bluuebunny/crossref_metadata_2025 huggingface dataset:
A Systematic Review of Select Social Science and Humanities Literature: The Presence and Positioning of Latina Professors
Authors: Gonzales Leslie D. , Saldivar Guadalupe
Published: December 2019

To understand the presence and positioning of Latina faculty in humanities and social science scholarship, the authors analyzed articles published between 2000 and 2016 and developed three findings. First, few papers centered Latina professors. Second, when Latina faculty were featured in scholarship, it was often in the context of research concerning other minoritized and underrepresented faculty, more generally. Third, Latina faculty were frequently elevated as intellectuals when Latina-identifying scholars conducted the work.
The Effects of Music-Contingent Gait Training on Cognition and Mood in Parkinson Disease: A Feasibility Study
Authors: Burt Jacqueline , Ravid Einat (Natalie) , Bradford Sandra , Fisher Nancy J. , Zeng Yiye , Chomiak Taylor , Brown Lesley , McKeown Martin J. , Hu Bin , Camicioli Richard
Published: December 2019

Background. In Parkinson disease (PD), gait impairments often coexist with nonmotor symptoms such as anxiety and depression. Biofeedback training may improve gait function in PD, but its effect on nonmotor symptoms remains unclear. This study explored the cognitive and global effects of Ambulosono, a cognitive gait training method utilizing step size to contingently control the real-time play of motivational music. Objective. This study examined the feasibility of music-contingent gait training and its effects on neuropsychological test performance and mood in persons with PD. Methods. A total of 30 participants with mild to moderate PD were semirandomized via sequential alternating assignment into an experimental training group or control music group. The training group received 12 weeks of music-contingent training, whereby music play was dependent on the user achieving a set stride length, adjusted online based on individual performance. The control group received hybrid training beginning with 6 weeks of noncontingent music walking, whereby music played continuously regardless of step size, followed by 6 weeks of music-contingent training. Global cognition, memory, executive function, attention, and working memory assessments were completed by blinded assessors at baseline, 6 weeks, and 12 weeks. Motor function, mood, and anxiety were assessed. Results. Average training adherence was 97%, with no falls occurring during training sessions. Improvements on cognitive measures were not clinically significant; however, significant decreases in depression and anxiety were observed in both groups over time ( P < .05). Conclusions. Music-contingent gait training is feasible and safe in individuals with PD. Further investigation into potential therapeutic applications of this technology is recommended.
Digital Texts and Moral Questions About Immigration: Papers, Please and the Capacity for a Video Game to Stimulate Sociopolitical Discussion
Authors: McKernan Brian
Published: December 2019

Scholars and critics have praised the video game, Papers, Please ( PP), for raising critical awareness of sociopolitical issues, including immigration. To begin to determine whether PP stimulated public discussions of pertinent social issues, I adopt insights and techniques from cultural sociology to study how posters in an online forum engage with PP. I use computational topic modeling to reveal the topics forum members discuss and qualitative content analysis to gain a deeper sense of how posters explore these issues. I find the forum does discuss social issues, including immigration. Sociopolitical topics, however, are far from the forum’s primary focus. Moreover, posts primarily rely on the same limited set of immigration frames that major U.S. media outlets use. These findings demonstrate how a game’s social meanings will be shaped not only by the game’s design but also by social factors internal to the public under analysis and broader social dynamics.
Understanding Diverse Perspectives on Genetic Research Through Focus Group Talk
Authors: Ridgeway Jennifer L. , Albertie Monica , Pantoja Elizabeth , Prescott Darin , Zhu Xuan , Breitkopf Carmen Radecki
Published: December 2019

While genetic research (GR) is fueling discoveries in fields like precision medicine, there is a growing concern that underrepresentation of racial and ethnic populations in GR will limit access to its benefits and subsequently worsen health disparities. This study aimed to understand GR perceptions among members from underrepresented communities by studying discourse and language use in focus group discussions. Nine focus groups were conducted with adults from three populations: African American, Hispanic/Latino, and Native American; 53 women and 15 men participated. Data were analyzed using methods of discourse and content analysis. Discourse analysis highlighted how conceptualization of science and family—rooted in historical experiences—can influence views on GR risks and benefits to self and others. The use of focus group discourse in particular provided an opportunity for group sense making around the science and ethics of GR. Content analysis highlighted differences between the language use of focus group moderators, who spoke about scientific discovery and research oversight, and that of participants, whose talk highlighted ancestral bloodline, personal risk, and ethical concerns. The findings can inform efforts to bolster GR participation, including recruitment and educational campaigns. However, they also challenge researchers to consider areas of discordance between their own and community members’ conceptualization of the risks and benefits of GR participation, including the notion of future and family benefit.
Formulation parameters effects on the performances of concrete equivalent mortars incorporating different ratios of recycled sand
Authors: Ghorbel Elhem , Wardeh George , Gomart Hector , Matar Pierre
Published: December 2019

The present research investigates the feasibility of manufacturing masonry mortars with recycled sand. The primary aim is to study the effect of fine recycled aggregates on fresh and hardened states with properties. Two series of mortars were designed by substituting natural sand with recycled sand, with variable sand replacement ratios ranging from 0% to 100%. One series, named variable workability series, has variable workability with constant water to cement ratio ( W/C), while the other series, called constant workability series, has a constant workability with variable W/C. The density, air content, and slump of mortars in fresh state were measured with a special attention devoted to the effect of pre-saturation of recycled sand on the slump. In the hardened state, the microstructure was studied by means of water accessible porosity test and mercury intrusion porosimetry test. Flexural and compressive strength as well as the dynamic modulus of elasticity were also examined and the correlations between these properties and the microstructure have been established. It was found that the properties of mortars with recycled sand are lower than those obtained for the natural sand mortar (−20% for variable workability series and −45% for constant workability series at the age of 28 days). For the series with variable workability, mechanical properties decrease to a step starting from 30% replacement ratio, while linearly decrease for the mortars with constant workability. The difference between the two series lies in the difference in total porosities and the pore size distribution.
Synthesis and biological properties of novel 3-(pyrazol-1-yl)-6-oxopyridazine derivatives
Authors: Shainova Roza S , Gomktsyan Tiruhi A , Karapetyan Armen V , Yengoyan Aleksandr P
Published: December 2019

The affordable and efficient methods for the syntheses of acyclic derivatives of 2-(3-(3,5-dimethyl-1H-pyrazol-1-yl)-6-oxopyridazin-1(6H)-yl)acetohydrazine as well as compounds with a combination of pyrazolyl-pyridazine fragment with various azoles in the molecules have been developed. The synthesized compounds showed a stimulating action on plant growth.
Treatment of chronic thromboembolic pulmonary hypertension in a multidisciplinary team
Authors: Siennicka Anna , Darocha Szymon , Banaszkiewicz Marta , Kędzierski Piotr , Dobosiewicz Anna , Błaszczak Piotr , Peregud-Pogorzelska Małgorzata , Kasprzak Jarosław Damian , Tomaszewski Michał , Mroczek Ewa , Zięba Bożena , Karasek Danuta , Ptaszyńska-Kopczyńska Katarzyna , Mizia-Stec Katarzyna , Mularek-Kubzdela Tatiana , Doboszyńska Anna , Lewicka Ewa , Ruchała Marcin , Lewandowski Maciej , Łukasik Sylwia , Chrzanowski Łukasz , Zieliński Dariusz , Torbicki Adam , Kurzyna Marcin
Published: December 2019

Background:

Chronic thromboembolic pulmonary hypertension (CTEPH) may be treated with pulmonary endarterectomy (PEA), balloon pulmonary angioplasty (BPA) and medical therapy (MT). Assessment in a multidisciplinary team of experts (CTEPH team) is currently recommended for treatment decision making. The aim of the present study was to report the effects of such an interdisciplinary concept.

Methods and results:

A total of 160 patients were consulted by the CTEPH team between December 2015 and September 2018. Patient baseline characteristics, CTEPH team decisions and implementation rates of diagnostic and therapeutic procedures were analysed. Change in World Health Organization (WHO) functional class and survival rates were evaluated by treatment strategy. A total of 51 (32%) patients were assessed as operable and 109 (68%) were deemed inoperable. Thirty-one (61% of operable patients) underwent PEA. Patients treated with PEA, BPA(+MT) and MT alone were 50.9 ± 14.7, 62.9 ± 15.1 and 68.9 ± 12.7 years old, respectively. At the follow-up, PEA patients had the highest WHO functional class improvement. Patients treated with BPA(+MT) had significantly better survival than PEA ( p = 0.04) and MT patients ( p = 0.04; 2-year survival of 92%, 79% and 79%, respectively).

Conclusions:

The CTEPH team ensures that necessary diagnostic procedures are performed. A relatively low proportion of patients was assessed by the CTEPH team as operable and underwent surgery, which in survivors resulted in the best functional improvement. Although patients undergoing BPA(+MT) were older than patients treated with PEA, their survival was better than patients subjected to PEA or MT alone. The reviews of this paper are available via the supplemental material section.
Using Models to Predict Cultural Evolution From Emotional Selection Mechanisms
Authors: Eriksson Kimmo , Strimling Pontus
Published: December 2019

Cultural variants may spread by being more appealing, more memorable, or less offensive than other cultural variants. Empirical studies suggest that such “emotional selection” is a force to be reckoned with in cultural evolution. We present a research paradigm that is suitable for the study of emotional selection. It guides empirical research by directing attention to the circumstances under which emotions influence the likelihood that an individual will influence another individual to acquire a cultural variant. We present a modeling framework to translate such knowledge into specific and testable predictions of population-level change. A set of already analyzed basic cases can serve as a toolbox.
Effect of stud shape on lower limb kinetics during football-related movements
Authors: Lv Xiang , He Yuqi , Sun Dong , Baker Julien S , Xuan Rongrong , Gu Yaodong
Published: December 2019

Different football shoe designs used under the same turf condition can impact athletic performance and influence the risk of injury. The purpose of this study was to investigate the effect of different shape studs of football shoes on lower limb kinetics during straight-ahead running and 45° left sidestep cutting movements. Twelve male football players were recruited from university football teams. They were asked to perform six trials using straight-ahead running and a 45° left sidestep cutting movement on artificial turf while wearing football shoes with the following three stud configurations: knife stud, triangle stud and round stud. The contact time of knife stud was longer than triangle stud and round stud. In the straight-ahead running task, the ground force in the direction of movement of knife stud and round stud was lower than triangle stud. The peak pressure on the lateral forefoot (5 metatarsal region) in knife stud was higher than triangle stud and round stud in the cutting movements. The peak pressure and force–time integral on the medial (1 metatarsal region) and central (2–4 metatarsal region) forefoot in triangle stud were smaller than round stud. The different stud shapes of firm ground soccer shoes have little effect on the traction force. Knife stud has a higher risk of fifth metatarsal bone injury. The triangle stud shows good explosive force and provides the ability to change direction quickly. The round stud generally produces the minimum peak vertical ground reaction force and has a good capability of changing direction among the three shoes.
Dynamic Amodal Completion Through the Magic Wand Illusion
Authors: Tyler Christopher W.
Published: December 2019

In the Magic Wand effect, an overlying figure of the same color as its background is revealed by the motion of a wand behind it. The occluding figure is inferred by integration of the occluding edge information over time. The overlying figure is perceived by modal completion, while the wand and the background underneath are perceived by amodal completion. This illusion is compared with its predecessor from nearly two centuries ago, the Plateau Anorthoscopic Illusion, in which an object is recognizable when moved behind a slit.
Teaching physicians the GPGP method promotes deprescribing in both inpatient and outpatient settings
Authors: Bilek Aaron Jason , Levy Yuval , Kab Haneen , Andreev Pavel , Garfinkel Doron
Published: December 2019

Background

In complex older patients, inappropriate medication use and polypharmacy (IMUP) are commonplace and increasing exponentially. Reducing IMUP is a challenge in multiple clinical contexts, including acute admission and family practice, due to several key barriers. In the global effort against this epidemic, educational programs geared toward changing physicians’ prescribing patterns represent an important means of promoting deprescribing.

Methods

This is a nonrandomized, controlled interventional study investigating polypharmacy outcomes and prescribing patterns in patients whose physicians were trained in the Good Palliative-Geriatric Practice (GPGP) method, an algorithm for the reduction of polypharmacy, with patients whose physicians were not. Training involved a one-time, full-day workshop led by a senior geriatrician. Two separate settings were examined. In the inpatient setting, one internal medicine ward was trained and compared with another ward which was not trained. In the family practice setting, 28 physicians were trained and compared with practices of 15 physicians not trained. Patients were above the age of 70, representative of the general geriatric population, and not terminally ill.

Results

In the inpatient arm, the intervention group ( n = 100) experienced a decrease in medications prescribed from admission to discharge of 18.5%, compared with a decrease of 1.9% in the control group ( n = 100, difference between groups p < 0.0001). In the outpatient arm, the intervention group ( n = 100) experienced a decrease in medication number of 6.1% compared with 0.07% in the control group ( n = 100, difference between groups p = 0.001) over a 6-month period. Preferential decreases in specific drug classes were observed in both groups, including benzodiazepines, psychotropics, and antihypertensives.

Conclusions

A one-time educational intervention based on GPGP can change prescribing patterns in both outpatient and inpatient settings leading to a moderate reduction in polypharmacy. Future work should focus on longitudinal interventions, and longer-term clinical outcomes such as morbidity, mortality, and quality of life.
Arthroscopic Circumferential Labral Repair for Patients With Multidirectional Instability: A Comparative Outcome Study
Authors: Wall Andrew , McGonigle Owen , Gill Thomas J.
Published: December 2019

Background:

Circumferential tears of the glenohumeral labrum are an uncommon injury, comprising 2.4% of all labral lesions. Currently, the clinical outcomes of arthroscopic circumferential labral repair for patients with instability and combined anterior, posterior, and superior labral tears are not well-known.

Hypothesis:

Patients treated with arthroscopic circumferential shoulder labral repairs will have inferior clinical outcomes and higher failure rates compared with patients who have isolated arthroscopic anterior labral repairs.

Study Design:

Cohort study; Level of evidence, 3.

Methods:

A retrospective cohort study was performed to identify patients aged 18 years and older who underwent circumferential arthroscopic stabilization for recurrent instability as compared with an age-matched control group of arthroscopic primary anterior labral repairs. Age at surgery, American Shoulder and Elbow Surgeons (ASES) Standardized Shoulder Assessment Form score, Simple Shoulder Test (SST) score, 12-Item Short Form Health Survey (SF-12) score (mental and physical), and overall patient satisfaction with surgery were assessed for each group.

Results:

A total of 35 consecutive patients (36 shoulders) who underwent an arthroscopic 360° circumferential labral repair were compared with a matched group of 31 patients who underwent an isolated arthroscopic anterior labral repair. The mean follow-up period was 34.3 and 56.8 months, respectively. No significant difference was found between the 2 groups for overall satisfaction with the surgery or recurrent instability. At the time of the follow-up survey, 22% of the patients experienced pain and 25% of the patients experienced instability in the circumferential repair group, whereas 15% of the patients experienced some level of pain and 30% of patients experienced a subjective sense of subtle instability in the isolated repair group. The ASES scores were 87.3 in the combined labral repair group and 93.3 in the isolated anterior group ( P = .35), SST scores were 10.7 and 11.3 ( P = .70), SF-12 mental scores were 54.6 and 56.8 ( P = .80), SF-12 physical scores were 53.2 and 54.2 ( P = .98), and age at time of the surgery was 26.7 and 24.6 years ( P = .33), respectively. There was no difference between the 2 groups in pre- and postoperative range of motion ( P > .05).

Conclusion:

There was no difference in shoulder stability and function in patients after 360° combined labral repairs versus anterior labral repair alone. With proper patient selection, patients can expect similar outcomes despite the more extensive surgical procedure and complex postoperative rehabilitation protocol for circumferential repairs.
A case of bortezomib-associated thrombotic microangiopathy in a multiple myeloma patient
Authors: Moreira Fonseca Nuno , Cardoso Filipa , Monteiro Manuel , Góis Mário , Sousa Helena , Fidalgo Teresa , Calado Joaquim , Nolasco Fernando
Published: December 2019

Bortezomib is a first-generation proteasome inhibitor used in the treatment of multiple myeloma. We present a case of a 70-year-old woman with multiple myeloma, who presented thrombotic microangiopathy with multi-organ involvement thrombotic microangiopathy (ocular, cardiac, and renal) after bortezomib initiation. A kidney biopsy confirmed the diagnosis of thrombotic microangiopathy. A temporal relation between bortezomib exposure and thrombotic microangiopathy onset was seen in the absence of other concurrent medication or disease known to cause thrombotic microangiopathy, and thrombotic microangiopathy was only resolved after drug discontinuation. The exact pathophysiological mechanism remains unknown. To our knowledge, this is the second biopsy-proven published case of bortezomib-associated thrombotic microangiopathy. Since bortezomib is extensively used for treating patients with multiple myeloma, prescribing clinicians should maintain a high index of suspicion of this potentially fatal complication.
Mutational profile and benefit of gemtuzumab ozogamicin in acute myeloid leukemia
Authors: Fournier Elise , Duployez Nicolas , Ducourneau Benoît , Raffoux Emmanuel , Turlure Pascal , Caillot Denis , Thomas Xavier , Marceau-Renaut Alice , Chantepie Sylvain , Malfuson Jean-Valère , Lemasle Emilie , Cheok Meyling , Celli-Lebras Karine , Guerin Estelle , Terré Christine , Lambert Juliette , Pautas Cécile , Dombret Hervé , Castaigne Sylvie , Preudhomme Claude , Boissel Nicolas
Published: December 2019

Acute myeloid leukemia (AML) is a highly heterogeneous disease both in terms of genetic background and response to chemotherapy. Although molecular aberrations are routinely used to stratify AML patients into prognostic subgroups when receiving standard chemotherapy, the predictive value of the genetic background and co-occurring mutations remains to be assessed when using newly approved antileukemic drugs. In the present study, we retrospectively addressed the question of the predictive value of molecular events on the benefit of the addition of gemtuzumab ozogamicin (GO) to standard front-line chemotherapy. Using the more recent European LeukemiaNet (ELN) 2017 risk classification, we confirmed that the benefit of GO was restricted to the favorable (hazard ratio [HR], 0.54, 95% confidence interval [CI], 0.30-0.98) and intermediate (HR, 0.57; 95% CI, 0.33-1.00) risk categories, whereas it did not influence the outcome of patients within the adverse risk subgroup (HR, 0.93; 95% CI, 0.61-1.43). Interestingly, the benefit of GO was significant for patients with activating signaling mutations (HR, 0.43; 95% CI, 0.28-0.65), which correlated with higher CD33 expression levels. These results suggest that molecular aberrations could be critical for future differentially tailored treatments based on integrated genetic profiles that are able to predict the benefit of GO on outcome.
Certainties and uncertainties in accessing toxicity of non-extractable residues (NER) in soil
Authors: Harmsen Joop , Hennecke Dieter , Hund-Rinke Kerstin , Lahr Joost , Deneer John
Published: December 2019

Background

Discussion concerning the bioavailability and ecotoxicological relevance of non-extractable residues (NER) in soil is still ongoing. Is NER formation a detoxification process or a hidden hazard? The use of radiolabelled chemicals enables detection of NER, but the identity of NER is usually unknown. Regulations require clear measurable parameters and the approach of Ortega-Calvo et al. (Environ Sci Technol 49:10255–10264, 2015) defines these.

Results

Following that approach, we studied the fate of three ecotoxic, NER-forming chemicals over a period of 6 months after application to three different soils. Initial 14C experiments showed formation of NER for all chemicals. For the chemical 2,4,6-trinitrotoluene (TNT), NER-formation was reproducible in all soils. We applied a recently standardized method using Tenax® to remove the bioavailable fraction of the chemical at test start and test end. Removing the bioavailable fractions also removed toxicity. Further experiments without radiolabelled TNT clearly showed that the toxicity measured in applied soils was caused by the bioavailable chemical and not by NER.

Conclusions

The tool developed can be used if the fate of the chemical including NER formation is well known and reproducible. The other selected chemicals, cypermethrin and carbendazim, showed unexpected behaviour in 14C-fate experiments. The degree of biodegradation was not reproducible for cypermethrin and unexpected losses occurred with carbendazim. This indicated a very large uncertainty when using non-radiolabelled compounds in NER experiments and thus the tool is not suitable in non-radiolabelled experiments.
Diffuse unilateral subacute neuroretinitis: review article
Authors: Mazzeo Thiago José Muniz Machado , dos Santos Motta Mario Martins , Curi André Luiz Land
Published: December 2019

Diffuse unilateral subacute neuroretinitis (DUSN) is an ocular infectious disease that can lead to severe visual impairment and blindness. It usually occurs in healthy young individuals and depending on the stage of the disease, it may present as vitritis, multifocal gray-white lesions in the outer retina, and derangement of the retinal pigment epithelium, narrowing of the retinal vessels and optic atrophy. Parasites of different sizes and species have been proposed as the etiologic agent of DUSN, including Ancylostoma caninum, Toxocara canis, and others. Thus, it is hypothesized that different infectious worms may be considered as the likely cause of both an autoimmune and toxic form of nematode retinopathy. Because serologic testing is variable, the definitive diagnosis is made when clinical characteristics of DUSN are found in conjunction with an intraocular worm. Ancillary tests can assist in the differential diagnosis when the nematode cannot be visualized, such as fluorescein and indocyanine green angiography, electrophysiological tests, visual field studies, and more recently, optical coherence tomography angiography. Cases in which the worm can be identified, it is defined as confirmed DUSN, and eyes with the typical clinical features but without identification of the worm should be classified as presumed DUSN. In confirmed DUSN, the classic treatment is directly photocoagulation of the worm; however, it can only be visualized in 30% (to 40%) of cases. Treatment of presumed DUSN cases with high-dose oral albendazole has shown encouraging results. However, perhaps due to the disease’s rarity or its underdiagnosis, there are no studies comparing current treatment modalities in both presumed and confirmed DUSN. Due to the possibility of this disease being, in part, autoimmune nematode retinopathy, corticosteroids associated with both albendazole or laser therapy, could be in any way beneficial. Thus, further comparative studies are necessary to elucidate the best treatment for this potentially blinding disease.
Population structure and genetic history of Tibetan Terriers
Authors: Janeš Mateja , Zorc Minja , Cubric-Curik Vlatka , Curik Ino , Dovc Peter
Published: December 2019

Background

Tibetan Terrier is a popular medium-sized companion dog breed. According to the history of the breed, the western population of Tibetan Terriers includes two lineages, Lamleh and Luneville. These two lineages derive from a small number of founder animals from the native Tibetan Terrier population, which were brought to Europe in the 1920s. For almost a century, the western population of Tibetan Terriers and the native population in Tibet were reproductively isolated. In this study, we analysed the structure of the western population of Tibetan Terriers, the original native population from Tibet and of different crosses between these two populations. We also examined the genetic relationships of Tibetan Terriers with other dog breeds, especially terriers and some Asian breeds, and the within-breed structure of both Tibetan Terrier populations.

Results

Our analyses were based on high-density single nucleotide polymorphism (SNP) array (Illumina HD Canine 170 K) and microsatellite (18 loci) genotypes of 64 Tibetan Terriers belonging to different populations and lineages. For the comparative analysis, we used 348 publicly available SNP array genotypes of dogs from other breeds. We found that the western population of Tibetan Terriers and the native Tibetan Terriers clustered together with other Asian dog breeds, whereas all other terrier breeds were grouped into a separate group. We were also able to differentiate the western Tibetan Terrier lineages (Lamleh and Luneville) from the native Tibetan Terrier population.

Conclusions

Our results reveal the relationships between the western and native populations of Tibetan Terriers and support the hypothesis that Tibetan Terrier belongs to the group of ancient dog breeds of Asian origin, which are close to the ancestors of the modern dog that were involved in the early domestication process. Thus, we were able to reject the initial hypothesis that Tibetan Terriers belong to the group of terrier breeds. The existence of this native population of Tibetan Terriers at its original location represents an exceptional and valuable genetic resource.
IILLS: predicting virus-receptor interactions based on similarity and semi-supervised learning
Authors: Yan Cheng , Duan Guihua , Wu Fang-Xiang , Wang Jianxin
Published: December 2019

Background

Viral infectious diseases are the serious threat for human health. The receptor-binding is the first step for the viral infection of hosts. To more effectively treat human viral infectious diseases, the hidden virus-receptor interactions must be discovered. However, current computational methods for predicting virus-receptor interactions are limited.

Result

In this study, we propose a new computational method (IILLS) to predict virus-receptor interactions based on Initial Interaction scores method via the neighbors and the Laplacian regularized Least Square algorithm. IILLS integrates the known virus-receptor interactions and amino acid sequences of receptors. The similarity of viruses is calculated by the Gaussian Interaction Profile (GIP) kernel. On the other hand, we also compute the receptor GIP similarity and the receptor sequence similarity. Then the sequence similarity is used as the final similarity of receptors according to the prediction results. The 10-fold cross validation (10CV) and leave one out cross validation (LOOCV) are used to assess the prediction performance of our method. We also compare our method with other three competing methods (BRWH, LapRLS, CMF).

Conlusion

The experiment results show that IILLS achieves the AUC values of 0.8675 and 0.9061 with the 10-fold cross validation and leave-one-out cross validation (LOOCV), respectively, which illustrates that IILLS is superior to the competing methods. In addition, the case studies also further indicate that the IILLS method is effective for the virus-receptor interaction prediction.
Model-based cell clustering and population tracking for time-series flow cytometry data
Authors: Minoura Kodai , Abe Ko , Maeda Yuka , Nishikawa Hiroyoshi , Shimamura Teppei
Published: December 2019

Background

Modern flow cytometry technology has enabled the simultaneous analysis of multiple cell markers at the single-cell level, and it is widely used in a broad field of research. The detection of cell populations in flow cytometry data has long been dependent on “manual gating” by visual inspection. Recently, numerous software have been developed for automatic, computationally guided detection of cell populations; however, they are not designed for time-series flow cytometry data. Time-series flow cytometry data are indispensable for investigating the dynamics of cell populations that could not be elucidated by static time-point analysis. Therefore, there is a great need for tools to systematically analyze time-series flow cytometry data.

Results

We propose a simple and efficient statistical framework, named CYBERTRACK (CYtometry-Based Estimation and Reasoning for TRACKing cell populations), to perform clustering and cell population tracking for time-series flow cytometry data. CYBERTRACK assumes that flow cytometry data are generated from a multivariate Gaussian mixture distribution with its mixture proportion at the current time dependent on that at a previous timepoint. Using simulation data, we evaluate the performance of CYBERTRACK when estimating parameters for a multivariate Gaussian mixture distribution, tracking time-dependent transitions of mixture proportions, and detecting change-points in the overall mixture proportion. The CYBERTRACK performance is validated using two real flow cytometry datasets, which demonstrate that the population dynamics detected by CYBERTRACK are consistent with our prior knowledge of lymphocyte behavior.

Conclusions

Our results indicate that CYBERTRACK offers better understandings of time-dependent cell population dynamics to cytometry users by systematically analyzing time-series flow cytometry data.
SpliceFinder: ab initio prediction of splice sites using convolutional neural network
Authors: Wang Ruohan , Wang Zishuai , Wang Jianping , Li Shuaicheng
Published: December 2019

Background

Identifying splice sites is a necessary step to analyze the location and structure of genes. Two dinucleotides, GT and AG, are highly frequent on splice sites, and many other patterns are also on splice sites with important biological functions. Meanwhile, the dinucleotides occur frequently at the sequences without splice sites, which makes the prediction prone to generate false positives. Most existing tools select all the sequences with the two dimers and then focus on distinguishing the true splice sites from those pseudo ones. Such an approach will lead to a decrease in false positives; however, it will result in non-canonical splice sites missing.

Result

We have designed SpliceFinder based on convolutional neural network (CNN) to predict splice sites. To achieve the ab initio prediction, we used human genomic data to train our neural network. An iterative approach is adopted to reconstruct the dataset, which tackles the data unbalance problem and forces the model to learn more features of splice sites. The proposed CNN obtains the classification accuracy of 90.25%, which is 10% higher than the existing algorithms. The method outperforms other existing methods in terms of area under receiver operating characteristics (AUC), recall, precision, and F1 score. Furthermore, SpliceFinder can find the exact position of splice sites on long genomic sequences with a sliding window. Compared with other state-of-the-art splice site prediction tools, SpliceFinder generates results in about half lower false positive while keeping recall higher than 0.8. Also, SpliceFinder captures the non-canonical splice sites. In addition, SpliceFinder performs well on the genomic sequences of Drosophila melanogaster, Mus musculus, Rattus, and Danio rerio without retraining.

Conclusion

Based on CNN, we have proposed a new ab initio splice site prediction tool, SpliceFinder, which generates less false positives and can detect non-canonical splice sites. Additionally, SpliceFinder is transferable to other species without retraining. The source code and additional materials are available at https://gitlab.deepomics.org/wangruohan/SpliceFinder.
Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation
Authors: Hasan A. B. M. Shamim Ul , Kurata Hiroyuki , Pechmann Sebastian
Published: December 2019

Background

Cellular memory is a ubiquitous function of biological systems. By generating a sustained response to a transient inductive stimulus, often due to bistability, memory is central to the robust control of many important biological processes. However, our understanding of the origins of cellular memory remains incomplete. Stochastic fluctuations that are inherent to most biological systems have been shown to hamper memory function. Yet, how stochasticity changes the behavior of genetic circuits is generally not clear from a deterministic analysis of the network alone. Here, we apply deterministic rate equations, stochastic simulations, and theoretical analyses of Fokker-Planck equations to investigate how intrinsic noise affects the memory function in a mutual repression network.

Results

We find that the addition of negative autoregulation improves the persistence of memory in a small gene regulatory network by reducing stochastic fluctuations. Our theoretical analyses reveal that this improved memory function stems from an increased stability of the steady states of the system. Moreover, we show how the tuning of critical network parameters can further enhance memory.

Conclusions

Our work illuminates the power of stochastic and theoretical approaches to understanding biological circuits, and the importance of considering stochasticity when designing synthetic circuits with memory function.
A generative model for constructing nucleic acid sequences binding to a protein
Authors: Im Jinho , Park Byungkyu , Han Kyungsook
Published: December 2019

Background

Interactions between protein and nucleic acid molecules are essential to a variety of cellular processes. A large amount of interaction data generated by high-throughput technologies have triggered the development of several computational methods either to predict binding sites in a sequence or to determine whether a pair of sequences interacts or not. Most of these methods treat the problem of the interaction of nucleic acids with proteins as a classification problem rather than a generation problem.

Results

We developed a generative model for constructing single-stranded nucleic acids binding to a target protein using a long short-term memory (LSTM) neural network. Experimental results of the generative model are promising in the sense that DNA and RNA sequences generated by the model for several target proteins show high specificity and that motifs present in the generated sequences are similar to known protein-binding motifs.

Conclusions

Although these are preliminary results of our ongoing research, our approach can be used to generate nucleic acid sequences binding to a target protein. In particular, it will help design efficient in vitro experiments by constructing an initial pool of potential aptamers that bind to a target protein with high affinity and specificity.
A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
Authors: Troll Christopher J. , Kapp Joshua , Rao Varsha , Harkins Kelly M. , Cole Charles , Naughton Colin , Morgan Jessica M. , Shapiro Beth , Green Richard E.
Published: December 2019

Background

Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming.

Results

Here we present an efficient ligation-based single-stranded library preparation method that is engineered to produce complex libraries in under 2.5 h from as little as 1 nanogram of input DNA without alteration to the native ends of template molecules. Our method, called Single Reaction Single-stranded LibrarY or SRSLY, ligates uniquely designed Next-Generation Sequencing (NGS) adapters in a one-step combined phosphorylation/ligation reaction that foregoes end-polishing. Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation patterns to deduce nucleosome positioning and transcription factor binding.

Conclusions

SRSLY is a versatile tool for converting short and fragmented DNA molecules, like cfDNA fragments, into sequencing libraries while retaining native lengths and ends.
Putative biomarkers for predicting tumor sample purity based on gene expression data
Authors: Li Yuanyuan , Umbach David M. , Bingham Adrienna , Li Qi-Jing , Zhuang Yuan , Li Leping
Published: December 2019

Background

Tumor purity is the percent of cancer cells present in a sample of tumor tissue. The non-cancerous cells (immune cells, fibroblasts, etc.) have an important role in tumor biology. The ability to determine tumor purity is important to understand the roles of cancerous and non-cancerous cells in a tumor.

Methods

We applied a supervised machine learning method, XGBoost, to data from 33 TCGA tumor types to predict tumor purity using RNA-seq gene expression data.

Results

Across the 33 tumor types, the median correlation between observed and predicted tumor-purity ranged from 0.75 to 0.87 with small root mean square errors, suggesting that tumor purity can be accurately predicted υσινγ expression data. We further confirmed that expression levels of a ten-gene set (CSF2RB, RHOH, C1S, CCDC69, CCL22, CYTIP, POU2AF1, FGR, CCL21, and IL7R) were predictive of tumor purity regardless of tumor type. We tested whether our set of ten genes could accurately predict tumor purity of a TCGA-independent data set. We showed that expression levels from our set of ten genes were highly correlated (ρ = 0.88) with the actual observed tumor purity.

Conclusions

Our analyses suggested that the ten-gene set may serve as a biomarker for tumor purity prediction using gene expression data.
Phenotypic and molecular characterization of antimicrobial resistance in Trueperella pyogenes strains isolated from bovine mastitis and metritis
Authors: Rezanejad Mobin , Karimi Sepideh , Momtaz Hassan
Published: December 2019

Background

Trueperella pyogenes is one of the most clinically imperative bacteria responsible for severe cases of mastitis and metritis, particularly in postpartum dairy cows. The bacterium has emergence of antibiotic resistance and virulence characters. The existing research was done to apprise the phenotypic and genotypic evaluation of antibiotic resistance and characterization of virulence factors in the T. pyogenes bacteria of bovine mastitis and metritis in postpartum cows.

Methods

Two-hundred and twenty-six bovine mastitic milk and 172 uterine swabs were collected and transferred to laboratory. Samples were cultured and T. pyogenes isolates were subjected to disk diffusion and DNA extraction. Distribution of virulence and antibiotic resistance genes was studied by PCR.

Results

Thirty-two out of 226 (14.15%) mastitic milk and forty-one out of 172 (23.83%) uterine swab samples were positive for T. pyogenes. Isolates of mastitic milk harbored the highest prevalence of resistance toward gentamicin (100%), penicillin (100%), ampicillin (90.62%), amoxicillin (87.50%) and trimethoprim-sulfamethoxazole (87.50%), while those of metritis harbored the highest prevalence of resistance toward ampicillin (100%), amoxicillin (100%), gentamicin (97.56%), penicillin (97.56%) and cefalexin (97.56%). AacC, aadA1, aadA2 and tetW were the most generally perceived antibiotic resistance genes. All bacteria harbored plo (100%) and fimA (100%) virulence factors. NanP, nanH, fimC and fimE were also the most generally perceived virulence factors.

Conclusions

All bacteria harbored plo and fimA virulence factors which showed that they can use as specific genetic markers with their important roles in pathogenicity of T. pyogenes bacteria. Phenotypic pattern of antibiotic resistance was confirmed by genotypic characterization of antibiotic resistance genes.
Genome-wide analysis of polygalacturonase gene family from pear genome and identification of the member involved in pear softening
Authors: Zhang Suling , Ma Min , Zhang Huping , Zhang Shaoling , Qian Ming , Zhang Zhen , Luo Weiqi , Fan Jinbu , Liu Zhiqiang , Wang Libin
Published: December 2019

Background

Polygalacturonase (PG), as an important hydrolase participating in the degradation of pectin, plays an important role in softening process of fruit. However, information on PG gene family in pear genome and the specific member involved in fruit softening is still rudimentary.

Results

In this study, a total of 61 PG genes, which could be divided into six subclasses, were identified from the pear genome with diverse chromosome locations, gene structures, motifs and cis-acting elements. Most PbrPGs were derived from WGD/segmental duplication blocks, and purifying selection was the main driving force for their expansion. The expression profiles of PbrPGs in pear were tissue/development-stage/cultivar-dependent. During ‘Housui’ pear storage, associated with the reduction of firmness was the accumulation of PG activity. Totally, 28 PbrPGs were expressed during fruit storage, which could be classified into five categories based on different expression patterns; most demonstrated an increased trend. Of these, PbrPG6 were proposed to account for pear softening in combination of the phylogenetic and correlation analysis among firmness, PG activity and PbrPGs. By constructing the silencing vector, a higher firmness was observed in PbrPG6-silenced fruit when compared with that of the control (empty vector). In a further study, we found that the expression of PbrPG6 was regulated by postharvest 1-MCP/ethrel treatment, and several PbrERFs might function in this process.

Conclusions

We identified 61 PbrPG genes from pear genome; of these, PbrPG6 was involved in fruit softening process; furthermore, the expression of PbrPG6 might be under the control of PbrERF. This study provides a foundation for future work aimed at elucidating the molecular mechanism underlying pear softening.
Sex differences in 10-year ischemic cardiovascular disease risk prediction in Chinese patients with prediabetes and type 2 diabetes
Authors: Yang Lihong , Fish Anne F. , Zhu Yuanyuan , Yuan Xiaodan , Li Jianing , Wang Xiaoyun , Yuan Li , Jia Zhumin , Liu Chao , Xu Yunchen , Lou Qingqing
Published: December 2019

Background

Cardiovascular disease has become a serious public health problem in recent years in China. The aim of the study was to examine sex differences in cardiovascular risk factors and 10-year ischemic cardiovascular disease (ICVD) risk in Chinese patients with prediabetes (PreDM) and type 2 diabetes mellitus (T2DM).

Methods

This was a multi-site retrospective case-control study conducted from April–November 2016 using an electronic medical record database, involving 217 PreDM and 900 T2DM patients admitted to endocrinology units in four hospitals in China. CVD risk was estimated using the Chinese 10-year ICVD risk model. The differences in 10-year absolute ICVD risk according to PreDM, T2DM < 1 year, T2DM 1–5 years or T2DM ≥5 years and sex were analyzed using ANOVA.

Results

When compared to PreDM females, males with PreDM had significantly higher 10-year ICVD risk In contrast, the opposite pattern of 10-year ICVD risk was observed in T2DM; males had significantly lower 10-year ICVD risk. Moreover, compared to T2DM females, males with T2DM had a lower proportion s with moderate or greater ICVD risk (p < 0.001). When compared to PreDM males, males with T2DM < 1 year, and with T2DM 1–5 years had no difference in 10-year ICVD risk, but had higher ICVD risk with T2DM ≥5 years (p < 0.05). Compared to PreDM females, females with T2DM in all subgroups had higher ICVD risk (p < 0.05). Among those with T2DM, hypertension rates of awareness, treatment and control were 78.60%, 65.38% and 31.10%, respectively; hyperlipidemia rates of awareness, treatment and control were lower (29.15%, 8.30% and 3.47%, respectively). Females with T2DM had higher prevalence, awareness and treatment of hypertension and hyperlipidemia than males with T2DM (p < 0.001).

Conclusions

There is a greater need for cardiovascular risk reduction programs for females with T2DM at diagnosis. Given the low numbers for awareness, treatment and control of hypertension and hyperlipidemia in both males and females, significant resources focused on them must be expended, specifically improving regular assessment of blood pressure and blood lipids. Strengthening the management of chronic diseases through adherence to evidence-based guidelines to enhance clinical treatment may reduce 10-year ICVD in patients with T2DM in China.