bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of Bethesda system in thyroid aspirate: A cyto-histopathological correlation study
Authors: Choudhary PK , Nepal N , Mainali N , Meenakshi B 
Published: September 2016

Background: Thyroid lump is a common clinical problem in Nepal. The risk of malignancy has to be judged prior to surgery for which fine needle aspiration cytology is widely used. To bring the uniform reporting of thyroid aspirates, the Bethesda system for reporting thyroid cytopathology (TBSRTC) was introduced in 2007. This study was done to evaluate the various cytomorphological patterns of thyroid aspirate and to correlate the Bethesda system with final histopathology report.Materials and Methods: Fine needle aspiration were performed and were evaluated as per TBSRTC criteria. Fine needle aspiration cytology report were compared with biopsy specimen whenever possible. Result: A total of 386 cases were studied. The sensitivity, specificity, positive predictive value, negative predictive value and overall accuracy of TBSRTC were 75.2%, 98.2%, 90.0%, 94.7% and 94.03% respectively. Conclusion: Use of TBSRTC in reporting thyroid cytopathology has a greater accuracy; however, benign cases need regular follow up as there are false negative cases.
Impact of urothelial carcinoma with divergent differentiation on tumor stage
Authors: Chalise S , Jha A , Neupane PR , Pradhan SB , Pathak R 
Published: September 2016

Background: Urinary bladder cancer is classified as urothelial or non-urothelial. Ninenty percent of bladder cancer are urothelial and has propensity for divergent differentiation. Squamous differentiation is associated with unfavourable prognostic features. The aim of this study is to determine the significance of urothelial carcinoma with divergent differentiation in relation to tumor stage and lymphovascular as well as perineural invasion in radical cystectomy and partial cystectomy specimen.Materials and methods: This prospective study was done among 51 patients who underwent radical cystectomy or partial cystectomy at Bhaktapur Cancer Hospital from 1st August 2013 to 31st December 2015. Received specimen was grossed following standard protocol and histopathological evaluation was done in relation to tumor type, depth of invasion, Lymphovascular and perineural invasion.Results: Pure urothelial carcinoma comprises 47.1% of cases. Among the divergent differentiation, urothelial carcinoma with squamous differentiation was the commonest one (39.2%) followed by glandular differentiation (5.9%), sarcomatoid differentiation (3.9%), clear cell variant (2.0%) and squamous along with sarcomatoid variant (2.0%). Statistical significant correlation was found between urothelial carcinoma with divergent differentiation and tumor stage (p<0.012). Statistically significant correlation was also found between urothelial carcinoma with divergent differentiation and lymphovascular invasion (p=0.012) as well as perineural invasion (p=0.037).Conclusion: Most common divergent differentiation was squamous differentiation. Urothelial carcinoma with divergent differentiation was associated with higher stage and lymphovascular as well as perineural invasion. So it is mandatory to search for the divergent differentiation in urothelial carcinoma as this may be associated with unfavourable prognosis.
Histopathological evaluation of ulcerative colitis in colonoscopic biopsies
Authors: Dhakhwa R , Shrestha HG , Acharya IL 
Published: September 2016

Background: Histopathologic evaluation of colonoscopic mucosal biopsy remains one of the earliest modalities of investigation in patients clinically suspected of ulcerative colitis. Pathologists should be aware of classical histomorphological features to avoid misdiagnosis. The aim of the present study was to evaluate histopathologic features as well as to determine possible atypical presentation.Materials and Methods: Forty newly diagnosed cases of ulcerative colitis were included in the study. Colonoscopic biopsies taken from rectum as well as various areas of colon and ileum depending upon clinical extent of involvement were submitted for histopathological evaluation. Diagnosis of ulcerative colitis was made by correlating clinical, endoscopic and histopathologic findings.Results: Out of 47 cases suspected of ulcerative colitis, histopathologic features were consistent with Ulcerative colitis in 40 cases. Almost all cases (97.5%) showed diffuse active colitis. Cryptitis (100%), crypt abscesses (75%) and basal plasmacytosis (85%) along with crypt architectural abnormalities (75%) and goblet cell depletion (70%) were classical histological changes associated with ulcerative colitis in active phase. Atypical presentations noticed were focal active colitis (2.5%), backwash ileitis (2.5%), rectal sparing (2.5%) and skip areas (5%).Conclusion: Accurate diagnosis of ulcerative colitis requires elaborate knowledge of histopathologic features along with awareness of possible atypical presentation.
Prevalence of Helicobacter pylori among patients with dyspepsia and correlation between endoscopic and histological diagnosis
Authors: K.C. Shiva Raj , Lakhey A , Koirala K , Amatya GL 
Published: September 2016

Background: Dyspepsia is a prevalent complaint in general practice and gastrointestinal clinics. Helicobacter pylori have major causal relationship with gastro duodenal disease. The following study seeks to identify the prevalence of H. pylori based on histology and to correlate endoscopic findings with histopathology.Materials and Methods: This was a cross-sectional observational study conducted in GRP Polyclinic and Om Hospital and research centre from April 2015-September 2015. The upper gastrointestinal endoscopic findings were recorded and were correlated with histopathological findings. All the relevant data were collected and analysed using Statistical Package of Social Sciences version 16 for windows. Results: Endoscopy finding was divided into reflux esophagitis, antral gastritis, duodenitis, duodenal ulcer, gastric ulcer, and gastric cancer. Duodenal ulcer and gastric ulcer was noted more frequently in males than in females (55.0% vs. 45.0% and 58.2% vs. 41.8%), respectively, P < 0.001).Chronic follicular gastritis was the most common in gastric ulcer (41.7%), whereas chronic persistent gastritis was common in non-ulcerative disease. Chronic active gastritis and chronic follicular gastritis were more common in ulcerative diseases, whereas chronic persistent gastritis was more common in gastritis and duodenitis (P < 0.001). The overall prevalence of H. pylori infection was 68.1% with male preponderance. Chronic active gastritis had highest prevalence of H. pylori (84.8%), followed by chronic follicular gastritis (84.1%) and chronic persistent gastritis (p value < 0.001.Conclusion: Rate of H. pylori infected patients with dyspepsia was high. Ulcerative lesions were more common in males than in females with higher rate of infection with H. Pylori. Histological diagnosis of chronic active gastritis and chronic follicular gastritis was the most common pathologies in ulcerative lesions.
The Paris System – A new insight into reporting urine cytology
Authors: Ghosh A 
Published: September 2016

Urine cytology helps in the diagnosis of urothelial malignancies. There were no universally accepted reporting system despite several systems were suggested in the past. As a part of irst international effort to standardize urine cytology, The Paris System Working Group was formed comprising pathologists and urologists who met in 2013 at the International Congress of Cytology in Paris and proposed The Paris System (TPS). It was unanimously decided that the main aim of urine cytology was to detect high grade urothelial carcinoma. TPS consists of 7 diagnostic categories and also tries to deine several morphological criteria. TPS Atlas was published in 2016. This article tries to summarize and highlight essential points of The Paris System.
Extra nodal Rosai Dorfman disease of nasal septal mucosa without lymphadenopathy
Authors: Raje P , Vyas P 
Published: September 2016

Rosai–Dorman disease, also known as sinus histiocytosis with massive lymphadenopathy, typically presents as massive enlargement of lymph nodes accompanied by systemic symptoms. Extranodal involvement is also known usually in head and neck regions. Rarely the disease presents at extranodal sites only without involvement of lymph nodes.We present a case of 58 years-old female who presented with mass in nasal septum without involvement of lymph nodes. The mass was removed surgically and diagnosis was made on histological grounds with classical indings of histiocytic proliferation and emperipolesis.
Seasonal changes in tissue‐water relations for eight species of ferns during historic drought in California
Authors: Holmlund Helen I. , Lekson Victoria M. , Gillespie Breahna M. , Nakamatsu Nicole A. , Burns Amanda M. , Sauer Kaitlyn E. , Pittermann Jarmila , Davis Stephen D. 
Published: September 2016

PREMISE OF THE STUDY:California experienced severe drought between 2012 and 2016. During this period, we compared seasonal changes in tissue‐water relations among eight fern species in the Santa Monica Mountains of southern California to elucidate differential mechanisms of drought survival and physiological performance during extreme water deficits.METHODS:We monitored seasonal changes in water potential (Ψmd) and dark‐adapted chlorophyll fluorescence (Fv/Fm), assessed tissue‐water relations including osmotic potential at saturation and the turgor loss point (Ψπ, sat and Ψπ, tlp), and measured, for two evergreen species, xylem‐specific and leaf‐specific hydraulic conductivity (Ks and Kl) and vulnerability of stem xylem to water stress‐induced embolism (water potential at 50% loss hydraulic conductivity, Ψ50).KEY RESULTS:Species grew in either riparian or chaparral understory. The five chaparral species had a wider range of seasonal water potentials, root depths, and frond phenological traits, including one evergreen, two summer‐deciduous, and two desiccation‐tolerant (resurrection) species. Evergreen species were especially diverse, with an evergreen riparian species maintaining seasonal water potentials above −1.3 MPa, while an evergreen chaparral species had seasonal water potentials below −8 MPa. In those two species the Ψ50 values were −2.5 MPa and −4.3 MPa, respectively.CONCLUSIONS:Observed differences in physiological performance among eight fern species reflected niche partitioning in water utilization and habitat preference associated with distinct phenological traits. We predict differential survival among fern species as future drought events in California intensify, with desiccation‐tolerant resurrection ferns being the most resistant.
Lost crops of the Incas: Origins of domestication of the Andean pulse crop tarwi, Lupinus mutabilis
Authors: Atchison Guy W. , Nevado Bruno , Eastwood Ruth J. , Contreras‐Ortiz Natalia , Reynel Carlos , Madriñán Santiago , Filatov Dmitry A. , Hughes Colin E. 
Published: September 2016

PREMISE OF THE STUDY:The Andean highlands are a hotspot of domestication, yet our understanding of the origins of early Andean agriculture remains fragmentary. Key questions of where, when, how many times, and from what progenitors many Andean crops were domesticated remain unanswered. The Andean lupine crop tarwi (Lupinus mutabilis) is a regionally important pulse crop with exceptionally high seed protein and oil content and is the focus of modern breeding efforts, but its origins remain obscure.METHODS:A large genome‐wide DNA polymorphism data set was generated using nextRADseq to infer relationships among more than 200 accessions of Andean Lupinus species, including 24 accessions of L. mutabilis and close relatives. Phylogenetic and demographic analyses were used to identify the likely progenitor of tarwi and elucidate the area and timing of domestication in combination with archaeological evidence.KEY RESULTS:We infer that tarwi was domesticated once in northern Peru, most likely in the Cajamarca region within, or adjacent to the extant distribution of L. piurensis, which is the most likely wild progenitor. Demographic analyses suggest that tarwi split from L. piurensis around 2600 BP and suffered a classical domestication bottleneck. The earliest unequivocal archaeological evidence of domesticated tarwi seeds is from the Mantaro Valley, central Peru ca. 1800 BP.CONCLUSIONS:A single origin of tarwi from L. piurensis in northern Peru provides a robust working hypothesis for the domestication of this regionally important crop and is one of the first clear‐cut examples of a crop originating in the highlands of northern Peru.
The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae)
Authors: Chaney Lindsay , Mangelson Ryan , Ramaraj Thiruvarangan , Jellen Eric N. , Maughan Peter J. 
Published: September 2016

Premise of the study:The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome.Methods and Results:A high‐quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long‐read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A. caudatus) and their putative progenitor (A. hybridus). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single‐copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single‐nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes.Conclusions:This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus.
Inhibition of Acid Sphingomyelinase Allows for Selective Targeting of CD4+ Conventional versus Foxp3+ Regulatory T Cells
Authors: Hollmann Claudia , Werner Sandra , Avota Elita , Reuter Dajana , Japtok Lukasz , Kleuser Burkhard , Gulbins Erich , Becker Katrin Anne , Schneider-Schaulies Jürgen , Beyersdorf Niklas 
Published: September 2016

Abstract
CD4+ Foxp3+ regulatory T cells (Tregs) depend on CD28 signaling for their survival and function, a receptor that has been previously shown to activate the acid sphingomyelinase (Asm)/ceramide system. In this article, we show that the basal and CD28-induced Asm activity is higher in Tregs than in conventional CD4+ T cells (Tconvs) of wild-type (wt) mice. In Asm-deficient (Smpd1−/−; Asm−/−) mice, as compared with wt mice, the frequency of Tregs among CD4+ T cells, turnover of the effector molecule CTLA-4, and their suppressive activity in vitro were increased. The biological significance of these findings was confirmed in our Treg-sensitive mouse model of measles virus (MV) CNS infection, in which we observed more infected neurons and less MV-specific CD8+ T cells in brains of Asm−/− mice compared with wt mice. In addition to genetic deficiency, treatment of wt mice with the Asm inhibitor amitriptyline recapitulated the phenotype of Asm-deficient mice because it also increased the frequency of Tregs among CD4+ T cells. Reduced absolute cell numbers of Tconvs after inhibitor treatment in vivo and extensive in vitro experiments revealed that Tregs are more resistant toward Asm inhibitor–induced cell death than Tconvs. Mechanistically, IL-2 was capable of providing crucial survival signals to the Tregs upon inhibitor treatment in vitro, shifting the Treg/Tconv ratio to the Treg side. Thus, our data indicate that Asm-inhibiting drugs should be further evaluated for the therapy of inflammatory and autoimmune disorders.
Lower Extremity Landing Biomechanics in Both Sexes After a Functional Exercise Protocol
Authors: Wesley Caroline A. , Aronson Patricia A. , Docherty Carrie L. 
Published: September 2016

Context
Sex differences in landing biomechanics play a role in increased rates of anterior cruciate ligament (ACL) injuries in female athletes. Exercising to various states of fatigue may negatively affect landing mechanics, resulting in a higher injury risk, but research is inconclusive regarding sex differences in response to fatigue.

Objective
To use the Landing Error Scoring System (LESS), a valid clinical movement-analysis tool, to determine the effects of exercise on the landing biomechanics of males and females.

Design
Cross-sectional study.

Setting
University laboratory.

Patients or Other Participants
Thirty-six (18 men, 18 women) healthy college-aged athletes (members of varsity, club, or intramural teams) with no history of ACL injury or prior participation in an ACL injury-prevention program.

Intervention(s)
Participants were videotaped performing 3 jump-landing trials before and after performance of a functional, sportlike exercise protocol consisting of repetitive sprinting, jumping, and cutting tasks.

Main Outcome Measure(s)
Landing technique was evaluated using the LESS. A higher LESS score indicates more errors. The mean of the 3 LESS scores in each condition (pre-exercise and postexercise) was used for statistical analysis.

Results
Women scored higher on the LESS (6.3 ± 1.9) than men (5.0 ± 2.3) regardless of time (P = .04). Postexercise scores (6.3 ± 2.1) were higher than preexercise scores (5.0 ± 2.1) for both sexes (P = .01), but women were not affected to a greater degree than men (P = .62).

Conclusions
As evidenced by their higher LESS scores, females demonstrated more errors in landing technique than males, which may contribute to their increased rate of ACL injury. Both sexes displayed poor technique after the exercise protocol, which may indicate that participants experience a higher risk of ACL injury in the presence of fatigue.
A Longitudinal Examination of Work-Life Balance in the Collegiate Setting
Authors: Mazerolle Stephanie , Eason Christianne 
Published: September 2016

The literature regarding work-life balance (WLB) is plentiful, particularly in the National Collegiate Athletic Association Division I collegiate setting due to its demanding nature as defined by work hours and travel. Despite the comprehensive understanding of factors contributing to WLB for athletic trainers (ATs) in this setting, the effect of time of year has yet to be investigated.Context:
To determine the influence sport season timing (ie, preseason, in-season, off-season) can have on perceptions and experiences of WLB for ATs.Objective:
Qualitative, case-study design.Design:
Division I collegiate practice setting.Setting:
Six ATs employed in the Division I college setting (3 women, 3 men) volunteered and completed our study over 1 year. The average age of participants was 31.0 ± 3 years, and they had 9.0 ± 3 years of experience.Patients or Other Participants:
We conducted semistructured one-on-one phone interviews with each participant at 4 points during the year (August, November, February, June). All interviews were transcribed verbatim. Data were analyzed inductively, and we used peer review, multiple-analyst triangulation, and member checks for credibility.Data Collection and Analysis:
Time of year (eg, competitive in-season), organizational demands (eg, hours and travel), and life stage (eg, roles assumed) were factors that influenced WLB for ATs in the collegiate setting. Having a positive and adaptable mind-set; having coworker, supervisor, and personal support; and engaging in personal or family time were factors that counterbalanced the inhibitors.Results:
Our results indicate that a career as an AT in the collegiate setting can create WLB concerns; these concerns, however, seem to peak during the competitive in-season for the AT's primary coverage team. Additionally, conflict that arises for ATs seems to be stimulated by time, as work roles are often less accommodating due to the athletic atmosphere.Conclusions:
Injury Scheme Claims in Gaelic Games: A Review of 2007–2014
Authors: Roe Mark , Blake Catherine , Gissane Conor , Collins Kieran 
Published: September 2016

Gaelic games (Gaelic football and hurling) are indigenous Irish sports with increasing global participation in recent years. Limited information is available on longitudinal injury trends. Reviews of insurance claims can reveal the economic burden of injury and guide cost-effective injury-prevention programs.Context:
To review Gaelic games injury claims from 2007–2014 for male players to identify the costs and frequencies of claims. Particular attention was devoted to lower limb injuries due to findings from previous epidemiologic investigations of Gaelic games.Objective:
Descriptive epidemiology study.Design:
Open-access Gaelic Athletic Association Annual Reports from 2007–2014 were reviewed to obtain annual injury-claim data.Setting:
Gaelic Athletic Association players.Patients or Other Participants:
Player age (youth or adult) and relationships between lower limb injury-claim rates and claim values, Gaelic football claims, hurling claims, youth claims, and adult claims.Main Outcome Measure(s):
Between 2007 and 2014, €64 733 597.00 was allocated to 58 038 claims. Registered teams had annual claim frequencies of 0.36 with average claim values of €1158.4 ± 192.81. Between 2007 and 2014, average adult claims were always greater than youth claims (6217.88 versus 1036.88), while Gaelic football claims were always greater than hurling claims (5395.38 versus 1859.38). Lower limb injuries represented 60% of all claims. The number of lower limb injury claims was significantly correlated with annual injury-claim expenses (r = 0.85, P = .01) and adult claims (r = 0.96, P = .01) but not with youth claims (r = 0.69, P = .06).Results:
Reducing lower limb injuries will likely reduce injury-claim expenses. Effective injury interventions have been validated in soccer, but whether such changes can be replicated in Gaelic games remains to be investigated. Injury-claim data should be integrated into current elite injury-surveillance databases to monitor the cost effectiveness of current programs.Conclusions: