaji Kumi , Sasano Mina , Kodama Eiichi N
Published: April 2020

Human adenovirus type 19 (HAdV-19) is a major cause of the epidemic keratoconjunctivitis. Outbreaks of keratoconjunctivitis are problematic to human health, especially for infants, the elderly, and immunocompromised individuals. However, the development of anti-HAdV drugs has been hampered by inconvenient screening systems; therefore, development of a simple screening method is highly desirable. In this study, we identified that HAdV-19 can infect a human lymphoid cell line transformed with human T-cell leukemia virus (MT-2 cells). MT-2 cells supported HAdV-19 replication and showed apparent cytopathic effects within five days post-infection. Using a thiazolyl blue tetrazolium bromide (MTT)-based colorimetric assay on MT-2 cells, we were able to detect the anti-HAdV-19 activities of previously reported nucleoside/tide compounds, including (S)-1–(3-hydroxy-2-phosphonylmethoxypropyl)cytosine (cidofovir), 2′,3′-dideoxycytidine (zalcitabine) and 3′-deoxy-3′-fluorothymidine (trifluridine). Compared with previous methods, this system represents a more simple and rapid method to screen anti-HAdV-19 agents.
Prehospital cardiopulmonary resuscitation duration and neurological outcome after adult out-of-hospital cardiac arrest by location of arrest
Authors: Kishimori Takefumi , Matsuyama Tasuku , Kiyohara Kosuke , Kitamura Tetsuhisa , Shida Haruka , Kiguchi Takeyuki , Nishiyama Chika , Kobayashi Daisuke , Okabayashi Satoe , Shimamoto Tomonari , Sado Junya , Kawamura Takashi , Iwami Taku
Published: April 2020

Background

Little is known about the association between prehospital cardiopulmonary resuscitation duration for adults with out-of-hospital cardiac arrest and outcome by the location of arrests. This study aimed to investigate the association between prehospital cardiopulmonary resuscitation duration and one-month survival with favourable neurological outcome.

Methods

We analysed 276,391 adults aged 18 years and older with out-of-hospital cardiac arrest of medical origin before emergency medical service arrival. Prehospital cardiopulmonary resuscitation duration was defined as the time from emergency medical service-initiated cardiopulmonary resuscitation to prehospital return of spontaneous circulation or to hospital arrival. The primary outcome was one-month survival with favourable neurological outcome (cerebral performance category 1 or 2). The association between prehospital cardiopulmonary resuscitation duration and favourable neurological outcome was assessed using univariable and multivariable logistic regression analyses.

Results

The proportion of favourable neurological outcomes was 2.3% in total, 7.6% in public locations, 1.5% in residential locations and 0.7% in nursing homes (P < 0.001). In univariable and multivariable logistic regression analyses, longer prehospital cardiopulmonary resuscitation duration was associated with poor neurological outcome, regardless of arrest location (P for trend < 0.001). Patients with shockable rhythm in both public and residential locations had better neurological outcome than those in nursing homes at any time point, and residential and public locations had a similar neurological outcome tendency among patients with shockable rhythm.

Conclusions

Longer prehospital cardiopulmonary resuscitation duration was independently associated with a lower proportion of patients with favourable neurological outcomes. Moreover, the association between prehospital cardiopulmonary resuscitation duration and neurological outcome differed according to the location of arrest and the first documented rhythm.
Effect of dimethyl fumarate on lymphocyte subsets in patients with relapsing multiple sclerosis
Authors: Buckle Guy , Bandari Daniel , Greenstein Jeffrey , Gudesblatt Mark , Khatri Bhupendra , Kita Mariko , Repovic Pavle , Riser Emily , Weinstock-Guttman Bianca , Thrower Ben , Loring Sherrill , Riester Katherine , Everage Nick , Prada Claudia , Koulinska Irene , Mann Monica
Published: April 2020

Background

In patients treated with dimethyl fumarate, absolute lymphocyte count decline typically occurs during the first year and then plateaus; early drops have been associated with the development of severe prolonged lymphopenia.

Objective

We investigated the effect of dimethyl fumarate on absolute lymphocyte counts and CD4+/CD8+ T cells in patients with relapsing–remitting multiple sclerosis treated with dimethyl fumarate in routine practice.

Methods

Lymphocyte data were collected via medical chart abstraction. Primary endpoint: change from baseline in absolute lymphocyte count and CD4+/CD8+ counts at 6‐month intervals following dimethyl fumarate initiation.

Results

Charts of 483 patients were abstracted and 476 patients included in the analysis. Mean baseline absolute lymphocyte count (2.23 × 109/l) decreased by ∼39% (95% confidence interval: –41.1 to –37.2) by month 6 and 44% (95% confidence interval: –46.6 to –42.1) by month 12. CD4+ and CD8+ T-cell subsets strongly correlated with absolute lymphocyte count, with greater decreases from baseline to 6 months vs 6–12 months, and in CD8+ vs CD4+ T cells. Prior natalizumab was not a risk factor for lymphopenia.

Conclusion

Dimethyl fumarate-associated decline in absolute lymphocyte count in the first 12 months correlated with decline in CD4+ and CD8+ T cells and was independent of prior natalizumab. Absolute lymphocyte count monitoring continues to be an effective strategy to identify patients at risk of prolonged lymphopenia.
The efficacy of spinal anaesthesia with fentanyl supplementation for arthroscopic knee surgery: A meta-analysis of randomized controlled studies
Authors: Chen Jianfeng , Yan Chao , Luo Chaosong , Li Guizhen , Yang Zong
Published: April 2020

Introduction:

The efficacy of spinal anaesthesia with fentanyl supplementation for arthroscopic knee surgery remains controversial. We conducted a systematic review and meta-analysis to explore the influence of fentanyl supplementation for arthroscopic knee surgery.

Methods:

We searched PubMed, Embase, Web of Science, EBSCO and Cochrane Library databases through May 2019 for randomized controlled trials (RCTs) assessing the efficacy and safety of fentanyl supplementation for arthroscopic knee surgery. This meta-analysis is performed using the random-effects model.

Results:

Five RCTs are included in the meta-analysis. Overall, compared with the control group for knee arthroscopy, fentanyl supplementation is associated with decreased time for sensory block regression to S1 (mean difference (MD) = −47.38; 95% confidence interval (CI) = −56.74 to −38.02; p < 0.00001), first ambulation (MD = −41.65; 95% CI = −65.11 to −18.19; p = 0.0005), first urination (MD = −23.45; 95% CI = −32.16 to −14.74; p < 0.00001) and hospital discharge (MD = −29.39; 95% CI = −44.73 to −14.06; p = 0.0002) but has no substantial influence on onset time of anaesthesia (MD = 0.50; 95% CI = −1.71 to 2.70; p = 0.66), duration for motor blockade (MD = −42.56; 95% CI = −119.18 to 34.07; p = 0.28), pruritus (risk ratio (RR) = 2.17; 95% CI = 0.28 to 16.90; p = 0.46) or nausea (RR = 0.42; 95% CI = 0.10 to 1.81; p = 0.25).

Conclusions:

Fentanyl supplementation benefits postoperative recovery after knee arthroscopy.
Femoral Tunnel Placement Analysis in ACL Reconstruction Through Use of a Novel 3-Dimensional Reference With Biplanar Stereoradiographic Imaging
Authors: Montreuil Julien , Saleh Joseph , Cresson Thierry , De Guise Jacques A. , Lavoie Frédéric
Published: April 2020

Background:

The femoral-sided anatomic footprint of the anterior cruciate ligament (ACL) has been widely studied during the past decades. Nonanatomic placement is an important cause of ACL reconstruction (ACLR) failure.

Purpose:

To describe femoral tunnel placement in ACLR through use of a comprehensive 3-dimensional (3D) cylindrical coordinate system combining both the traditional clockface technique and the quadrant method. Our objective was to validate this technique and evaluate its reproducibility.

Study Design:

Descriptive laboratory study.

Methods:

The EOS Imaging System was used to make 3D models of the knee for 37 patients who had undergone ACLR. We designed an automated cylindrical reference software program individualized to the distal femoral morphology of each patient. Cylinder parameters were collected from 2 observers’ series of 3D models. Each independent observer also manually measured the corresponding parameters using a lateral view of the 3D contours and a 2-dimensional stereoradiographic image for the corresponding patient.

Results:

The average cylinder produced from the first observer’s EOS 3D models had a 30.0° orientation (95% CI, 28.4°-31.5°), 40.4 mm length (95% CI, 39.3-41.4 mm), and 19.3 mm diameter (95% CI, 18.6-20.0 mm). For the second observer, these measurements were 29.7° (95% CI, 28.1°-31.3°), 40.7 mm (95% CI, 39.7-41.8 mm), and 19.7 mm (95% CI, 18.8-20.6 mm), respectively. Our method showed moderate intertest intraclass correlation among all 3 measuring techniques for both length ( r = 0.68) and diameter ( r = 0.63) but poor correlation for orientation ( r = 0.44). In terms of interobserver reproducibility of the automated EOS 3D method, similar results were obtained: moderate to excellent correlations for length ( r = 0.95; P < .001) and diameter ( r = 0.66; P < .001) but poor correlation for orientation ( r = 0.29; P < .08). With this reference system, we were able to describe the placement of each individual femoral tunnel aperture, averaging a difference of less than 10 mm from the historical anatomic description by Bernard et al.

Conclusion:

This novel 3D cylindrical coordinate system using biplanar, stereoradiographic, low-irradiation imaging showed a precision comparable with standard manual measurements for ACLR femoral tunnel placement. Our results also suggest that automated cylinders issued from EOS 3D models show adequate accuracy and reproducibility.

Clinical Relevance:

This technique will open multiple possibilities in ACLR femoral tunnel placement in terms of preoperative planning, postoperative feedback, and even intraoperative guidance with augmented reality.
Nonoperative Treatment of Fracture of the Entire Posterior Process of the Talus With Subtalar Dislocation: Case Report
Authors: McCoy Jordan S. , Meyers Amy L. , Marquart Matthew
Published: April 2020

Level of Evidence:

Level V, expert opinion.
Ballistic limit velocity of tungsten alloy spherical fragment penetrating Ti/Al3Ti-laminated composite target plates
Authors: Liu Yingbin , Yin Chufan , Hu Xiaoyan , Yuan Meini
Published: April 2020

To determine the ballistic limit velocity of titanium–titanium tri-aluminide (Ti/Al3Ti)-laminated composites under the action of tungsten alloy spherical fragments, a type of 12.7 mm ballistic gun loading system was used to test the tungsten alloy spherical fragments vertically impacting the Ti/Al3Ti-laminated composite targets with different thickness. The relationship between the ballistic limit velocity and the target area density of the Ti/Al3Ti-laminated composite was obtained. As the area density increased, the ballistic limit velocity and the ballistic energy absorbed by the target plate also enhanced. Based on the dimensional analysis and similarity theory, a simulation law of tungsten alloy spherical fragments penetrating Ti/Al3Ti-laminated composite targets with different thickness was studied and an empirical formula for the ballistic limit velocity was obtained. The research results had an important application value for the optimal design of the light armor protection structure.
Intrinsic limitations in mainstream methods of identifying network motifs in biology
Authors: Fodor James , Brand Michael , Stones Rebecca J. , Buckle Ashley M.
Published: April 2020

Background

Network motifs are connectivity structures that occur with significantly higher frequency than chance, and are thought to play important roles in complex biological networks, for example in gene regulation, interactomes, and metabolomes. Network motifs may also become pivotal in the rational design and engineering of complex biological systems underpinning the field of synthetic biology. Distinguishing true motifs from arbitrary substructures, however, remains a challenge.

Results

Here we demonstrate both theoretically and empirically that implicit assumptions present in mainstream methods for motif identification do not necessarily hold, with the ramification that motif studies using these mainstream methods are less able to effectively differentiate between spurious results and events of true statistical significance than is often presented. We show that these difficulties cannot be overcome without revising the methods of statistical analysis used to identify motifs.

Conclusions

Present-day methods for the discovery of network motifs, and, indeed, even the methods for defining what they are, are critically reliant on a set of incorrect assumptions, casting a doubt on the scientific validity of motif-driven discoveries. The implications of these findings are therefore far-reaching across diverse areas of biology.
SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
Authors: Bergenstråhle Joseph , Bergenstråhle Ludvig , Lundeberg Joakim
Published: April 2020

Background

Technological developments in the emerging field of spatial transcriptomics have opened up an unexplored landscape where transcript information is put in a spatial context. Clustering commonly constitutes a central component in analyzing this type of data. However, deciding on the number of clusters to use and interpreting their relationships can be difficult.

Results

We introduce SpatialCPie, an R package designed to facilitate cluster evaluation for spatial transcriptomics data. SpatialCPie clusters the data at multiple resolutions. The results are visualized with pie charts that indicate the similarity between spatial regions and clusters and a cluster graph that shows the relationships between clusters at different resolutions. We demonstrate SpatialCPie on several publicly available datasets.

Conclusions

SpatialCPie provides intuitive visualizations of cluster relationships when dealing with Spatial Transcriptomics data.
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
Authors: Mih Nathan , Monk Jonathan M. , Fang Xin , Catoiu Edward , Heckmann David , Yang Laurence , Palsson Bernhard O.
Published: April 2020

Background

The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studiedEscherichia coliK-12 MG1655 strain. The combination of the two leads to the formation of a structural systems biology framework, which we have used to analyze differences between the reactive oxygen species (ROS) sensitivity of the proteomes of sequenced strains ofE. coli. As proteins are one of the main targets of oxidative damage, understanding how the genetic changes of different strains of a species relates to its oxidative environment can reveal hypotheses as to why these variations arise and suggest directions of future experimental work.

Results

Creating a reference structural proteome forE. coliallows us to comprehensively map genetic changes in 1764 different strains to their locations on 4118 3D protein structures. We use metabolic modeling to predict basal ROS production levels (ROStype) for 695 of these strains, finding that strains with both higher and lower basal levels tend to enrich their proteomes with antioxidative properties, and speculate as to why that is. We computationally assess a strain’s sensitivity to an oxidative environment, based on known chemical mechanisms of oxidative damage to protein groups, defined by their localization and functionality. Two general groups - metalloproteins and periplasmic proteins - show enrichment of their antioxidative properties between the 695 strains with a predicted ROStype as well as 116 strains with an assigned pathotype. Specifically, proteins that a) utilize a molybdenum ion as a cofactor and b) are involved in the biogenesis of fimbriae show intriguing protective properties to resist oxidative damage. Overall, these findings indicate that a strain’s sensitivity to oxidative damage can be elucidated from the structural proteome, though future experimental work is needed to validate our model assumptions and findings.

Conclusion

We thus demonstrate that structural systems biology enables a proteome-wide, computational assessment of changes to atomic-level physicochemical properties and of oxidative damage mechanisms for multiple strains in a species. This integrative approach opens new avenues to study adaptation to a particular environment based on physiological properties predicted from sequence alone.
The genetic basis of hybrid male sterility in sympatric Primulina species
Authors: Feng Chen , Yi Huiqin , Yang Lihua , Kang Ming
Published: April 2020

Background

Sympatric sister species provide an opportunity to investigate the genetic mechanisms and evolutionary forces that maintain species boundaries. The persistence of morphologically and genetically distinct populations in sympatry can only occur if some degree of reproductive isolation exists. A pair of sympatric sister species of Primulina (P. depressa and P. danxiaensis) was used to explore the genetic architecture of hybrid male sterility.

Results

We mapped one major- and seven minor-effect quantitative trait loci (QTLs) that underlie pollen fertility rate (PFR). These loci jointly explained 55.4% of the phenotypic variation in the F2 population. A Bateson–Dobzhansky–Muller (BDM) model involving three loci was observed in this system. We found genotypic correlations between hybrid male sterility and flower morphology, consistent with the weak but significant phenotypic correlations between PFR and floral traits.

Conclusions

Hybrid male sterility in Primulina is controlled by a polygenic genetic basis with a complex pattern. The genetic incompatibility involves a three-locus BDM model. Hybrid male sterility is genetically correlated with floral morphology and divergence hitchhiking may occur between them.
Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23
Authors: Taslima Khanam , Wehner Stefanie , Taggart John B. , de Verdal Hugues , Benzie John A. H. , Bekaert Michaël , McAndrew Brendan J. , Penman David J.
Published: April 2020

Background

Tilapias (Family Cichlidae) are the second most important group of aquaculture species in the world. They have been the subject of much research on sex determination due to problems caused by early maturation in culture and their complex sex-determining systems. Different sex-determining loci (linkage group 1, 20 and 23) have been detected in various tilapia stocks. The ‘genetically improved farmed tilapia’ (GIFT) stock, founded from multiple Nile tilapia (Oreochromis niloticus) populations, with some likely to have been introgressed withO. mossambicus, is a key resource for tilapia aquaculture. The sex-determining mechanism in the GIFT stock was unknown, but potentially complicated due to its multiple origins.

Results

A bulk segregant analysis (BSA) version of double-digest restriction-site associated DNA sequencing (BSA-ddRADseq) was developed and used to detect and position sex-linked single nucleotide polymorphism (SNP) markers in 19 families from the GIFT strain breeding nucleus and two Stirling families as controls (a single XY locus had been previously mapped to LG1 in the latter). About 1500 SNPs per family were detected across the genome. Phenotypic sex in Stirling families showed strong association with LG1, whereas only SNPs located in LG23 showed clear association with sex in the majority of the GIFT families. No other genomic regions linked to sex determination were apparent. This region was validated using a series of LG23-specific DNA markers (five SNPs with highest association to sex from this study, the LG23 sex-associated microsatelliteUNH898andARO172,and the recently isolatedamhymarker for individual fish (n = 284).

Conclusions

Perhaps surprisingly given its multiple origins, sex determination in the GIFT strain breeding nucleus was associated only with a locus in LG23. BSA-ddRADseq allowed cost-effective analysis of multiple families, strengthening this conclusion. This technique has potential to be applied to other complex traits. The sex-linked SNP markers identified will be useful for potential marker-assisted selection (MAS) to control sex-ratio in GIFT tilapia to suppress unwanted reproduction during growout.
P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB)
Authors: Ellis J. Christopher
Published: April 2020

Background

The rnpB gene encodes for an essential catalytic RNA (RNase P). Like other essential RNAs, RNase P’s sequence is highly variable. However, unlike other essential RNAs (i.e. tRNA, 16 S, 6 S,...) its structure is also variable with at least 5 distinct structure types observed in prokaryotes. This structural variability makes it labor intensive and challenging to create and maintain covariance models for the detection of RNase P RNA in genomic and metagenomic sequences. The lack of a facile and rapid annotation algorithm has led to the rnpB gene being the most grossly under annotated essential gene in completed prokaryotic genomes with only a 24% annotation rate. Here we describe the coupling of the largest RNase P RNA database with the local alignment scoring algorithm to create the most sensitive and rapid prokaryote rnpB gene identification and annotation algorithm to date.

Results

Of the 2772 completed microbial genomes downloaded from GenBank only 665 genomes had an annotated rnpB gene. We applied P Finder to these genomes and were able to identify 2733 or nearly 99% of the 2772 microbial genomes examined. From these results four new rnpB genes that encode the minimal T-type P RNase P RNAs were identified computationally for the first time. In addition, only the second C-type RNase P RNA was identified in Sphaerobacter thermophilus. Of special note, no RNase P RNAs were detected in several obligate endosymbionts of sap sucking insects suggesting a novel evolutionary adaptation.

Conclusions

The coupling of the largest RNase P RNA database and associated structure class identification with the P Finder algorithm is both sensitive and rapid, yielding high quality results to aid researchers annotating either genomic or metagenomic data. It is the only algorithm to date that can identify challenging RNAse P classes such as C-type and the minimal T-type RNase P RNAs. P Finder is written in C# and has a user-friendly GUI that can run on multiple 64-bit windows platforms (Windows Vista/7/8/10). P Finder is free available for download at https://github.com/JChristopherEllis/P-Finder as well as a small sample RNase P RNA file for testing.
Genomic characterization of Lactobacillus fermentum DSM 20052
Authors: Brandt Katelyn , Nethery Matthew A. , O’Flaherty Sarah , Barrangou Rodolphe
Published: April 2020

Background

Lactobacillus fermentum, a member of the lactic acid bacteria complex, has recently garnered increased attention due to documented antagonistic properties and interest in assessing the probiotic potential of select strains that may provide human health benefits. Here, we genomically characterize L. fermentum using the type strain DSM 20052 as a canonical representative of this species.

Results

We determined the polished whole genome sequence of this type strain and compared it to 37 available genome sequences within this species. Results reveal genetic diversity across nine clades, with variable content encompassing mobile genetic elements, CRISPR-Cas immune systems and genomic islands, as well as numerous genome rearrangements. Interestingly, we determined a high frequency of occurrence of diverse Type I, II, and III CRISPR-Cas systems in 72% of the genomes, with a high level of strain hypervariability.

Conclusions

These findings provide a basis for the genetic characterization of L. fermentum strains of scientific and commercial interest. Furthermore, our study enables genomic-informed selection of strains with specific traits for commercial product formulation, and establishes a framework for the functional characterization of features of interest.
Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches
Authors: Babenko Vladislav V. , Podgorny Oleg V. , Manuvera Valentin A. , Kasianov Artem S. , Manolov Alexander I. , Grafskaia Ekaterina N. , Shirokov Dmitriy A. , Kurdyumov Alexey S. , Vinogradov Dmitriy V. , Nikitina Anastasia S. , Kovalchuk Sergey I. , Anikanov Nickolay A. , Butenko Ivan O. , Pobeguts Olga V. , Matyushkina Daria S. , Rakitina Daria V. , Kostryukova Elena S. , Zgoda Victor G. , Baskova Isolda P. , Trukhan Vladimir M. , Gelfand Mikhail S. , Govorun Vadim M. , Schiöth Helgi B. , Lazarev Vassili N.
Published: April 2020

Background

Salivary cell secretion (SCS) plays a critical role in blood feeding by medicinal leeches, making them of use for certain medical purposes even today.

Results

We annotated the Hirudo medicinalis genome and performed RNA-seq on salivary cells isolated from three closely related leech species, H. medicinalis, Hirudo orientalis, and Hirudo verbana. Differential expression analysis verified by proteomics identified salivary cell-specific gene expression, many of which encode previously unknown salivary components. However, the genes encoding known anticoagulants have been found to be expressed not only in salivary cells. The function-related analysis of the unique salivary cell genes enabled an update of the concept of interactions between salivary proteins and components of haemostasis.

Conclusions

Here we report a genome draft of Hirudo medicinalis and describe identification of novel salivary proteins and new homologs of genes encoding known anticoagulants in transcriptomes of three medicinal leech species. Our data provide new insights in genetics of blood-feeding lifestyle in leeches.
Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing
Authors: Fan Yixuan , Liang Yaxu , Deng Kaiping , Zhang Zhen , Zhang Guomin , Zhang Yanli , Wang Feng
Published: April 2020

Background

DNA methylation is an epigenetic regulatory form that plays an important role in regulating the gene expression and the tissues development.. However, DNA methylation regulators involved in sheep muscle development remain unclear. To explore the functional importance of genome-scale DNA methylation during sheep muscle growth, this study systematically investigated the genome-wide DNA methylation profiles at key stages of Hu sheep developmental (fetus and adult) using deep whole-genome bisulfite sequencing (WGBS).

Results

Our study found that the expression levels of DNA methyltransferase (DNMT)-related genes were lower in fetal muscle than in the muscle of adults. The methylation levels in the CG context were higher than those in the CHG and CHH contexts, and methylation levels were highest in introns, followed by exons and downstream regions. Subsequently, we identified 48,491, 17, and 135 differentially methylated regions (DMRs) in the CG, CHG, and CHH sequence contexts and 11,522 differentially methylated genes (DMGs). The results of bisulfite sequencing PCR (BSP) correlated well with the WGBS-Seq data. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis revealed that some DMGs were involved in regulating skeletal muscle development and fatty acid metabolism. By combining the WGBS-Seq and previous RNA-Seq data, a total of 159 overlap genes were obtained between differentially expressed genes (DEGs) and DMGs (FPKM > 10 and fold change > 4). Finally, we found that 9 DMGs were likely to be involved in muscle growth and metabolism of Hu sheep.

Conclusions

We systemically studied the global DNA methylation patterns of fetal and adult muscle development in Hu sheep, which provided new insights into a better understanding of the epigenetic regulation of sheep muscle development.