bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Biology Information Service: an innovative medical library-based bioinformatics support service for biomedical researchers
Authors: Chattopadhyay Ansuman , Iwema Carrie L , Epstein Barbara A , Lee Adrian V , Levine Arthur S 
Published: March 2019

Abstract
Biomedical researchers are increasingly reliant on obtaining bioinformatics training in order to conduct their research. Here we present a model that academic institutions may follow to provide such training for their researchers, based on the Molecular Biology Information Service (MBIS) of the Health Sciences Library System, University of Pittsburgh (Pitt). The MBIS runs a four-facet service with the following goals: (1) identify, procure and implement commercially licensed bioinformatics software, (2) teach hands-on workshops using bioinformatics tools to solve research questions, (3) provide in-person and email consultations on software/databases and (4) maintain a web portal providing overall guidance on the access and use of bioinformatics resources and MBIS-created webtools. This paper describes these facets of MBIS activities from 2006 to 2018, including outcomes from a survey measuring attitudes of Pitt researchers about MBIS service and performance.
Phosphodiesterase 1 Bridges Glutamate Inputs with NO- and Dopamine-Induced Cyclic Nucleotide Signals in the Striatum
Authors: Betolngar Dahdjim B , Mota Élia , Fabritius Arne , Nielsen Jacob , Hougaard Charlotte , Christoffersen Claus T , Yang Jun , Kehler Jan , Griesbeck Oliver , Castro Liliana R V , Vincent Pierre 
Published: March 2019

AbstractThe calcium-regulated phosphodiesterase 1 (PDE1) family is highly expressed in the brain, but its functional role in neurones is poorly understood. Using the selective PDE1 inhibitor Lu AF64196 and biosensors for cyclic nucleotides including a novel biosensor for cGMP, we analyzed the effect of PDE1 on cAMP and cGMP in individual neurones in brain slices from male newborn mice. Release of caged NMDA triggered a transient increase of intracellular calcium, which was associated with a decrease in cAMP and cGMP in medium spiny neurones in the striatum. Lu AF64196 alone did not increase neuronal cyclic nucleotide levels, but blocked the NMDA-induced reduction in cyclic nucleotides indicating that this was mediated by calcium-activated PDE1. Similar effects were observed in the prefrontal cortex and the hippocampus. Upon corelease of dopamine and NMDA, PDE1 was shown to down-regulate the D1-receptor mediated increase in cAMP. PDE1 inhibition increased long-term potentiation in rat ventral striatum, showing that PDE1 is implicated in the regulation of synaptic plasticity. Overall, our results show that PDE1 reduces cyclic nucleotide signaling in the context of glutamate and dopamine coincidence. This effect could have a therapeutic value for treating brain disorders related to dysfunctions in dopamine neuromodulation.
Sex Differences in the Incidence and Clearance of Anogenital Human Papillomavirus Infection in Liuzhou, China: An Observational Cohort Study
Authors: Wei Feixue , Guo Meng , Huang Shoujie , Li Mingqiang , Cui Xuelian , Su Yingying , Wu Xin , Ma Xinjing , Zheng Ya , Huang Yue , Wang Lin , Pan Lili , Wu Ting , Zhang Jun , Xia Ningshao 
Published: March 2019

Abstract

Background
Human papillomavirus (HPV) causes anogenital warts and cancers in men and women. However, little is known about sex differences regarding the natural history of anogenital HPV infection.

Methods
Starting in May 2014, an observational cohort study including 2309 men and 2378 women aged 18–55 years was conducted in Liuzhou, China. Samples from anogenital sites were tested for HPV genotypes by multicolor real-time polymerase chain reaction and melting curve analysis biannually for ~1 year.

Results
The incidence of oncogenic HPV infection was similar in men and women (10.3 and 11.5/1000 person-months; P = .275), whereas the incidence of HPV-6/11 infection was higher in men than in women (2.0 vs 1.1; P = .018). The incidence of both oncogenic HPV and HPV-6/11 infections was significantly higher in women in the 18- to 25-year age group than in the older age groups (P = .006 and .011, respectively), whereas it did not vary by age among men (P = .552 and .425, respectively). Additionally, men were more likely than women to clear oncogenic infections (101.5 vs 58.6/1000 person-months; P &lt; .001), but no significant difference was found in the clearance of HPV-6/11 by sex (111.7 vs 84.8; P = .266). The median time to clearance of oncogenic type and type 6/11 infections was not age dependent for either sex (all P &gt; .05).

Conclusions
The natural history of oncogenic and nononcogenic HPV infection differs by sex, which implies that sex-specific vaccination strategies should be considered for oncogenic and nononcogenic HPV.

Clinical Trials Registration
NCT02188004.
Use and Success of In Vitro Fertilisation Following Restorative Proctocolectomy and Ileal Pouch-anal Anastomosis. A Nationwide 17-year Cohort Study
Authors: Pachler Frederik R , Toft Gunnar , Bisgaard Thue , Laurberg Søren 
Published: March 2019

Abstract

Background and Aims
Fertility decreases in women following restorative proctocolectomy for ulcerative colitis. The use and success of in vitro fertilisation [IVF] after restorative proctocolectomy for ulcerative colitis is not systematically studied. We aimed to estimate the use and success of in vitro fertilisation treatment in female ulcerative colitis patients, with and without restorative proctocolectomy.

Methods
Women of fertile age [15–49 years] with restorative proctocolectomy for ulcerative colitis were compared with females with ulcerative colitis without restorative proctocolectomy. Data from the IVF registry from 1994–2010 were cross-linked with data from the National Danish Patient Registry and the Medical Birth Registry.

Results
In vitro fertilisation is significantly more frequent in females with restorative proctocolectomy compared with females without restorative proctocolectomy, adjusted hazard ratio 3.2, 95% confidence interval [CI] [2.5;4.0]. The odds for having a live birth after in vitro fertilisation are no different in females with restorative proctocolectomy compared with females without restorative proctocolectomy, adjusted odds ratio 0.8, 95% CI [0.6;1.1]. The percentage of children born as a result of in vitro fertilisation is significantly higher in females with restorative proctocolectomy compared with females without restorative proctocolectomy (31.0%, 95% CI [24.1; 37.7] vs 5.0%, 95% CI [4.4; 5.6]).

Conclusions
Females with restorative proctocolectomy for ulcerative colitis have increased incidence of in vitro fertilisation by more than a factor three, the odds that a treatment results in a live birth are similar and six times more children are born as a result of in vitro fertilisation compared with females without restorative proctocolectomy.
Long-term results of ventricular septation for double-inlet left ventricle†
Authors: Shimada Masatoshi , Hoashi Takaya , Nakata Tomohiro , Kurosaki Kenichi , Kanzaki Suzu , Shiraishi Isao , Ichikawa Hajime 
Published: March 2019

AbstractOBJECTIVESTo review the long-term surgical outcomes of ventricular septation for double-inlet left ventricle and reconsider the possibility of ventricular septation as an option of surgical treatments.METHODSBetween 1978 and 1994, 22 patients with double-inlet left ventricle underwent ventricular septation. The mean age at operation was 5.3 years (range 0–22 years). Follow-up was carried out in 20 of 22 patients (91%) and the mean follow-up period was 14.7 years (range 0–39 years).RESULTSActuarial survival and reoperation-free survival rates at 30 years were 49% and 21%, respectively. To date, 8 patients have been followed up. Among them, atrioventricular valve replacement and permanent pacemaker were required in 4 and 7 patients, respectively. Late cardiac catheter examination at 25.5 years after surgery showed that the median cardiac index was 2.6 l/min/m2 (range 2.1–3.4 l/min/m2), left ventricular end-diastolic pressure was 7 mmHg (range 4–11 mmHg), left ventricular ejection fraction was 50% (range 27–63%), right ventricular ejection fraction was 53% (range 31–66%) and central venous pressure was 6 mmHg (range 4–11 mmHg). At the latest follow-up, the New York Heart Association Functional Classification was I for 5 patients, II for 2 patients and III for 1 patient. The median peak oxygen uptake was 52.9% (range 44.1–93.5%).CONCLUSIONSSome patients with double-inlet left ventricle were able to maintain low central venous pressure and a sufficient cardiac index long after ventricular septation. Although the single ventricle strategy remains a first-line treatment, ventricular septation can be a surgical treatment option.
A century of changing fire management alters ungulate forage in a wildfire-dominated landscape
Authors: Proffitt Kelly M , DeVoe Jesse , Barker Kristin , Durham Rebecca , Hayes Teagan , Hebblewhite Mark , Jourdonnais Craig , Ramsey Philip , Shamhart Julee 
Published: March 2019

AbstractForestry practices such as prescribed fire and wildfire management can modify the nutritional resources of ungulates across broad landscapes. To evaluate the influences of fire and forest management on ungulate nutrition, we measured and compared forage quality and abundance among a range of land cover types and fire histories within 3 elk ranges in Montana. We used historical fire data to assess fire-related variations in elk forage from 1900 to 2015. Fire affected summer forage more strongly than winter forage. Between 1900–1990 and 1990–2015, elk summer range burned by wildfire increased 242–1772 per cent, whereas the area on winter range burned by wildfire was low across all decades. Summer forage quality peaked in recently burned forests and decreased as time since burn increased. Summer forage abundance peaked in dry forests burned 6–15 years prior and mesic forests burned within 5 years. Forests recently burned by wildfire had higher summer forage quality and herbaceous abundance than those recently burned by prescribed fire. These results suggest that the nutritional carrying capacity for elk varies temporally with fire history and management practices. Our methods for characterizing nutritional resources provide a relatively straightforward approach for evaluating nutritional adequacy and tracking changes in forage associated with disturbances such as fire.
A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes
Authors: Dussert Yann , Mazet Isabelle D , Couture Carole , Gouzy Jérôme , Piron Marie-Christine , Kuchly Claire , Bouchez Olivier , Rispe Claude , Mestre Pere , Delmotte François 
Published: March 2019

AbstractDowny mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant–pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.
Embedding C*-Algebras Into the Calkin Algebra
Authors: Farah Ilijas , Katsimpas Georgios , Vaccaro Andrea 
Published: March 2019

Abstract
We prove that, under Martin’s axiom, every ${\mathrm{C}}^\ast $-algebra of density character less than continuum embeds into the Calkin algebra. Furthermore, we show that it is consistent with Zermelo-Fraenkel set theory plus the axiom of choice, ZFC, that there is a $\mathrm{C}^\ast $-algebra of density character less than continuum that does not embed into the Calkin algebra.
How to optimize the therapeutic effect of free autogenous fibula graft and wrist arthroplasty for giant cell tumors of distal radius?
Authors: Liu Qing , Luo Wei , Zhang Can , Liao Zhan , Liu Yupeng , He Hongbo 
Published: March 2019

AbstractObjectiveThe purpose of this study is to retrospectively analyze the clinical efficacy of free fibula autograft and wrist arthroplasty in the treatment of giant cell tumors (GCT) of distal radius.MethodsWe retrospectively reviewed 26 patients with GCT of distal radius who underwent free autogenous fibula graft and wrist arthroplasty for repairing residual defect after en-block resection. The length of the fibula graft was 8.2 cm (6–10 cm). Postoperative follow-up regularly for an mean of 66.9 months. Bone healing was assessed by radiographs, pain was assessed by Visual Analog Scale (VAS) score and limb function was evaluated by Musculoskeletal Tumor Society (MSTS) score and disabilites of the arm, shoulder and hand (DASH) score. The range of motion (ROM) of wrist and grip strength were also evaluated.ResultThere were four males and 22 females with an mean age of 36.7 years (19–60 years); the mean length of lesions was 4.8 cm (2.3–6.6 cm); 21 primary cases and five recurrent cases; eight cases of Campanacci Grade II, 18 cases of Grade III. We had no postoperative lung metastasis and only one case had a local recurrence, three cases (11%) with subluxation of lower ulnoradial joints and five cases (19%) showed narrowing of wrist joint space. The mean postoperative VAS pain score was 0.7 ± 0.7 and grip strength retained 71% of the normal hand, MSTS score was 27.7 ± 1.1 and DASH score was 9.0 ± 3.7. The ROM of the involved wrist only slightly restricted and no donor complications. Postoperative wrist joint function was significantly improved.ConclusionStrict surgical resection boundary and solid reconstruction of wrist joint capsule are the key to achieving excellent oncological prognosis and function of distal radius GCT.
Comparing Asset Pricing Models by the Conditional Hansen-Jagannathan Distance*
Authors: Gagliardini Patrick , Ronchetti Diego 
Published: March 2019

AbstractWe compare nonnested parametric specifications of the stochastic discount factor (SDF) using the conditional Hansen–Jagannathan (HJ-) distance. This distance measures the discrepancy between a parametric model-implied SDF and the admissible SDF’s satisfying all the conditional (dynamic) no-arbitrage restrictions, instead of just few unconditional no-arbitrage restrictions for managed portfolios chosen through the instrument selection. We estimate the conditional HJ-distance by a generalized method of moments estimator and establish its large sample properties for model selection purposes. We compare empirically several SDF models including multifactor beta pricing specifications and some recently proposed SDF models that are conditionally linear in consumption growth.
The synchrotron maser emission from relativistic shocks in Fast Radio Bursts: 1D PIC simulations of cold pair plasmas
Authors: Plotnikov Illya , Sironi Lorenzo 
Published: March 2019

ABSTRACT
The emission process of Fast Radio Bursts (FRBs) remains unknown. We investigate whether the synchrotron maser emission from relativistic shocks in a magnetar wind can explain the observed FRB properties. We perform particle-in-cell (PIC) simulations of perpendicular shocks in cold pair plasmas, checking our results for consistency among three PIC codes. We confirm that a linearly polarized X-mode wave is self-consistently generated by the shock and propagates back upstream as a precursor wave. We find that at magnetizations σ ≳ 1 (i.e. ratio of Poynting flux to particle energy flux of the pre-shock flow) the shock converts a fraction $f_\xi ^{\prime } \approx 7 \times 10^{-4}/\sigma ^2$ of the total incoming energy into the precursor wave, as measured in the shock frame. The wave spectrum is narrow-band (fractional width ≲1−3), with apparent but not dominant line-like features as many resonances concurrently contribute. The peak frequency in the pre-shock (observer) frame is $\omega ^{\prime \prime }_{\rm peak} \approx 3 \gamma _{\rm s | u} \omega _{\rm p}$, where γs|u is the shock Lorentz factor in the upstream frame and ωp the plasma frequency. At σ ≳ 1, where our estimated $\omega ^{\prime \prime }_{\rm peak}$ differs from previous works, the shock structure presents two solitons separated by a cavity, and the peak frequency corresponds to an eigenmode of the cavity. Our results provide physically grounded inputs for FRB emission models within the magnetar scenario.
Global PD-L1 Signals and Tumor-Infiltrating Lymphocytes: Markers of Immunogenicity in Different Subsets of Merkel Cell Carcinoma and Potential Therapeutic Implications
Authors: Walsh Noreen M. , Castonguay Mathieu C. , Carter Michael D. , Pasternak Sylvia , Ly Thai Yen , Doucette Steve , Hanly John G. , Saggini Andrea , Cerroni Lorenzo 
Published: March 2019

Abstract:
We previously studied the genetic and immunohistochemical profiles of subsets of Merkel cell carcinoma (MCC) stratified by morphology and Merkel cell polyomavirus (MCPyV) status. Recent advances in the immunotherapy of this disease prompted us to examine markers of immunogenicity [PD-L1 expression and tumor-infiltrating lymphocytes (TILS) in these subsets]. The observed clinical responses to checkpoint inhibition of the PD-1/PD-L1 pathway have not correlated with PD-L1 expression by MCC cells, and recent evidence suggests that functions of this pathway within the immune tumor microenvironment may be relevant. We conducted a semiquantitative (high, moderate, and minimal) immunohistochemical evaluation of the global PD-L1 signal in 52 cases of MCC, segregated in 3 subsets [pure MCPyV-positive (n = 28), pure MCPyV-negative (n = 9), and combined MCPyV-negative (n = 15)]. TILS were categorized as brisk, nonbrisk, or absent. Intersubset comparisons revealed that high global PD-L1 signals were exclusively associated with pure MCPyV-positive MCCs contrasted with virus-negative cases (P = 0.0003). Moderate signals were seen across all 3 groups. Brisk TILS were significantly associated with MCPyV-positive MCCs compared with MCPyV-negative cases (P = 0.029). Neither parameter (PD-L1 or TILS) was significantly different between the MCPyV-negative groups. Of potential clinical relevance, MCPyV seems to convey greater immunogenicity to MCCs than the high mutational burden/greater neoantigen load of MCPyV-negative cases. Interesting too is the fact that subset-related profiles of these markers mirrored those noted at genetic and immunohistochemical levels, separating pure MCPyV-positive MCCs from the virus-negative subsets.
Differential Expression of PLAG1 in Apocrine and Eccrine Cutaneous Mixed Tumors: Evidence for Distinct Molecular Pathogenesis
Authors: Russell-Goldman Eleanor , Dubuc Adrian , Hanna John 
Published: March 2019

Abstract:
Cutaneous mixed tumors, also known as chondroid syringomas, are benign adnexal neoplasms that share histomorphologic features with pleomorphic adenomas of the salivary gland. Recent work suggests that the similarity between these 2 tumor types extends to the molecular level because both harbor identical chromosomal rearrangements involving the PLAG1 gene. The resulting nuclear PLAG1 overexpression can be detected by immunohistochemistry and has become a useful diagnostic adjunct for both tumor types. In the skin, however, there are 2 morphologically distinct types of mixed tumor, which have been referred to as apocrine-type cutaneous mixed tumor (AMT) and eccrine-type cutaneous mixed tumor (EMT). Previous studies of PLAG1 expression in cutaneous mixed tumor did not distinguish between these types. Here, we evaluated PLAG1 expression by immunohistochemistry in a cohort of 25 cutaneous mixed tumors stratified by type. PLAG1 was overexpressed in the majority of AMT cases (14 of 16) but in none of the EMT cases (0 of 9). A second gene, HMGA2, known to be upregulated in a subset of salivary gland pleomorphic adenomas, was overexpressed in only 1 case of AMT (1 of 16) and in none of the cases of EMT (0 of 9). Our results indicate that apocrine- and eccrine-type mixed tumors are associated with different pathways of molecular pathogenesis and suggest that the emerging relationship between skin and salivary gland mixed tumors is likely limited to those of apocrine type.
Expression of Connexin 43 (Cx43) in Benign Cutaneous Tumors With Follicular Differentiation
Authors: Fernandez-Flores Angel , Varela-Vazquez Adrian , Mayan Maria D. , Fonseca Eduardo 
Published: March 2019

Introduction:
Benign cutaneous tumors with follicular differentiation are alleged to differentiate toward parts of the hair follicle. Connexin 43 (Cx43) is a gap junction protein, the tumoral role of which has been investigated in several types of tumors.

Objective:
To study the pattern of expression of Cx43 in benign cutaneous tumors with follicular differentiation and to compare it with that shown by their alleged anatomical counterparts of the hair follicle.

Materials and Methods:
Five cases each of trichofolliculoma, trichilemmoma, fibrofolliculoma/trichodiscoma, trichoblastoma, trichoepithelioma, pilomatrixoma, and proliferating trichilemmal tumor, 3 cases of pilar sheath acanthoma, and 1 case of tumor of the follicular infundibulum were examined. Anti-Cx43 antibody was used.

Results:
Cx43 was expressed by all follicular tumors studied. Comparisons between trichoblastoma and trichoepithelioma and their respective normal counterparts could not be made. In 3 tumors (trichofolliculoma, pilomatrixoma, and the spectrum fibrofolliculoma/trichodiscoma), there was a parallelism between their Cx43 expression pattern and that of their alleged anatomical counterparts. In pilar sheath acanthoma, trichilemmoma, and the tumor of the follicular infundibulum, we only found partial similarities in Cx43 expression. Only the proliferating trichilemmal tumor showed a discordant pattern of expression.

Conclusions:
Cx43 expression is preserved in benign cutaneous tumors with follicular differentiation and the patterns of Cx43 expression in benign cutaneous tumors with follicular differentiation parallel those of their alleged anatomical counterparts in 5 types (either totally or partially). This preservation might be related to the good behavior of the entities studied.
IgG4-Related Skin Disease Presenting as a Pseudolymphoma in a White Adolescent Girl
Authors: Shakeri Aria , Kindley Kimball Jade , Noland Mary Margaret , Gru Alejandro Ariel 
Published: March 2019

Abstract:
Immunoglobulin gamma (Ig) type 4–related disease (IgG4-RD) is a chronic immunologic systemic disorder that has gained worldwide recognition in the past decade. This entity can affect almost every organ system, and its characteristic lesions have been found in a variety of organs such as lacrimal and salivary glands, pancreas, liver, bile ducts, lungs, kidneys, retroperitoneum, breast, aorta, thyroid, and prostate. This case reports a very rare case of IgG4-RD presenting with a cutaneous lesion in a young female patient mimicking a lymphoproliferative disorder. IgG4-RD affecting the skin is a rare entity and has mostly been reported in Japanese men of middle to older age. IgG4-RD with cutaneous involvement should be in the differential of non-neoplastic, lymphomas, autoimmune, and infectious disorders of the skin.