Reviewability and supportability: New complementary principles to empower research software practices.

In today's scientific landscape, research software has evolved from being a supportive tool to becoming a fundamental driver of discovery, particularly in life sciences. Beyond its roots in software engineering, research software now plays a crucial role in facilitating efficient data analysis and enabling the exploration of complex natural phenomena. The advancements in simulations and modeling through research software have significantly accelerated the pace of scientific research while reducing associated costs.

scAEGAN: Unification of single-cell genomics data by adversarial learning of latent space correspondences.

Recent progress in Single-Cell Genomics has produced different library protocols and techniques for molecular profiling. We formulate a unifying, data-driven, integrative, and predictive methodology for different libraries, samples, and paired-unpaired data modalities. Our design of scAEGAN includes an autoencoder (AE) network integrated with adversarial learning by a cycleGAN (cGAN) network.

The Regulators of Peroxisomal Acyl-Carnitine Shuttle CROT and CRAT Promote Metastasis in Melanoma.

Circulating tumor cells are the key link between a primary tumor and distant metastases, but once in the bloodstream, loss of adhesion induces cell death. To identify the mechanisms relevant for melanoma circulating tumor cell survival, we performed RNA sequencing and discovered that detached melanoma cells and isolated melanoma circulating tumor cells rewire lipid metabolism by upregulating fatty acid (FA) transport and FA beta-oxidation‒related genes. In patients with melanoma, high expression of FA transporters and FA beta-oxidation enzymes significantly correlates with reduced progression-free and overall survival.

Functional and transcriptomic analysis of extracellular vesicles identifies calprotectin as a new prognostic marker in peripheral arterial disease (PAD).

Peripheral arterial disease (PAD) is associated with a high risk of cardiovascular events and death and is postulated to be a critical socioeconomic cost in the future. Extracellular vesicles (EVs) have emerged as potential candidates for new biomarker discovery related to their protein and nucleic acid cargo. In search of new prognostic and therapeutic targets in PAD, we determined the prothrombotic activity, the cellular origin and the transcriptomic profile of circulating EVs.

Immunophenotypic identification and characterization of tumor cells and infiltrating cell populations in meningiomas.

Meningiomas are primary tumors of the central nervous system composed of both neoplastic and other infiltrating cells. We determined the cellular composition of 51 meningioma samples by multiparameter flow cytometric (MFC) immunophenotyping and investigated the potential relationship between mRNA and protein expression levels of neoplastic cells. For immunophenotypic, morphologic, and cytogenetic characterization of individual cell populations, a large panel of markers was used together with phagocytic/endocytic functional assays and MFC sorting.

Delineation of commonly deleted chromosomal regions in meningiomas by high-density single nucleotide polymorphism genotyping arrays.

Despite recent advances in the identification of the cytogenetic profiles of meningiomas, a significant group of tumors still show normal karyotypes or few chromosomal changes. The authors analyzed the cytogenetic profile of 50 meningiomas using fluorescence in situ hybridization and high-density (500 K) single nucleotide polymorphism (SNP) arrays. Our results confirm that del(22q) (52%) and del(1p) (16%) (common deleted regions: 22q11.

[Aneurysmal subarachnoid hemorrhage: group of study of cerebrovascular pathology of the Spanish society of neurosurgery management guideline].

An actualized revision of the most important aspects of aneurismal subarachnoid hemorrhage is presented from the guidelines previously published by the group of study of cerebrovascular pathology of the Spanish Society of Neurosurgery. The proposed recommendations should be considered as a general guide for the management of this pathological condition. However, they can be modified, even in a significant manner according to the circumstances relating each clinical case and the variations in the therapeutic and diagnostic procedures available in the center attending each patient.

Idiopathic subarachnoid hemorrhage: a multicentre series of 220 patients.

BACKGROUND. The Spanish neurosurgical society created a multicentre data base on spontaneous SAH to analyze the real problematic of this disease in our country. This paper focuses on the group of patients with idiopathic SAH (ISAH).

[Spontaneous Subarachnoid Haemorrhage multicenter database from the Group for the Study of Vascular Pathology of the Spanish Society for Neurosurgery: presentation, inclusion criteria and development of an internet-based registry].

Introduction: Subarachnoid haemorrhage is one of the most severe neurosurgical diseases. Its study is crucial for improving the care of these patients in our environment. With this goal the Group for the Study of Neurovascular Pathology of the Spanish Society for Neurosurgery (SENEC) decided to create a multicenter registry for the study of this disease.

Gene expression profiles of meningiomas are associated with tumor cytogenetics and patient outcome.

Cytogenetic analysis is a powerful tool for predicting recurrence in meningiomas, even among histologically benign/grade I tumors. Despite this, no study has been reported in which the impact of tumor cytogenetics on the gene expression profiles (GEP) has been analyzed in meningiomas. Here, we analyzed the GEP of 47 tumors and correlated them with the most clinical relevant cytogenetic subgroups of meningiomas, as confirmed through the analysis of 172 patients.

Array-based comparative genomic hybridization of mapped BAC DNA clones to screen for chromosome 14 copy number abnormalities in meningiomas.

Chromosome 14 loss in meningiomas are associated with more aggressive tumour behaviour. To date, no studies have been reported in which the entire chromosome 14q of meningioma tumour cells has been studied by high-resolution array comparative genomic hybridization (a-CGH). Here, we used a high-resolution a-CGH to define the exact localization and extent of numerical changes of chromosome 14 in meningioma patients.

Changes in ventricular size after endoscopic third ventriculostomy.

Background: There is general consensus that a successful endoscopic third ventriculostomy is usually followed by a decrease of ventricular size without reaching their normal size. This study was performed to determine how the change related to clinical outcome, how it developed chronologically and whether the change in ventricular size was different in acute and chronic forms of hydrocephalus.

Method: Fifty-five of 74 patients who had undergone endoscopic third ventriculostomy during the period 1997-2004 were selected by the criterion that they had both pre-operative and post-operative films and no neurosurgical manoeuvre other than a surgically successful endoscopic third ventriculostomy in the time span between both radiological studies.

Patient gender is associated with distinct patterns of chromosomal abnormalities and sex chromosome linked gene-expression profiles in meningiomas.

The female predominance of meningiomas has been established, but how this is affected by hormones is still under discussion. We analyzed the characteristics of meningiomas from male (n = 53) and female (n = 111) patients by interphase fluorescence in situ hybridization (iFISH). In addition, in a subgroup of 45 (12 male and 33 female) patients, tumors were hybridized with the Affymetrix U133A chip.

Early recurrences in histologically benign/grade I meningiomas are associated with large tumors and coexistence of monosomy 14 and del(1p36) in the ancestral tumor cell clone.

Tumor recurrence is the major clinical complication in meningiomas, and its prediction in histologically benign/grade I tumors remains a challenge. In this study, we analyzed the prognostic value of specific chromosomal abnormalities and the genetic heterogeneity of the tumor, together with other clinicobiological disease features, for predicting early relapses in histologically benign/grade I meningiomas. A total of 149 consecutive histologically benign/grade I meningiomas in patients who underwent complete tumor resection were prospectively analyzed.

[Cytogenetic alterations in meningioma tumors and their impact on disease outcome].

In recent years important advances have been achieved in the understanding of the genetic abnormalities present in meningioma tumors and its association with the ontogeny and progression of these tumor. Accordingly, while the presence of monosomy 22/22q-, associated with mutation of the NF2, BAM22, RRP22, GAR22, MN1, SMARCB1, CLH22 and/or LARGE genes, is associated with neoplasic transformation, other alterations such us monosomy 14, del(1p), different chromosomal abnormalities localized at 9p, 10q and 17q and complex karyotypes are frequently related to tumor progression. From the clinical point of view, currently available information about the impact of the different cytogenetic abnormalities on disease behavior and patient outcome is still scanty; nevertheless, the presence of gains of chromosome 22 in the context of a hyperdiploid karyotype, as well as del(1p) and monosomy 14 have been associated with a statistically significantly shorter recurrence-free survival, this later abnormality showing an independent prognostic value.

Microarray-based analysis of spinal versus intracranial meningiomas: different clinical, biological, and genetic characteristics associated with distinct patterns of gene expression.

It has long been recognized that spinal meningiomas show particular clinical and histological features. Here, we compare the clinico-biological characteristics as well as the genetic abnormalities and patterns of gene expression of spinal and intracranial meningiomas. Fourteen spinal and 141 intracranial meningioma patients were analyzed at diagnosis.

The cytogenetic relationship between primary and recurrent meningiomas points to the need for new treatment strategies in cases at high risk of relapse.

Purpose: Recurrence is the major factor influencing the clinical outcome of meningioma patients although the exact relationship between primary and recurrent tumors still needs to be clarified. The aim of the present study is to analyze the cytogenetic relationship between primary and subsequent recurrent meningiomas developed within the same individual.

Experimental Design: Multicolor interphase fluorescence in situ hybridization was done for the identification of numerical abnormalities of 12 chromosomes in single-cell suspensions from 59 tumor samples corresponding to 25 recurrent meningioma patients.

[Skull base meningiomas: a predictive system to know the extent of their surgical resection and patient outcome].

Objective: The aim of this study was to build a preoperative predictive system which could provide reliable information about: 1 degrees which skull base meningiomas can be total or partially removed, and 2 degrees their surgical outcome.

Method: Patient histories and imaging data were reviewed retrospectively from 85 consecutive skull base meningiomas patients who underwent surgery from 1990 and 2002. From the preoperative data, nine variables were selected for conventional statistical analysis as regards their relationship with: 1 degrees total vs partial tumor resection and 2 degrees with patients outcome according to the degree of tumour removal.

Characterization of chromosome 14 abnormalities by interphase in situ hybridization and comparative genomic hybridization in 124 meningiomas: correlation with clinical, histopathologic, and prognostic features.

We analyzed quantitative chromosome 14 abnormalities in 124 meningiomas by interphase fluorescence in situ hybridization (iFISH) and confirmed the nature of abnormalities by comparative genomic hybridization (CGH). We correlated the abnormalities with clinical, histopathologic, and prognostic factors. Of 124 cases, 50 (40.

Intratumoral patterns of clonal evolution in meningiomas as defined by multicolor interphase fluorescence in situ hybridization (FISH): is there a relationship between histopathologically benign and atypical/anaplastic lesions?

Meningiomas are cytogenetically heterogeneous tumors in which chromosome gains and losses frequently occur. Based on the intertumoral cytogenetic heterogeneity of meningiomas, hypothetical models of clonal evolution have been proposed in these tumors which have never been confirmed at the intratumoral cell level. The aim of this study was to establish the intratumoral patterns of clonal evolution associated with chromosomal instability in individual patients as a way to establish tumor progression pathways in meningiomas and their relationship with tumor histopathology and behavior.

[Intracerebral hemorrhage following chronic subdural hematoma evacuation: report of two cases and review of the literature].

Intracerebral hemorrhage ocurring after chronic subdural hematoma evacuation, is a rare and very serious postoperative complication. The sudden increase of cerebral blood flow in the hemisphere beneath the hematoma, is the most likely mechanism responsible for this situation. Two new cases of intracerebral hemorrage after evacuation of chronic subdural hematomas are reported.

New classification scheme for the prognostic stratification of meningioma on the basis of chromosome 14 abnormalities, patient age, and tumor histopathology.

Purpose: Meningiomas are usually considered benign tumors. However, relapses occur in 10% to 20% of all patients, including both histopathologically aggressive and benign tumors. This study explored the value of numerical abnormalities for 10 different chromosomes in meningiomas for predicting relapse-free survival (RFS).

[Analysis of cerebrospinal fluid related complications (hydrocephalus, fistula, pseudomeningocele and infection) following surgery for posterior fossa tumors].

Introduction: Hydrocephalus, cerebrospinal fluid (CSF) leak, pseudomeningocele and CSF infection are potential complications related to surgical treatment of posterior fossa tumors. The objectives of this study were to review the incidence of such complications and to identify contributing factors related to them.

Material And Methods: This study is based on a retrospective review of the medical records of 71 consecutive patients who underwent posterior fossa surgery for a tumor between the period January 1997 and December 2001.

[Evaluation of microsurgical treatment in a series of 121 intracranial aneurysms].

Objective: The results obtained with therapy of intracranial aneurysms, in terms of morbidity and mortality, are very important when the patient has to choose between microsurgical techniques or endovascular management. The aim of this paper is to review the information regarding current microsurgical treatment of intracranial aneurysms, and presenting our experience over the last five years.

Material And Methods: We studied 101 consecutive patients with 121 intracranial aneurysms admitted between 1996 and 2000 with the initial diagnosis of subarachnoid hemorrhage.