bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Timing and Direction of Introgression Under the Multispecies Network Coalescent
Authors: Hibbins Mark S , Hahn Matthew W 
Published: January 2019

Abstract
Introgression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics, D1 and D2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively. D1 may find use in evaluating cases of homoploid hybrid speciation (HHS), while D2 provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply the D1 statistic to genomic data from the wild yeast Saccharomyces paradoxus—a proposed example of HHS—demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.
Modelling Sex-Specific Crossover Patterning inArabidopsis
Authors: Lloyd Andrew , Jenczewski Eric 
Published: January 2019

AbstractMales and females of many organisms show distinct patterns of inheritance. Here, Lloyd and Jenczewski model crossover patterning in Arabidopsis to gain insights into what causes the large differences in recombination rates and patterns...“Interference” is a major force governing the patterning of meiotic crossovers. A leading model describing how interference influences crossover patterning is the beam-film model, a mechanical model based on the accumulation and redistribution of crossover-promoting “stress” along the chromosome axis. We use the beam-film model in conjunction with a large Arabidopsis reciprocal backcross data set to gain “mechanistic” insights into the differences between male and female meiosis, and crossover patterning. Beam-film modeling suggests that the underlying mechanics of crossover patterning and interference are identical in the two sexes, with the large difference in recombination rates and distributions able to be entirely explained by the shorter chromosome axes in females. The modeling supports previous indications that fewer crossovers occur via the class II pathway in female meiosis and that this could be explained by reduced DNA double-strand breaks in female meiosis, paralleling the observed reduction in synaptonemal complex length between the two sexes. We also demonstrate that changes in the strength of suppression of neighboring class I crossovers can have opposite effects on “effective” interference depending on the distance between two genetic intervals.
Gerybinių stemplės anastomozės striktūrų gydymas
Authors: Stratilovas Eugenijus , Sangaila Egidijus 
Published: January 2019

Eugenijus Stratilovas, Egidijus SangailaVilniaus universiteto Onkologijos instituto Bendrosios ir abdominalinės chirurgijosir onkologijos skyrius, Santariškių g. 1, LT-08660 VilniusEl paštas: eugenijus.stratilatovas@loc.lt
Įvadas
Viena iš dažniausiai pasitaikančių vėlyvųjų komplikacijų po stemplės rezekcinio pobūdžio operacijų yra gerybinė anastomozės striktūra. Dėl striktūros išsivysčiusi disfagija ilgam pablogina ligonio gyvenimo kokybę. Pagrindiniai šios komplikacijos gydymo metodai išlieka dažnos endoskopijos, dilatacijos bužais sukėlus nejautrą. Autoriai siūlo taikyti gana paprastą šių striktūrų gydymo metodą – dilataciją Folley kateteriu.
Rezultatai
Šiuo būdu gydyti keturi pacientai. Visi procedūrą pakėlė gerai, gydymo komplikacijų nebuvo. Po dviejų procedūrų rijimas tapo normalus, toliau procedūros tęstos ambulatoriškai, praėjus 3 mėn. rijimas išliko normalus.
Išvada
Anastomozės striktūros dilatacija Folley kateteriu yra saugus, veiksmingas ir pigus metodas.
Reikšminiai žodžiai: stemplės vėžys, anastomozės striktūra, dilatacija
The treatment of the benign esophagus anastomosis strictures
Eugenijus Stratilovas, Egidijus SangailaVilnius University, Institute of Oncology, Department of Generaland Abdominal Surgery and Oncology, Santariškių str. 1, LT-08660 Vilnius, LithuaniaE-mail: eugenijus.stratilatovas@loc.lt
Background
One of the most frequent late complications after the resectable type of esophageal surgery is benign anastomosis stricture. The subsequent dysphagia worsens the patients’ quality of life for a long time. The main treatment modalities for this complication remain frequent endoscopy, dilatation using weighted bougies under anesthesia. Authors recommend use a simple mode of treatment – dilatation with the Folley catheter.
Results
Four patients underwent the treatment. All patients felt well, there were no treatment complications. Swallowing after two procedures became normal, the treatment was continued in outpatient clinic; after three months the swallowing was good.
Conclusions
Dilatation of a stricture with the Folley catheter is a safe and cost-effective method.
Key words: esophageal cancer, anastomosis benign stenosis, dilatation
Имя Великого Князя Литовского Витовта в названиях Северного Причерноморья XVI–XVIII веков
Authors: Белецкая Ольга 
Published: January 2019

[full article and abstract in Russian; abstract in English]
This research deals with the study of the toponyms of the Northern Black Sea Region, in which the name of Vytautas, Grand Duke of Lithuania, is fixed. The data of written (documentary, narrative, cartographic) and archaeological sources are considered concerning nine objects: The Bathhouse of Vytautas (1, 2, 3), the Wade of Vytautas, the Bridge of Vytautas, the Hillfort of Vytautas, Vytautas’s Tower, Vitovka and Lake Vidovo. The author has come to the conclusion that all the names are mentioned in the later sources. The results of the article may be interesting to all who study the activity of Vytautas as well as to scholars dealing with the historical geography of the Northern Black Sea Region.
Bazilijonų vienuolijos ryšiai su Vilniaus universitetu
Authors: Kažuro Ina 
Published: January 2019

[full article and abstract in Lithuanian; abstract in English]
Vilnius University has been the preeminent high school of The Grand Duchy of Lithuania for several centuries, spreading its influence across different areas of public life – religion, politics, culture. This article analyzes the influence of the Vilnius Alma Mater on the development of the Order of Saint Basil the Great (which had operated between 1617–1839). To that end, three aspects, revealing the connections of the two establishments, are distinguished: Basilians as university students, Basilians as university professors, and Basilians as university partners in the field of education. The research indicates that over a hundred young Basilians were studying in Vilnius University between 1617 and 1832. The members of the Basilian Order constituted a significant group of monk students from the mid-18th to the early 19th centuries. Cooperation in administering secondary schools yielded mutual benefits for both Vilnius University, which supervised the Vilnius educational district in 1803–1832, and the Basilian Order. The Order secured maintenance and provided support for a certain part of the Vilnius educational district schools, while the University became the protector and representative of the Order’s interests in Russian governmental institutions. The employment of Basilian lecturers (professors and vice-professors) at Vilnius University indicates the public recognition of the Order.
Motiejaus Kazimiero Sarbievijaus Akmens pašventinimas (Sacra Lithothesis): žanro problema
Authors: Šarkauskienė Skirmantė 
Published: January 2019

The article attempts to define the genre of one of the earliest creations by Sarbievijus – Consecration of the Stone. Consecration of the Stone is a collection of poems illustrated with prints. Sarbievijus included these texts into his poetry collections, and therefore these poems are to be considered a significant part of the poet’s lyric creation. Due to formal similarity with the emblem genre (the prints correspond to icons, the inscription – to lemmas, and rhymed texts – to subscriptions), Consecration of the Stone may be analyzed as an emblematic creation.Taking into consideration the circumstances of the appearance of the creation and the peculiarities of the text itself, the author of this article tries to prove that the poems included in the collection were recited during festivities. In such case Consecration of the Stone is to be considered a dramatic creation. An important circumstance is that the creation reflects festivities that were organized by the Jesuits of Kraþiai college. Theatre and the forms common to it was the important range of the cultural programme pursueted by the Jesuits order. In addition to that, there are numerous similarities betweenConsecration of the Stone and another creation by Sarbievijus – an epithalamium Hymenodora(Wedding Gifts) – that has a number of characteristics of a dramatic creation. It includes descriptions of live pictures, and references showing that rhymed texts are speeches of characters. This is a dramatic pageant with antique mythological deities and personifications of abstract concepts expressing virtues acting as characters. Consecration of the Stone is associated with Wedding Gift through the emblematic structure (a feature typical of all theatrical activity of Jesuits), and the compositions of the reflection and the text meant for the glorification of some virtue performing the role of a character. The poems ofConsecration of the Stone feature appeals to the dedicate – the audience that sees and hears the recited texts.On the basis of the existing typology of paratheatrical works, Consecration of the Stone should be attributed to the genre of declamatory dialogue: here four personified virtues are acting, but there is no conversation between them that would serve as a means of disclosing the action.
Intertekstinis Margaretos Atwood romano Tarnaitės pasakojimas skaitymas
Authors: Šlapkauskaitė Rūta 
Published: January 2019

Since its publication in 1985, Margaret Atwood’s dystopia The Handmaid’s Tale has prominently secured its place among the most widely read novels of Canadian literature. The present article offers a reading of Atwood’s The Handmaid’s Tale as a narrative built on intertextual relationships with other texts, which are directly or implicitly referred to in the novel. This analysis of the novel emphasizes reading as a dynamic semiotic process and employs Gérard Genette’s notion of transtextuality to look into the narrative’s semantic field from the perspective of its paratextual, intertextual and metatextualrelationships. While focusing on the Bible as the major intertext that structures the semantic space of Atwood’s narrative, this intertextual reading of The Handmaid’s Tale also looks at the ways in which the biblical context of Atwood’s novel correlates with the paratexts of Jonathan Swift’s essay A Modest Proposal and sufi philosophy to delineate the dominant strategies of the reading and interpreting of Atwood’s text. Finally, the article analyzes the metatextual level of Atwood’s novel and points out the ways in which the writer ironizes the intertextual nature of her own text and fictionalizes its intertexts, thereby suggesting the impossibility of narrative and interpretative closure.
Автобио-реконструктивная маска в письмах М. И. Цветаевой
Authors: Туганова Наталия 
Published: January 2019

Teatrinis kodas yra vienas iš M. Cvetajevos kūrybos kodų ir išryškinamas įvairiuose jos tekstų lygmenyse. Šiame straipsnyje analizuojamas toks teatrinio kodo elementas kaip vaidmuo ir prieinama išvados, kad toks teatro elementas kaip vaidmuo Cvetajevos laiškuose yra susijęs su N. Jevreinovo teatrine novacija – autobiorekonstruktyvia kauke. M. Cvetajevos laiškuose A. Bahrahui tai Fedros autobio-rekonstruktyvi kaukė.
Bifidobacterium Abundance in Early Infancy and Vaccine Response at 2 Years of Age
Authors: Huda M. Nazmul , Ahmad Shaikh M. , Alam M. Jahangir , Khanam Afsana , Kalanetra Karen M. , Taft Diana H. , Raqib Rubhana , Underwood Mark A. , Mills David A. , Stephensen Charles B. 
Published: January 2019

BACKGROUND:
The intestinal microbiome in early infancy affects immunologic development and thus may affect vaccine memory, though few prospective studies have examined such associations. We examined the association of Bifidobacterium levels in early infancy with memory responses to early vaccination measured at 2 years of age.

METHODS:
In this prospective observational study, we examined the association of Bifidobacterium abundance in the stool of healthy infants at 6 to 15 weeks of age, near the time of vaccination, with T-cell and antibody responses measured at 6 weeks, 15 weeks, and 2 years of age. Infants were vaccinated with Bacillus Calmette-Guérin (BCG) (at birth), oral polio virus (at birth and at 6, 10, and 14 weeks), tetanus toxoid (TT) (at 6, 10, and 14 weeks), and hepatitis B virus (at 6, 10, and 14 weeks). Fecal Bifidobacterium was measured at 6, 11, and 15 weeks. Bifidobacterium species and subspecies were measured at 6 weeks.

RESULTS:
Mean Bifidobacterium abundance in early infancy was positively associated with the CD4 T-cell responses to BCG, TT, and hepatitis B virus at 15 weeks, with CD4 responses to BCG and TT at 2 years, and with plasma TT-specific immunoglobulin G and stool polio-specific immunoglobulin A at 2 years. Similar associations were seen for the predominant subspecies, Bifidobacterium longum subspecies infantis.

CONCLUSIONS:
Bifidobacterium abundance in early infancy may increase protective efficacy of vaccines by enhancing immunologic memory. This hypothesis could be tested in clinical trials of interventions to optimize Bifidobacterium abundance in appropriate populations.
Prognostic criteria of variceal bleeding in patients with portal hypertension
Authors: Zhigalova S. B. , Manukiyan G. V. , Shertsinger A. G. , Fandeyev E. E. , Semenova T. S. , Korshunov I. B. , Martirosyan R. A. 
Published: January 2019

Aim. To determine prognostic criteria of variceal bleeding in patients with portal hypertension.Material and methods. There were 53 patients with portal hypertension and the threat of variceal bleeding from the esophagus and stomach without previous hemorrhage. Univariate and multivariate analysis was applied to determine prognostic criteria of the first bleeding. Patients with esophageal and gastroesophageal varices were analyzed separately. The following prognostic criteria were considered: dimensions of the veins, vasculopathy and gastropathy, liver function.Results. Incidence of hemorrhage was 72.7% in patients with esophageal varices grade 3, in case of vasculopathy — 80%. Child-Pugh class A was followed by incidence of hemorrhage near 12.5%, class B — 44%, C — 100%. MELD score < 9 was associated with bleeding rate 28.6%, 10—19 — 39.3%, over 20 scores — 100%. According to multivariate analysis consisting of Child—Pugh classification, in patients with < 11 scores 1-year incidence of bleeding was 13.3%, in case of MELD classification — 16.7%. The same values in patients with 11—16 scores were 77.8% and 31.3%, respectively. Analysis including both classifications (overall score over 16) was associated with incidence of hemorrhage up to 100%. Gastroesophageal varices grade 3 were associated with the risk of hemorrhage near 44.4% within 12 months, in case of vasculopathy — 60%, gastropathy — 37.5%. Incidence of hemorrhage in patients with Child-Pugh class A was 12.5%, class B — 44%, class C — 100%. In patients with MELD score < 9 bleeding rate was 28.6%, 10—19 scores — 39.3%, over 20 scores — 100%. According to multivariate analysis consisting of Child—Pugh classification, patients with gastroesophageal varices and less than 11 scores have the probability of hemorrhage near 15.4% within 12 months, in case of MELD score — 23%. The same values were 55.6% and 50%, respectively in case of 11—18 scores. In patients with more than 18 scores incidence of hemorrhage was 75% considering Child-Pugh classification and 100% for the MELD classification.Conclusion. The group of patients with threat of bleeding within 12 months was determined that makes possible a differentiated approach to patients who for need primary prevention of bleeding.
Quadriceps Weakness in Individuals with Coexisting Medial and Lateral Osteoarthritis
Authors: Iijima Hirotaka , Suzuki Yusuke , Aoyama Tomoki , Takahashi Masaki 
Published: January 2019

Background:
This study examined whether individuals who have mild medial osteoarthritis (OA) of the knee with coexisting lateral OA have less muscle strength than individuals who do not have lateral OA.

Methods:
A series of 153 individuals (84% of whom were women) between 48 and 88 years old who had Kellgren and Lawrence (KL) grade-2 OA in the medial compartment of the knee underwent radiographic evaluation to assess the presence of lateral OA, which was graded with the system of the Osteoarthritis Research Society International (OARSI) atlas as well as the KL system. The isometric maximum strengths of the quadriceps, the hip abductors, and the hip extensors were evaluated with use of a handheld dynamometer.

Results:
Individuals who had coexisting medial and lateral OA had more severe knee pain and weaker quadriceps than those who did not have lateral OA. The study adjusted for age and sex both for the OARSI atlas system (adjusted difference in mean strength: 0.272 Nm/kg, 95% confidence interval [CI]: 0.143 to 0.401 Nm/kg) and for KL grading (adjusted difference in mean strength: 0.185 Nm/kg, 95% CI: 0.061 to 0.309 Nm/kg). Logistic regression analysis showed that weakness of the quadriceps increased the odds of the presence of lateral OA sevenfold after adjustments using the OARSI atlas were made for age, sex, anatomical axis, range of motion of the knee, and intensity of pain in the knee.

Conclusions:
Individuals who had coexisting medial and lateral OA had weaker quadriceps than individuals who had mild medial OA alone. Paying close attention to quadriceps weakness might provide a key to clarifying the pathogenesis of bicompartmental disease in the tibiofemoral joint.

Level of Evidence:
Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Team Approach: Treatment of Injuries in the Female Athlete
Authors: Tanaka Miho J. , Szymanski Linda M. , Dale John L. , Dixit Sameer , Jones Lynne C. 
Published: January 2019

* Women’s sports medicine programs are gaining interest throughout the United States. Despite growing interest in the topic, we continue to have limited knowledge about the epidemiology, etiology, and long-term outcomes of treatment of injuries in female athletes.* Currently, no sex-specific differences in the perioperative treatment of female athletes exist.* The role of a team approach to treat and prevent injuries in female athletes extends beyond the single episode of perioperative care. Athletic trainers can extend the scope of outreach and education for female athletes.* Postoperative counseling for female athletes may have a role in addressing psychological barriers during recovery and return to play.* The role of hormones and considerations in the treatment of injuries in pregnant athletes should be addressed in collaborative women’s sports medicine programs.
Trapeziometacarpal Arthrosis
Authors: Wilkens Suzanne C. , Meghpara Michael M. , Ring David , Coert J. Henk , Jupiter Jesse B. , Chen Neal C. 
Published: January 2019

* Trapeziometacarpal arthrosis is an expected part of normal human aging.* The radiographic severity of trapeziometacarpal arthrosis may not correlate with symptom intensity or magnitude of limitations.* Psychosocial factors may be important drivers of symptom intensity, magnitude of limitations, and seeking of treatment.* Nonoperative treatment is palliative and not disease-modifying, but may facilitate long-term adaptation.* Current surgical treatment strategies center around trapeziectomy, but it is unclear whether the addition of other stabilization or interposition techniques changes overall outcomes.
An healthy lifestyle consultant based on Traditional Chinese medicine versus routine patient education in the treatment of idiopathic sudden sensorineural hearing loss after failure of systemic therapy: Study protocol for a clinical randomized trial with a paired design
Authors: Fei Yingping , Zheng Yun , Lai Dan , Zhong Ping , Lu Jing-zhe , Li Gang , Liu Peng 
Published: January 2019

Abstract
Background: Idiopathic sudden sensorineural hearing loss (ISSNHL) is an important cause of deafness. Despite advances of systemic therapy, some ISSNHL patients remains ineffective since the exact etiology for SSNHL is still unclear. Traditional Chinese medicine (TCM) has been used for treating disease for thousands of years. It is popular and widely practiced in Asia. TCM contains guidance on people's healthy lifestyle. In recent decades, the relationship between lifestyle and disease has been emphasized and unhealthy lifestyle may lead to illness. Thus, this study aims to compare the efficacy of the lifestyle modification based on TCM to the usual consultation of the ISSNHL after failure of two weeks systemic therapy, to provide a scientific basis for clinical decisions.
Methods: This is a clinical randomized trial with a paired design which will include 58 patients diagnosed with ISSNHL, according to the American Academy of Otolaryngology-Head and Neck Surgery sudden hearing loss clinical guideline published in 2012, but incomplete recovery from ISSNHL after of initial management. Participants will be randomized to either healthy lifestyle modification group based on TCM or control group. All patients will be followed for 3 months. The primary outcome measure is the effective rate of hearing improvement (defined as the proportion of patients with at least 15- dB improvement in the average thresholds by the hearing loss frequency). Secondary outcome measures are the improvements in pure-tone average (PTA) of the impaired frequencies, Word Recognition Score (WRS), Tinnitus Handicap Inventory (THI) and ear blockage. The assessments of the participants will be made at baseline, after lifestyle modification in 1 month and 3 months.
Discussion: This trial will determine the efficacy of healthy lifestyle modification based on TCM program for ISSNHL patients with incomplete recovery from after failure of initial systemic therapy. The results, if it is yielding positive results, will provide clinical evidence and TCM based healthy lifestyle could be recommended as salvage therapy for patients with ISSNHL.
Trial Registration: ClinicalTrials.gov, ChiCTR-INR-17011459. Registered on May 22 2017.
Keywords: ISSNHL, TCM, healthy lifestyle, Study protocol, randomized controlled trial