bluuebunny/crossref_metadata_2025_split huggingface dataset:
(167) 3D Penile Reconstruction Imaging in Complex Peyronie’s Disease (PD): Proof of Concept Study
Authors: Nascimento B C G , Moraes C A D C , Neto R P , Rocha B A , Miranda E D P , Bessa J D , Nahas W C , Hallak J , Mulhall J P , Gomes C M 
Published: May 2023

Abstract

Introduction
The evaluation of penile deformity in PD is a critical step in therapeutic decision making and is generally the main outcome in PD clinical trials. 3D reconstruction is becoming increasingly common in the medical field, with highly accurate and long term accessible images. To date, there is no widely accepted 3D documentation protocol for penile deformity.

Objective
To evaluate the feasibility of 3D imaging and its accuracy in quantifying penile deformity.

Methods
Video images captured intraoperatively during saline-induced rigid erection were acquired from 4 PD patients undergoing penile surgery. Penile curvature measurements were obtained by the surgeon with a goniometer. Video images were obtained with an iPhone 11 (Apple Inc, Cupertino, CA) camera in full HD or 4k resolution, traveling in a circular 360o motion around the penile shaft. Video images were analysed by a team with 3D expertise using the open source software Blender (Blender Foundation, Amsterdan, NE) and its addon OrtogonBlender, and 3D reconstructed images were created. The 3D team performed curvature measurements using the software tools. A non-concordance magnitude was defined as a measurement difference (between physician measurement and 3D image) of 20% or 10o, whichever was smaller.

Results
The 3D reconstruction was possible in all cases and all videos used took &lt;1 minute to be captured. Images of 4 patients, 3 with bi-planar curvature, were obtained and therefore 7 measurements were available for caparison. The 3D images quality was good and volume loss deformities were visible. Measurements generated from those reconstructed images showed excellent concordance (100%, N=7 - Table 1). An example of curvature measurement in a 3D model is presented in Figure 1.

Conclusions
In this pilot study, deformity analysis and measurement with tolerable error was performed using video images acquired quickly intraoperatively, with a smartphone. With further development, this strategy may contribute to a more objective follow up of complex PD cases, as those with biplanar curvature or volume loss deformities.

Disclosure
No
(181) Combination Clomiphene Citrate and Anastrozole Therapy Iimproves Semen Parameters in a Multi-institutional Cohort of Men with Idiopathic Infertility
Authors: Eleswarapu S , Naelitz B , Jiang T , Munoz C , Parekh N , Andino J , Sigalos J , Modiri N , Mills J , Vij S , Lundy S 
Published: May 2023

Abstract

Introduction
Clomiphene citrate (CC), a selective estrogen receptor modulator, and anastrozole, a selective aromatase inhibitor, are common empiric medical therapies for men with idiopathic infertility. The effects of jointly administering these agents are not well understood.

Objective
The objective of this study is to compare semen parameters in men treated with clomiphene citrate and anastrozole (CC-A) combination therapy to those in men taking anastrozole alone.

Methods
We performed a multi-center, retrospective cohort study of men with idiopathic infertility prescribed anastrozole at two tertiary referral institutions. Demographic, laboratory, and prescription data were captured. The subset of patients taking CC at the time of anastrozole initiation were identified. Patients with pre-treatment normozoospermia, recent or current exogenous testosterone or human chorionic gonadotropin use, previous orchiectomy, and scrotal surgery during the treatment period were excluded. Outcome measures included changes in World Health Organization sperm concentration category (WHO-SCC) following initiation of anastrozole therapy. Linear and logistic regression models were constructed to evaluate the association of combination therapy with these outcomes.

Results
72 men were included in the analysis cohort, including 54 men taking anastrozole alone and 18 men on CC therapy who subsequently started taking anastrozole (CC-A). Men on CC-A relative to anastrozole monotherapy were older (40 vs. 35 years, p=0.03) and had a lower BMI (30 vs. 34 kg/m^2, p=0.05), respectively. Pre-treatment LH levels (5.6 vs. 7.6 IU/L, p=0.25) and testosterone (336 vs 263 ng/dL, p=0.32) were similar. Baseline semen parameters including sperm concentration (3.7 vs. 2.3 M/mL, p=0.26) and motility (41 vs. 36%, p= 0.17) were also comparable. However, post-treatment median sperm concentration (6.9 vs. 3.4M/mL, p=0.02) and the change in mean sperm concentration (17.5 vs. 6.2 M/mL, p=0.03) were significantly higher in the CC-A combination group. Univariate linear regression also revealed an association between the use of CCA combination therapy and increase in sperm concentration (p=0.05). Despite these differences, WHO-SCC upgrade rates between groups were comparable (56 vs. 39%, p=0.22) in the setting of similar post-treatment levels of LH (7.4 vs. 8.6 IU/L, p=0.5), FSH (8.6 vs. 9.4 IU/mL, p=0.19), and testosterone (537 vs. 415 ng/dL, p=0.09).

Conclusions
Combination therapy with clomiphene citrate and anastrozole was associated with modest benefits in post-treatment sperm concentration when compared to anastrozole monotherapy. Combination empiric medical therapy using clomiphene citrate and anastrozole offers a small, but significant, clinical benefit over anastrozole alone for infertile men

Disclosure
No
Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes
Authors: Barrett Kristian , Hunt Cameron J , Lange Lene , Grigoriev Igor V , Meyer Anne S 
Published: May 2023

Abstract
Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering method CUPP, Conserved Unique Peptide Patterns. CUPP operates synergistically with the CAZy family/subfamily categorizations to allow systematic exploration of CAZymes by defining small protein groups with shared sequence motifs. The updated CUPP library contains 21,930 of such motif groups including 3,842,628 proteins. The new implementation of the CUPP-webserver, https://cupp.info/, now includes all published fungal and algal genomes from the Joint Genome Institute (JGI), genome resources MycoCosm and PhycoCosm, dynamically subdivided into motif groups of CAZymes. This allows users to browse the JGI portals for specific predicted functions or specific protein families from genome sequences. Thus, a genome can be searched for proteins having specific characteristics. All JGI proteins have a hyperlink to a summary page which links to the predicted gene splicing including which regions have RNA support. The new CUPP implementation also includes an update of the annotation algorithm that uses only a fourth of the RAM while enabling multi-threading, providing an annotation speed below 1 ms/protein.
Conformational dynamics of RNA G4C2 and G2C4 repeat expansions causing ALS/FTD using NMR and molecular dynamics studies
Authors: Taghavi Amirhossein , Baisden Jared T , Childs-Disney Jessica L , Yildirim Ilyas , Disney Matthew D 
Published: May 2023

Abstract
G4C2 and G2C4 repeat expansions in chromosome 9 open reading frame 72 (C9orf72) are the most common cause of genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), or c9ALS/FTD. The gene is bidirectionally transcribed, producing G4C2 repeats [r(G4C2)exp] and G2C4 repeats [r(G2C4)exp]. The c9ALS/FTD repeat expansions are highly structured, and structural studies showed that r(G4C2)exp predominantly folds into a hairpin with a periodic array of 1 × 1 G/G internal loops and a G-quadruplex. A small molecule probe revealed that r(G4C2)exp also adopts a hairpin structure with 2 × 2 GG/GG internal loops. We studied the conformational dynamics adopted by 2 × 2 GG/GG loops using temperature replica exchange molecular dynamics (T-REMD) and further characterized the structure and underlying dynamics using traditional 2D NMR techniques. These studies showed that the loop's closing base pairs influence both structure and dynamics, particularly the configuration adopted around the glycosidic bond. Interestingly, r(G2C4) repeats, which fold into an array of 2 × 2 CC/CC internal loops, are not as dynamic. Collectively, these studies emphasize the unique sensitivity of r(G4C2)exp to small changes in stacking interactions, which is not observed in r(G2C4)exp, providing important considerations for further principles in structure-based drug design.
CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing
Authors: Zhou Fengxia , Yu Xiaorong , Gan Rui , Ren Kuan , Chen Chuangeng , Ren Chunyan , Cui Meng , Liu Yuchen , Gao Yiyang , Wang Shouyu , Yin Mingyu , Huang Tengjin , Huang Zhiwei , Zhang Fan 
Published: May 2023

Abstract
The CRISPR-Cas system is a highly adaptive and RNA-guided immune system found in bacteria and archaea, which has applications as a genome editing tool and is a valuable system for studying the co-evolutionary dynamics of bacteriophage interactions. Here introduces CRISPRimmunity, a new web server designed for Acr prediction, identification of novel class 2 CRISPR-Cas loci, and dissection of key CRISPR-associated molecular events. CRISPRimmunity is built on a suite of CRISPR-oriented databases providing a comprehensive co-evolutionary perspective of the CRISPR-Cas and anti-CRISPR systems. The platform achieved a high prediction accuracy of 0.997 for Acr prediction when tested on a dataset of 99 experimentally validated Acrs and 676 non-Acrs, outperforming other existing prediction tools. Some of the newly identified class 2 CRISPR-Cas loci using CRISPRimmunity have been experimentally validated for cleavage activity in vitro. CRISPRimmunity offers the catalogues of pre-identified CRISPR systems to browse and query, the collected resources or databases to download, a well-designed graphical interface, a detailed tutorial, multi-faceted information, and exportable results in machine-readable formats, making it easy to use and facilitating future experimental design and further data mining. The platform is available at http://www.microbiome-bigdata.com/CRISPRimmunity. Moreover, the source code for batch analysis are published on Github (https://github.com/HIT-ImmunologyLab/CRISPRimmunity).
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics
Authors: Ciecierski Lukasz , Stolarek Ireneusz , Figlerowicz Marek 
Published: May 2023

Abstract
Archeogenomics is a rapidly growing interdisciplinary research field driven by the development of techniques that enable the acquisition and analysis of ancient DNA (aDNA). Recent advances in aDNA studies have contributed significantly to increasing our understanding of the natural history of humans. One of the most significant challenges facing archeogenomics is the integration of highly heterogeneous genomic, archeological, and anthropological data and their comprehensive analysis, considering changes that occur in time and space. Only this complex approach can explain the relationship between past populations in the context of migration or cultural development. To address these challenges, we developed a Human AGEs web server. It focuses on creating comprehensive spatiotemporal visualizations of genomic, archeogenomic, and archeological information, which can be provided by the user or loaded from a graph database. The interactive map application at the center of Human AGEs can display multiple layers of data in various forms, such as bubble charts, pie charts, heatmaps, or tag clouds. These visualizations can be modified using various clustering, filtering, and styling options, and the map state can be exported to a high-resolution image or saved as a session file for later use. Human AGEs, along with their tutorial, are accessible at https://archeogenomics.eu/.
Large-scale expansions of Friedreich's ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers
Authors: Rastokina Anastasia , Cebrián Jorge , Mozafari Negin , Mandel Nicholas H , Smith C I Edvard , Lopes Massimo , Zain Rula , Mirkin Sergei M 
Published: May 2023

Abstract
Friedreich's ataxia (FRDA) is caused by expansions of GAA•TTC repeats in the first intron of the human FXN gene that occur during both intergenerational transmissions and in somatic cells. Here we describe an experimental system to analyze large-scale repeat expansions in cultured human cells. It employs a shuttle plasmid that can replicate from the SV40 origin in human cells or be stably maintained in S. cerevisiae utilizing ARS4-CEN6. It also contains a selectable cassette allowing us to detect repeat expansions that accumulated in human cells upon plasmid transformation into yeast. We indeed observed massive expansions of GAA•TTC repeats, making it the first genetically tractable experimental system to study large-scale repeat expansions in human cells. Further, GAA•TTC repeats stall replication fork progression, while the frequency of repeat expansions appears to depend on proteins implicated in replication fork stalling, reversal, and restart. Locked nucleic acid (LNA)-DNA mixmer oligonucleotides and peptide nucleic acid (PNA) oligomers, which interfere with triplex formation at GAA•TTC repeats in vitro, prevented the expansion of these repeats in human cells. We hypothesize, therefore, that triplex formation by GAA•TTC repeats stall replication fork progression, ultimately leading to repeat expansions during replication fork restart.
FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data
Authors: Zhang Zixuan , Zhu Haiqi , Dang Pengtao , Wang Jia , Chang Wennan , Wang Xiao , Alghamdi Norah , Lu Alex , Zang Yong , Wu Wenzhuo , Wang Yijie , Zhang Yu , Cao Sha , Zhang Chi 
Published: May 2023

Abstract
Quantitative assessment of single cell fluxome is critical for understanding the metabolic heterogeneity in diseases. Unfortunately, laboratory-based single cell fluxomics is currently impractical, and the current computational tools for flux estimation are not designed for single cell-level prediction. Given the well-established link between transcriptomic and metabolomic profiles, leveraging single cell transcriptomics data to predict single cell fluxome is not only feasible but also an urgent task. In this study, we present FLUXestimator, an online platform for predicting metabolic fluxome and variations using single cell or general transcriptomics data of large sample-size. The FLUXestimator webserver implements a recently developed unsupervised approach called single cell flux estimation analysis (scFEA), which uses a new neural network architecture to estimate reaction rates from transcriptomics data. To the best of our knowledge, FLUXestimator is the first web-based tool dedicated to predicting cell-/sample-wise metabolic flux and metabolite variations using transcriptomics data of human, mouse and 15 other common experimental organisms. The FLUXestimator webserver is available at http://scFLUX.org/, and stand-alone tools for local use are available at https://github.com/changwn/scFEA. Our tool provides a new avenue for studying metabolic heterogeneity in diseases and has the potential to facilitate the development of new therapeutic strategies.
Transformations of Workers’ Mobilization in Latin America
Authors: Ramírez Gallegos Franklin , Stoessel Soledad 
Published: May 2023

Abstract
This chapter explores the transformations of workers’ mobilization in Latin America from the end of the nineteenth century to the twenty-first century. For that purpose, the link is observed between changing economic connections, state-society relations, and workers’ collective action. The dynamics of mobilization and demobilization are considered from the inter-relationship of three dimensions: forms of organization, repertoires of state–society interaction, and ideological frameworks. The analysis focuses on four periods: 1890–1929: the emergence of workers’ organizations; 1930–1960: the strengthening of labor unions and processes of incorporation; 1970–1990: neoliberalism, democracy, and organizational breakdown; and 1999–2017: the return of the state and the calling into question of neoliberalism, the revitalization of labor unions, and new workers’ movements. In order to provide greater insight, the more industrialized countries (Argentina, Brazil, Mexico, Chile) are compared with others less industrialized (the Andean region and Central American countries such as Bolivia, Ecuador, Venezuela, Nicaragua, El Salvador, and Panama). The chapter concludes with three findings: (1) Latin American workers’ mobilization is not reduced to labor union dynamics nor is its role limited to extending workers’ rights; (2) the complex interactions of class, ethnicity, gender, and territory have produced successive waves of politicization of the “worker question”; and (3) beyond the constraints imposed by economic structures and state control, the political subjectivation of workers has evolved in contradictory ways in the different spheres of relationship with the left, populism, the church, and political institutions, as well as a product of the historical vicissitudes of the struggles.
Peasant Movements in Recent Latin American History
Authors: Welch Cliff 
Published: May 2023

Abstract
This chapter offers an historical synthesis of twentieth- and twenty-first-century peasant movements in Latin America and the Caribbean. Based mostly on secondary literature, the chapter follows overlapping developments in diverse locations generally determined by the intensity of the penetration of capitalist relations of production. The chapter recounts the experiences of distinct peasant movements through an analytical narrative that follows a periodization defined by the descriptive categories of “restoration,” “integration,” “revolution,” and “alternation.” Restoration movements were typical of the early twentieth century, wherein peasants joined together to halt change and restore conceptions of an earlier, often idealized order. From the 1920s to the 1950s, many peasants banded together in efforts to integrate themselves into national projects, struggling to shape incorporation instruments like political parties, labor unions, and agricultural policy. Often frustrated in these attempts, some peasant sectors participated in revolutionary movements from the 1950s to 1980s. During the most recent period analyzed, the 1980s to 2000s, a combination of transforming socialist icons, diversified practices, altered identities, and neoliberal restructuring fostered peasant movements intent on ensuring their livelihoods through the development of autonomous organizations and alternative social formations that sought greater control over their relationship to the capitalist political economy.
Environmental Mobilization in Latin America
Authors: Christel Lucas G. , Gutiérrez Ricardo A. 
Published: May 2023

Abstract
This chapter reviews and discusses the vast literature on environmental mobilization in Latin America and the Caribbean from the 1980s on. There is a tendency in the literature to use the term environmental “movement” as tantamount to “mobilization” or “organization,” while only a few studies elaborate what an environmental movement is and what the conditions for its existence are. Given this lack of precision in using the term movement and the fact that several studies do not use it at all, this chapter seeks to answer to what extent the concept of social movement is appropriate to understand environmental mobilization in Latin America and the Caribbean. Its starting point is the conceptual distinction between environmental mobilization and environmental movement. The chapter defines environmental mobilization as the collective action aiming to influence (in either contentious or institutionalized ways) the decisions regarding the political and economic regulation of the interactions between human beings and their environment. Based upon this definition, it first examines the general characteristics of environmental mobilization in the region and then discusses the analytical scope of the concept of social movement as used in the literature. Based on this review, the chapter contends that the concept of environmental mobilization is better equipped than the notion of social movement to grasp the singularities of Latin American and Caribbean environmentalism.
Transnational Social Movements in Latin America
Authors: von Bülow Marisa 
Published: May 2023

Abstract
Latin America has been an important cradle of transnational social movements since the beginning of the twentieth century. These movements not only launched reactive campaigns to counter threats, but also built new organizational fora and events to think about policy alternatives. They had substantial impacts on international negotiations and on the organizational infrastructure of civil society globally. Two examples discussed in this chapter are the creation of the Hemispheric Social Alliance, at the Inter-American level, and the World Social Forum meetings, at the global level. The scholarly literature on Latin American transnationalism has added to key debates about the emergence of transnational collective action and its consequences. It has also helped reach a better understanding of why and how actors shift through domestic and international scales, and the challenges they face as they do so. Important gaps remain, however, most importantly the study of conservative and right-wing transnational movements, and research on the impacts of the incorporation of digital repertoires on transnational collective action.
Education, Pedagogy, and Social Movements in Latin America
Authors: Tarlau Rebecca 
Published: May 2023

Abstract
This chapter provides an overview of the role of education within Latin American social movements over the past century. The first part discusses political education during the first half of the twentieth century, with a focus on the Communist Party and anarchist organizing efforts both before and after the Bolshevik Revolution. The emphasis is on urban and rural labor organizing in Brazil, as a lens into similar socialist organizing unfolding throughout the continent. This section also analyzes two important state-led educational initiatives during this period, the “socialist education” policies developed in Mexico during the 1930s and the 1961 Cuban Literacy campaign. The second part of the chapter discusses the authoritarian period in Latin America, from the mid-1960s to the early 1980s, and the impact of Paulo Freire’s Pedagogy of the Oppressed. The educational approach outlined in Freire’s book was taken up by Catholic clergy inspired by liberation theology, which facilitated the rapid spread of Freirean practices throughout Latin America. This section examines Freirean literacy programs and popular education among El Salvadoran guerrilla groups and under the Sandinista government. The final section is on social movements and education in contemporary Latin America, after the re-democratization of the region, focusing on both non-formal education, or formación, as well as social movement’s transformation and co-governance of public education. This long-term emphasis on education and pedagogy within Latin American social movements has been a major reason for their growth, continuity, and effectiveness.