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A large body of literature has established the benefits of undergraduate research experiences via the traditional apprenticeship model. More recently, several studies have shown that many of these benefits can be recapitulated in course-based undergraduate research experiences (CUREs) that are more scalable and easier for students to participate in, compared to the apprenticeship-based research experiences. Many Biology curricula also incorporate more traditional laboratory courses, where students learn to use common laboratory techniques through guided exercises with known outcomes. Indeed, many programs across the nation provide such programs or courses for students early in their careers, with a view toward increasing student interest and engagement in Biology. While there is general consensus that all lab experiences have some benefits for students, very few studies have examined whether either research experiences or learning biological techniques in more traditional lab courses directly impacts student performance in lecture courses. Here, we show that prior familiarity with laboratory techniques does not improve student performance in a lecture course, even if these techniques are directly related to content being taught in the course. However, having prior research experience improves performance in the course, irrespective of whether the research experience included the use of course-related laboratory techniques.

Clinical exome sequencing has the potential to identify pathogenic variants unrelated to the purpose of the study (secondary findings, SFs). Data describing actual choices of SFs in participants in a clinical setting and factors influencing their decision are virtually non-existant in Europe. In this work, we report the acceptance rate of SFs, calculate their prevalence and study factors associated with the decision in a cohort of patients affected with a rare genetic disorder in a Spanish Hospital. Finally, we re-examine the presence of previously non reported family history in positive cases. We retrospectively reviewed informed consent choices and SF results from 824 unrelated probands affected with rare genetic disorders who underwent whole-genome or exome sequencing. Ninety percent of families (740/824) affected with rare disorders wished to be informed of SFs. Declining SFs was associated with a prenatal setting (30% vs. 8.7%, p = 0.025), consanguinity (19% vs. 8.7%, p = 0.013), male gender (10.6% vs. 1.5%, p = 0.00865) and the proband being a minor (10.6% vs. 1.5%, p = 0.014). Overall, 27 pathogenic or likely pathogenic variants were identified in 27 individuals, with an SF prevalence of 3.6%. Disclosure of SFs increased the percentage of positive family histories and resulted in early diagnosis or changes in the management of 10 individuals from five families. We show that the acceptance of SFs in Spain is high and the disclosure of SFs leads to a clinically meaningful change in the medical management of individuals.

Intimacy is a key component of relational bonds, associated not only with sex but with every aspect of what each member of a family expresses –in the way he or she can do so–. How does it take place? What are the existing approaches towards the family to weigh intimacy? How is intimacy construed, and how can it be widely understood? Intimacy is not static: it changes through time and is different throughout the family life cycle, as well as through the various stages of each of the family members. Why is intimacy relevant? Intimacy is a value, and its nature goes beyond what is often expected: it constructs or deconstructs the family. Because it is deeply connected to feelings, thoughts, beliefs, traditions, culture, working with intimacy in each member may lead to the armor-plating of the family. Now, the construction of each person as a human individual does not just happen; it requires time, techniques, love, respect, and intimacy, which directly leads to self-fidelity. In turn, self-fidelity in each member of the family can produce what is known as a family coat of arms. While broken intimacy can destroy a person’s self-esteem and, consequently, meaningful, long-lasting relationships, armor-plating intimacy can develop deeply enriched human individuals who bring who they are and what they possess to ultimately weave a strong society. As a result, a society that protects and fosters intimacy, not only pays attention to what damages exist and should be prevented, but to what makes people live in generous self-donation. Intimacy lets a person know his/her value; therefore, intimacy is the strongest value and technique to assess what we are, what we need, what we want.

Spinal Muscular Atrophy (SMA) Type II is a neurodegenerative disease that leads to progressive muscle weakness. It prevents children from walking and affects their respiratory function and their activity tolerance, among other health problems. We aimed to assess the activity tolerance showed by a child with SMA using a pediatric gait exoskeleton at home when walking and performing activities.This study presents the case of a 6-year-old boy with SMA Type II and respiratory failure who used a pediatric gait exoskeleton at home for a period of two months. A nursing assessment was done before and during the use of the device to evaluate the child's activity tolerance during the sessions. Nursing interviews, performance, vital signs, fatigue, field notes, and functional scales were analyzed.The nursing assessment showed a good activity tolerance of the child. Performance using the device improved over time; vital signs did not vary significantly during the sessions; fatigue perception decreased over time; and the child reached a higher score on some functional outcomes.A first step has been taken to evaluate the impact of exoskeleton technology in children with SMA Type II from the nursing point of view, exposing the potential of this technology for the care of children with neuromuscular diseases, and the need for more research on the topic.The information in this study will be useful to nurses to know the effects of gait exoskeletons in pediatric care of children with neuromuscular diseases like SMA.

To compare toric intraocular lens (TIOL) implantation and femtosecond laser-assisted arcuate keratotomy (FSAK) during phacoemulsification surgery in correction of moderate astigmatism.Clinical research study.Prospective randomized comparison study.Patients with age-related cataract and moderate preoperative corneal astigmatism of 1.25 to 3.0 diopters (D) were randomized into a TIOL implantation group and an FSAK group with symmetrical paired corneal arcuate keratotomies. The preoperative evaluation included corrected distance visual acuity (CDVA), corneal topography, autokeratometry, and ocular biometry. Postoperative examinations were performed at 1 month and 3 months and included CDVA and uncorrected distance visual acuity, manifest refraction, autokeratometry, and corneal topography. Vector analysis of astigmatic changes was performed using the Alpins vector method.This study comprised 75 eyes from 67 patients. The mean residual refractive astigmatism at 3 months was -0.63 ± 0.55 D in the TIOL group and -0.90 ± 0.53 D in the FSAK group ( P = .037) and was ≤1.00 D in 32 eyes (84%) and 25 eyes (64%), respectively. There were no statistically significant differences between the 2 groups in difference vector, angle of error, magnitude error, or correction index in the 3-month follow-up. The index of success was 0.32 ± 0.33 D in the TIOL group and 0.48 ± 0.29 D in the FSAK group ( P = .029).TIOL implantation showed better results in correcting moderate astigmatism. Despite this, FSAK is shown to be a safe technique for reducing astigmatism.

To evaluate the ability of swept-source optical coherence tomography (SS-OCT) implemented with angiography analysis (SS-OCTA) to detect neuro-retinal and vasculature changes in patients with Parkinson's disease (PD) and essential tremor (ET), and to distinguish between both pathologies.A total 42 PD and 26 ET patients and 146 controls underwent retinal evaluation using SS-OCT plus OCT-Angio™. The macular (m) and peripapillary (p) retinal nerve fiber layer (RNFL) and ganglion cell layer (GCL), and macular vasculature were assessed. A Linear discriminant function (LDF) was calculated to evaluate the diagnostic ability of SS-OCTA in both PD and ET.PD patients presented a reduction in mRNFL (p 0.005), mGCL (all sectors, p 0.05) and pRNFL (p 0.005) vs healthy controls, and in mRNFL and pRNFL vs ET patients (p 0.001). ET patients showed a significant reduction in mGCL vs controls (p 0.001). No differences were observed in the macular vasculature between groups. Predictive diagnostic variables were significant only for PD and a LDF was obtained with an area under the ROC curve of 0.796.Neuro-retinal thinning is present in both diseases, being greater in PD. While SS-OCT could be useful in diagnosing ET and PD, the diagnostic potential for SS-OCTA based on an LDF applies only to PD, not ET.

Focal radiotherapy can promote cross-presentation of tumor antigens to T cells, but by itself, it is insufficient to induce therapeutically effective T-cell responses. The common gamma-chain cytokine IL15 promotes and sustains the proliferation and effector function of CD8+ T cells but has limited activity against poorly immunogenic tumors that do not elicit significant spontaneous T-cell responses. Here, we show that radiotherapy and subcutaneous IL15 had complementary effects and induced CD8+ T-cell–mediated tumor regression and long-term protective memory responses in two mouse carcinoma models unresponsive to IL15 alone. Mechanistically, radiotherapy-induced IFN type I production and Batf3-dependent conventional dendritic cells type 1 (cDC1) were required for priming of tumor-specific CD8+ T cells and for the therapeutic effect of the combination. IL15 cooperated with radiotherapy to activate and recruit cDC1s to the tumor. IL15 alone and in complex with a hybrid molecule containing the IL15α receptor have been tested in early-phase clinical trials in patients with cancer and demonstrated good tolerability, especially when given subcutaneously. Expansion of natural killer (NK) cells and CD8+ T cells was noted, without clear clinical activity, suggesting further testing of IL15 as a component of a combinatorial treatment with other agents. Our results provide the rationale for testing combinations of IL15 with radiotherapy in the clinic.

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Supplementary Fig. S3 from Efficacy and pharmacodynamic effects of bosutinib (SKI-606), a Src/Abl inhibitor, in freshly generated human pancreas cancer xenografts

Recently, Src tyrosine kinase has emerged as an attractive target for anticancer therapy, and Src is overexpressed in pancreatic cancer. The purpose of the study was to investigate the in vivo efficacy and pharmacodynamic effects of bosutinib (SKI-606), a Src/Abl inhibitor, using a panel of human pancreatic tumor xenografts. Surgically resected human pancreatic tumors were implanted into female nude mice and randomized to bosutinib versus control. Src and other pathways were analyzed by Western Blot, IHC, and Affymetrix U133 Plus 2.0 gene arrays. Of 15 patient tumors, 3 patient tumors were found to be sensitive to bosutinib, defined as tumor growth of

Background To evaluate alterations of the choroid in neurodegenerative disease patients versus healthy controls using a custom supervised algorithm based on superpixel segmentation. Methods The prospective study protocol and procedures were approved by the Aragon Research Ethics Committee (CEICA) according to Declaration of Helsinki. Informed consent was obtained from all participants included in the study. Swept-source optical coherence tomography (OCT) B-scan images obtained using a Triton (Topcon, Japan) device were compiled. Images were included from three cohorts: multiple sclerosis (MS) patients and Parkinson disease (PD) patients diagnosed by a neurologist, and healthy subjects. 104 OCT B-scan images were processed using a custom supervised superpixel segmentation (SpS) algorithm to detect boundary limits in the choroidal layer. The algorithm groups pixels with similar structural image properties to generate clusters with similar meaningful properties. SpS automatically selects and groups the superpixels in a segmented choroidal area, computing the choroidal optical image density (COID), the total choroidal area (CA), and choroid density (CD). Results CA and CD were significantly reduced in the two neurodegenerative diseases (higher in PD than in MS) versus healthy subjects (p

The antimicrobial resistance crisis calls for the discovery and production of new antimicrobials. Host defense peptides (HDPs) are small proteins with potent antibacterial and immunomodulatory activities that are attractive for translational applications, with several already under clinical trials. Traditionally, antimicrobial peptides have been produced by chemical synthesis, which is expensive and requires the use of toxic reagents, hindering the large-scale development of HDPs. Alternatively, HDPs can be produced recombinantly to overcome these limitations. Their antimicrobial nature, however, can make them toxic to the hosts of recombinant production. In this review we explore the different strategies that are used to fine-tune their activities, bioengineer them, and optimize the recombinant production of HDPs in various cell factories.

BACKGROUND: Cerebral Palsy (CP) and Spinal Muscular Atrophy (SMA) are common causes of motor disability in childhood. Gait exoskeletons are currently being used as part of rehabilitation for children with walking difficulties. OBJECTIVE: To assess the safety and efficacy and describe the main characteristics of the clinical articles using robot-assisted gait training (RAGT) with exoskeleton for children with CP or SMA. METHODS: A computer search was conducted in five bibliographic databases regarding clinical studies published in the last ten years. In order to be included in this review for further analysis, the studies had to meet the following criteria: (1) assess efficacy or safety of interventions; (2) population had to be children with CP or SMA aged between 3 and 14; (3) exoskeleton must be bilateral and assist lower limbs during walking. RESULTS: Twenty-one articles were selected, of which only five were clinical trials. 108 participants met the inclusion criteria for this study, all with a diagnosis of CP. The evidence level of the selected papers was commonly low. CONCLUSIONS: RAGT therapy seems to be safe for children with CP. However, further investigation is needed to confirm the results related to efficacy. There is no evidence of RAGT therapy for SMA children.

ObjectiveThe coronavirus disease 2019 (COVID-19) pandemic has demonstrated the value of real-world data for public health research. International federated analyses are crucial for informing policy makers. Common data models (CDMs) are critical for enabling these studies to be performed efficiently. Our objective was to convert the UK Biobank, a study of 500 000 participants with rich genetic and phenotypic data to the Observational Medical Outcomes Partnership (OMOP) CDM.Materials and MethodsWe converted UK Biobank data to OMOP CDM v. 5.3. We transformedparticipant research data on diseases collected at recruitment and electronic health records (EHRs) from primary care, hospitalizations, cancer registrations, and mortality from providers in England, Scotland, and Wales. We performed syntactic and semantic validations and compared comorbidities and risk factors between source and transformed data.ResultsWe identified 502 505 participants (3086 with COVID-19) and transformed 690 fields (1 373 239 555 rows) to the OMOP CDM using 8 different controlled clinical terminologies and bespoke mappings. Specifically, we transformed self-reported noncancer illnesses 946 053 (83.91% of all source entries), cancers 37 802 (70.81%), medications 1 218 935 (88.25%), and prescriptions 864 788 (86.96%). In EHR, we transformed 13 028 182 (99.95%) hospital diagnoses, 6 465 399 (89.2%) procedures, 337 896 333 primary care diagnoses (CTV3, SNOMED-CT), 139 966 587 (98.74%) prescriptions (dm+d) and 77 127 (99.95%) deaths (ICD-10). We observed good concordance across demographic, risk factor, and comorbidity factors between source and transformed data.Discussion and ConclusionOur study demonstrated that the OMOP CDM can be successfully leveraged to harmonize complex large-scale biobanked studies combining rich multimodal phenotypic data. Our study uncovered several challenges when transforming data from questionnaires to the OMOP CDM which require further research. The transformed UK Biobank resource is a valuable tool that can enable federated research, like COVID-19 studies.

Peer reviewed: True, Ordered Nanoporous Metals (ONMs) form a new family of nanoporous materials composed only of pure metals. The expected impact is considerable from combining the ordered nanopore structure of MOFs, zeolites and carbon schwartzites with the robustness and electronic conductivity of metals. Little is known about their stability and structural features. Here we address these points to provide clues toward their rational synthesis, introducing an automatic atomistic design that uses model building and molecular dynamics structural relaxation, and is validated against the experimentally known ONMs. Analysing the properties of the 10 stable structures out of the 17 studied (14 of which are designed in this work) using four noble metals (Pt, Pd, Au and Ag), we have deciphered some key elements and structural descriptors that provide guidelines for the experimental synthesis of ONMS. The long-lived metastability of the stable ONMs is evidenced by the high free energy landscape, computed via Metadynamic simulations. The new ONMs permit molecular diffusion of various molecules of industrial relevance, increasing the expectation for their use in catalysis, separation, nanofiltration, batteries, fuel cells, etc. Stable low-cost ONMs are predicted using Earth-abundant Ni metal, which maintains the main features of their relative noble metal forms.

Background: Current procedures for diagnosing multiple sclerosis (MS) present a series of limitations, making it critically important to identify new biomarkers. The aim of the study was to identify new biomarkers for the early diagnosis of MS using spectral-domain optical coherence tomography (OCT) and artificial intelligence. Methods: Spectral domain OCT was performed on 79 patients with relapsing-remitting multiple sclerosis (RRMS) (disease duration ≤ 2 years, no history of optic neuritis) and on 69 age-matched healthy controls using the posterior pole protocol that incorporates the anatomic Positioning System. Median retinal thickness values in both eyes and inter-eye difference in healthy controls and patients were evaluated by area under the receiver operating characteristic (AUROC) curve analysis in the foveal, parafoveal and perifoveal areas and in the overall area spanned by the three rings. The structures with the greatest discriminant capacity — retinal thickness and inter-eye difference — were used as inputs to a convolutional neural network to assess the diagnostic capability. Results: Analysis of retinal thickness and inter-eye difference in RRMS patients revealed that greatest alteration occurred in the ganglion cell (GCL), inner plexiform (IPL), and inner retinal (IRL) layers. By using the average thickness of the GCL (AUROC = 0.82) and the inter-eye difference in the IPL (AUROC = 0.71) as inputs to a two-layer convolutional neural network, automatic diagnosis attained accuracy = 0.87, sensitivity = 0.82, and specificity = 0.92. Conclusion: This study adds weight to the argument that neuroretinal structure analysis could be incorporated into the diagnostic criteria for MS.

Background and Aims: Anemia is a common complication of heart failure and Chronic Kidney Disease (CKD). Sacubitril-valsartan is a novel therapy for the treatment of chronic Heart Failure with a reduced Ejection Fraction (HFrEF). We have evaluated the short-term effects of sacubitril- valsartan on the anemia of CRS. Methods: The study group comprised 39 patients with HFrEF, who were followed-up for three months. The study is a retrospective analysis of clinical data. Data of 3 months’ and baseline visits were recorded including plasmatic creatinine, glomerular filtration rate, cystatin C, kaliemia, haemoglobin, pro-BNP, and albuminuria. Results: In all, 34 patients ended the follow-up. Mean sacubitril-valsartan dosage at baseline was 101 ± 62 mg/day and 126 ± 59 mg/day at end. Mean hemoglobin increased from 12.2 ± 1.1 g/dl at baseline to 12.9 ± 1.0 g/dl (p = 0.001,). Prevalence of anemia was 64.7% (95%CI, 47.9-78.5%) at baseline and 38.4 (95%CI, 23.9-55.0%) after the follow-up (p = 0.016). Serum cystatin C levels decreased from 2.71 ± 1.0 to 2.48 ± 1.0 mg/l (p = 0.028). Serum K levels remained unchanged (baseline 4.94 ± 0.60, three months visit 4.94 ± 0.61 mmol/l, p = 0.998). Conclusions: Sacubitril-valsartan improves anemia in CRS patients. An improvement in serum cystatin levels was observed. Few untoward effects were detected. These findings should be confirmed in wider clinical trials.

Often electronic tools are built with English proficient (EP) patients in mind. Cancer patients with limited English proficiency (LEP) experience gaps in care and are at risk for excess toxic effects if they are unable to effectively communicate with their care team.To evaluate whether electronic patient-reported outcome tools (ePROs) built to improve health outcomes for EP patients might also be acceptable for LEP patients in the context of oral cancer-directed therapies (OCDT).This qualitative study was conducted at a single National Cancer Institute-designated comprehensive cancer center. In 2019, English-speaking and Spanish-speaking LEP patients with cancer receiving oral chemotherapies were recruited to participate in a qualitative focus group examining patient attitudes toward ePROs and electronic tools that are used to manage adherence and symptoms related to oral therapies. Six focus groups were held for EP patients and 1 for Spanish-speaking LEP patients. LEP was defined as patients who self-identified as needing an interpreter to navigate the health care system. Data analysis was performed April through June of 2019.Enrolled patients participated in a focus group lasting approximately 90 minutes.The perspectives of patients with cancer treated with oral chemotherapies on integrating ePROs into their care management.Among the 46 participants included in the study, 46 (100%) were White, 10 (22%) were Latinx Spanish-speaking, 43 (93%) were female, and 37 (80%) were aged at least 50 years or older. Among the 6 focus groups with 6 to 8 EP patients (ranging from 6 to 8 participants) and 1 focus group with 10 Spanish-speaking LEP patients, this qualitative study found that EP and LEP patients had different levels of acceptability of using technology and ePRO tools to manage their OCDT. EP patients felt generally positive toward OCDT and were not generally interested in using electronic tools to manage their care. LEP patients generally disliked OCDT and welcomed the use of technology for health management, particularly when addressing gaps in symptom management by their oncology clinicians.Although most electronic interventions target EP patients, these findings reveal the willingness of LEP patients to participate in technology-based interventions. Expanding ePROs to LEP patients may help to manage gaps in communication about treatment and potential adverse events because of the willingness of LEP patients to use ePRO tools to manage their health. This qualitative assessment is a strategic step in determining the resources needed to narrow the digital health gap and extend the value of PROs to the LEP oncology population.

Introduction and objectives: Tumor infiltrating lymphocytes (TILs) and neutrophil-to-lymphocyte ratio (NLR) play a prognostic role in early stage breast cancer (BC). There is no evidence about the combined effect of both factors. Our objective was to evaluate the integrated clinical significance of TILs and NLR in patients with early BC treated with neoadjuvant therapy. Materials and methods: Retrospective, single-center analysis of a cohort of patients with early BC treated with neoadjuvant chemotherapy between 2001-2010. Pre-treatment TILs (CD3+-TIL count) was evaluated using a tumor tissue microarray. NLR was calculated within one month of cancer diagnosis. TILs (logarithmic transformed) and NLR were analyzed as continuous variables. Survival analysis was performed using multivariable Cox regression models. Results:A total of 121 patients were included. Median age: 56 years. Cancer stage at diagnosis: 16% IIA, 28% IIB, 33% IIIA, 7% IIIB and 16% IIIC. Molecular subtype: 64% hormone receptor(HR)-positive (12% HER2-positive), 11% HER2-positive HR-negative and 22% triple-negative. Pathological complete response (pCR): 16.5%. Median follow-up: 12 years. Pre-treatment TIL analysis was available in 71 patients (59%) and NLR in 101 (83%). There was no correlation between both variables (Spearman's Rho: 0.03, p = 0.98). In the univariate analysis, the NLR showed a negative prognostic value for overall survival (OS) (HR 1.23, 95%CI 1.11-1.36; p Citation Format: Esmeralda García-Torralba, Francisco Ayala de la Peña, Beatriz Alvarez-Abril, Pilar de la Morena Barrio, Alejandra Ivars Rubio, Elisa Garcia Garre, Gema Marin Zafra, Alberto Carmona-Bayonas, Elena Garcia Martinez. Prognostic significance of tumor-infiltrating lymphocytes and neutrophil-to-lymphocyte ratio in patients with breast cancer receivingneoadjuvant chemotherapy [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS6-45.

Introduction and objectives Pathologic complete response (pCR, ypT0/Tis ypN0) after neoadjuvant chemotherapy (nCT) in early breast cancer (BC) is associated with higher survival rate. Controversy about the prognostic significance of low-volume or micrometastatic axillary residual disease (ypN1mi-RD) exists. Essentially, it is considered equivalent to high-volume nodal disease (ypN1/ypN2-RD) for the indication of lymphadenectomy after nCT. Clarifying ypN1mi-RD prognostic value would be useful for planning adjuvant therapy. Thus, our objective was to assess the prognostic significance of ypN1mi-RD in the context of primary breast tumor pCR. Material and methodsRetrospective, single-center analysis of a cohort of early BC patients treated with nCT between 2010 and 2018 who achieved breast pCR (ypT0/Tis) combined with axillary pCR (ypN0) or ypN1mi-RD or ypN1/ypN2-RD. Cases with pre-nCT sentinel lymph node biopsy were excluded. 5-year disease-free survival (DFS) and overall survival (OS) were analyzed using Cox regression models.ResultsAmong 470 early BC patients treated with nCT, 134 (28.5%) had in-breast pCR, of whom: 97 (20.6%) were ypN0; 7 (1.5%) were ypN1mic; 10 (2.1%) were ypN1 and 5 (1.1%) were ypN2. Clinicopathological characteristics of the groups are shown in the Table. Median follow-up: 33 months. Eight patients relapsed, 4 of 97 with nodal pCR and 4 of 22 with axillary residual disease: 2/7 ypN1mic; 1/10 ypN1 and 1/5 ypN2. Patients who relapsed predominantly presented pre-nCT clinical lymph node involvement, hormone receptor negativity, ki67 Table. Clinicopathologic characteristics of the cohort of early BC patients treated with nCT betweenypT0/TisypT0/TisypN1mic-RDypN1/N2-RDpCR(N=7)(N=15)(N=97)Age (median, range)49 (25-83)47 (40-77)47 (25-80)Menstrual statusPostmenopausal3 (42,8%)4 (26,7%)42 (43,3%)Premenopausal4 (57,1%)11 (73,3%)55 (56,7%)ECOGECOG 05 (71,4%)13 (86,7%)78 (80,4%)ECOG 12 (28,5%)2 (13,3%)19 (19,6%)Histologic subtypeInvasive ductal carcinoma7(100,0%)14 (93,3%)95 (97,9%)Other subtypes0 (0,0%)1 (6,7%)2 (2,0%)Histologic gradeGrade 10 (0,0%)0 (0,0%)1 (1,0%)Grade 23 (42,9%)5 (33,3%)17 (17,5%)Grade 34 (57,1%)8 (53,3%)67 (69,1%)Unknown0 (0,0%)2 (13,3%)0 (0,0%)cTcT11 (14,2%)4 (26,7%)8 (8,2%)cT24 (57,1%)5 (33,3%)63 (64,9%)cT32 (28,6%)6 (40,0%)24 (24,7%)cT4a-d0 (0,0%)0 (0,0%)2 (2,1%)cNcN01 (14,3%)0 (0,0%)27 (27,8%)cN13 (42,9%)5 (33,3%)34 (35,1%)cN21 (14,3%)6 (40,0%)24 (24,7%)cN32 (28,6%)4 (26,7%)11 (11,3%)Molecular subtypeHR+ HER2-1 (14,3%)8 (53,3%)11 (11,3%)HR+ HER2+3 (42,9%)1 (6,7%)30 (30,9%)HR- HER2+2 (28,6%)3 (20,0%)21 (21,6%)TNBC1 (14,3%)3 (20,0%)35 (36,1%)Breast surgeryConservative7 (100%)10 (66,7%)67 (69,1%)Mastectomy0 (0,0%)5 (33,3%)30 (30,9%)Nodal surgerySLN biopsy0 (0,0%)0 (0,0%)22 (22,7%)ALND7 (100,0%)15 (100,0%)75 (77,3%)ypTypT05 (71,4%)7 (46,7%)80 (82,5%)ypTis2 (28,6%)8 (53,3%)17 (17,5%)Relapse typeMetastatic2 (28,6%)2 (28,6%)2 (2,1%)Local/contralateral0 (0,0%)0 (0,0%)2 (2,1%)Deaths0 (0,0%)1 (6,7%)1 (1,0%)BC: breast cancer. HR: hormone receptor. nCT: neoadjuvant chemotherapy. pCR: pathologic complete response. SLN: sentinel lymph node. TN: triple negative. ypN1mic-RD: micrometastatic axillary residual disease. ypN1/N2-RD: high-volume axillary residual disease. Citation Format: Esmeralda García-Torralba, Maria Esperanza Guirao Garcia, Pilar de la Morena Barrio, Alejandra Ivars Rubio, Elena Garcia Martinez, Elisa Garcia Garre, Gema Marin Zafra, Beatriz Alvarez Abril, Esther Navarro Manzano, Francisco Ayala de la Peña. Prognostic significance of residual micrometastatic axillary involvement with complete pathologic breast response after neoadjuvant chemotherapy for early breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS6-54.

Conventional anatomic models of the rodent (mammalian) amygdala are based on section planes oblique to its intrinsic radial glial organization. As a result, we still lack a model of amygdalar histogenesis in terms of radial units (progenitor domains and related radial migration and layering patterns). A radial model of the mouse pallial amygdala is first offered here, based on three logical steps: (1) analysis of amygdalar radial structure in variously discriminative genoarchitectonic material, using an optimal ad hoc section plane; (2) testing preliminary models with experiments labelling at the brain surface single packets of radial glia processes, to be followed into the ventricular surface across intervening predicted elements; (3) selection of 81 differential amygdalar gene markers and checking planar and radial aspects of their distribution across the model elements. This approach shows that subtle changes to the conventional schema of the amygdala allow a radial histogenetic model to be recognized, which is consistent with molecularly coded differential identities of its units and strata. It is expected that this model will help both causal studies of amygdalar developmental patterning and comparative evolutionary studies. It also may have potential impact on hodological and functional studies. Electronic supplementary material The online version of this article (10.1007/s00429-020-02097-4) contains supplementary material, which is available to authorized users.

The arrival of collaborative contexts to the global economic stage is a latent reality which threatens to change the traditional production models' operation. Likewise, concepts such as Industry 3.0 or even 4.0 refer to the possibility of providing customers and users with unimaginable possibilities compared to the industrial manufacturing inherited from the past centuries. Within this environment, the fabrication laboratories (FabLabs) emerge. In this chapter, the authors approach an exploratory perspective in order to make known the FabLab movement origin and further worldwide development with the intention to highlight their characteristics and the main difficulties they face nowadays. The growing importance that the FabLabs have achieved despite their novelty justifies the precise study of their characteristics according to the importance related to the strong expansion of these laboratories in this decade and its contribution to a major revolution in the collaborative environments associated with the digital manufacturing.

Data processing; DNA sequencing; Genomic analysis Tratamiento de datos; Secuenciación de ADN; Análisis genómico Tractament de dades; Seqüenciació d'ADN; Anàlisi genòmica Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Here we describe a method to target, multiplex and sequence at high coverage full-length human mitochondrial genomes as native single-molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks, that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. The long-read sequencing data is analysed with a pipeline where our custom-developed software, baldur, efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase and can accurately disentangle complex deletions. Our workflow is a tool for studying mtDNA variation and will accelerate mitochondrial research. This research has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824110 – EASI-Genomics (I.G.G.) and the ERC Synergy project BCLL@las under grant agreement No 810287 (I.G.G.). Institutional support was from the Spanish Instituto de Salud Carlos III, Fondo de Investigaciones Sanitarias and cofunded with ERDF funds (PI19/01772). We acknowledge the institutional support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the 2014–2020 Smart Growth Operating Program, to the EMBL partnership and institutional co-financing with the European Regional Development Fund (MINECO/FEDER, BIO2015-71792-P). We also acknowledge the support of the Centro de Excelencia Severo Ochoa, and the Generalitat de Catalunya through the Departament de Salut, Departament d’Empresa i Coneixement and the CERCA Programme to the institute.

To quantify visual and retinal changes in patients with bipolar disorder (BD) over 5 years, compared with controls.Thirty-eight patients with BD and 122 healthy subjects underwent visual acuity (VA) evaluation, contrast sensitivity vision testing (CSV) with the Pelli Robson and CSV 1000E tests, and retinal thicknesses measurement [ganglion cell layer (GCL) and retinal nerve fiber layer (RNFL)] using Spectralis Optical Coherence Tomography (OCT). All subjects were re-evaluated after 5 years. The relationship between progressive structural changes and disease duration was analyzed.Visual function parameters in BD patients remained unchanged during the follow-up period. A progressive decrease affecting macular and peripapillary RNFL thickness (Progressive axonal loss was detected in BD patients. Visual function parameters were not affected after the 5-year follow-up. Despite observed changes in the neuroretina of patients with BD, axonal degeneration in these patients seemed to be mild and might be slowed down by other factors, such as BD treatments.

Background CRISPR-based programmable transcriptional activators (PTAs) are used in plants for rewiring gene networks. Better tuning of their activity in a time and dose-dependent manner should allow precise control of gene expression. Here, we report the optimization of a Copper Inducible system called CI-switch for conditional gene activation in Nicotiana benthamiana. In the presence of copper, the copper-responsive factor CUP2 undergoes a conformational change and binds a DNA motif named copper-binding site (CBS). Results In this study, we tested several activation domains fused to CUP2 and found that the non-viral Gal4 domain results in strong activation of a reporter gene equipped with a minimal promoter, offering advantages over previous designs. To connect copper regulation with downstream programmable elements, several copper-dependent configurations of the strong dCasEV2.1 PTA were assayed, aiming at maximizing activation range, while minimizing undesired background expression. The best configuration involved a dual copper regulation of the two protein components of the PTA, namely dCas9:EDLL and MS2:VPR, and a constitutive RNA pol III-driven expression of the third component, a guide RNA with anchoring sites for the MS2 RNA-binding domain. With these optimizations, the CI/dCasEV2.1 system resulted in copper-dependent activation rates of 2,600-fold and 245-fold for the endogenous N. benthamiana DFR and PAL2 genes, respectively, with negligible expression in the absence of the trigger. Conclusions The tight regulation of copper over CI/dCasEV2.1 makes this system ideal for the conditional production of plant-derived metabolites and recombinant proteins in the field.

Hereditary spastic paraplegias (HSPs) are a group of inherited, progressive neurodegenerative conditions characterised by prominent lower-limb spasticity and weakness, caused by a length-dependent degeneration of the longest corticospinal upper motor neurons. While more than 80 spastic paraplegia genes (SPGs) have been identified, many cases arise from mutations in genes encoding proteins which generate and maintain tubular endoplasmic reticulum (ER) membrane organisation. The ER-shaping proteins are essential for the health and survival of long motor neurons, however the mechanisms by which mutations in these genes cause the axonopathy observed in HSP have not been elucidated. To further develop our understanding of the ER-shaping proteins, this study outlines the generation of novel in vivo and in vitro models, using CRISPR/Cas9-mediated gene editing to knockout the ER-shaping protein ADP-ribosylation factor-like 6 interacting protein 1 (ARL6IP1), mutations in which give rise to the HSP subtype SPG61. Loss of Arl6IP1 in Drosophila results in progressive locomotor deficits, emulating a key aspect of HSP in patients. ARL6IP1 interacts with ER-shaping proteins and is required for regulating the organisation of ER tubules, particularly within long motor neuron axons. Unexpectedly, we identified physical and functional interactions between ARL6IP1 and the phospholipid transporter oxysterol-binding protein-related protein 8 in both human and Drosophila model systems, pointing to a conserved role for ARL6IP1 in lipid homeostasis. Furthermore, loss of Arl6IP1 from Drosophila neurons results in a cell non-autonomous accumulation of lipid droplets in axonal glia. Importantly, treatment with lipid regulating liver X receptor-agonists blocked lipid droplet accumulation, restored axonal ER organisation, and improved locomotor function in Arl6IP1 knockout Drosophila. Our findings indicate that disrupted lipid homeostasis contributes to neurodegeneration in HSP, identifying a potential novel therapeutic avenue for the treatment of this disorder.

cBioPortal for Cancer Genomics is an open-source platform for interactive, exploratory analysis of large-scale clinico-genomic data sets. cBioPortal provides a suite of user-friendly visualizations and analyses, including OncoPrints, mutation “lollipop” plots, variant interpretation, group comparison, survival analysis, expression correlation analysis, alteration enrichment analysis, cohort and patient-level visualization. The public site (https://www.cbioportal.org) is accessed by >35,000 unique visitors each month and hosts data from >350 studies spanning individual labs and large consortia. In addition, at least 74 instances of cBioPortal are installed at academic institutions and companies worldwide. To better support all users, we unified our documentation (https://docs.cbioportal.org) and added a user guide and an ongoing series of ‘how-to’ videos to address common questions. In 2022 we added 32 studies (>38,000 samples) to the public site. In addition, we added a nonsynonymous tumor mutation burden (TMB) value for all samples and enhanced the TCGA PanCancer Atlas studies with DNA methylation and treatment data. All data is available in the cBioPortal Datahub: https://github.com/cBioPortal/datahub. We also host a dedicated instance for AACR Project GENIE, enabling access to the GENIE cohort of >165,000 clinically sequenced samples from 19 institutions (https://genie.cbioportal.org). The GENIE Biopharma Collaborative (BPC) enables the collection of comprehensive clinical annotations, including response, outcome, and treatment history. The first BPC cohorts are now available: ~2,000 non-small cell lung cancer samples and ~1,500 colorectal cancer samples. Support for multimodal data analysis has been a major focus, including several new integrations with external tools. Single cell data is now available in the CPTAC GBM study and can be visualized throughout cBioPortal, and via integration with cellxgene. On the patient page, H&E and mIF images can be visualized via integration with Minerva, and the genomic overview now integrates IGV. We continue to enhance existing features. In the study view, users can now add charts comparing categorical vs continuous data, and the plots tab includes a heatmap option. We replaced the existing fusion data type with a generalized structural variant data type that supports detailed information including breakpoints and orientation, to enable new visualizations and analyses. Pathway level analysis has been extended with a new integration with NDEx. cBioPortal is fully open source (https://github.com/cBioPortal/). Development is a collaborative effort among groups at Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children’s Hospital of Philadelphia, Princess Margaret Cancer Centre, Caris Life Sciences, Bilkent University and The Hyve. We welcome open source contributions from others in the cancer research community. Citation Format: Ino de Bruijn, Tali Mazor, Adam Abeshouse, Diana Baiceanu, Stephanie Carrero, Elena Garcia Lara, Benjamin Gross, David M. Higgins, Prasanna K. Jagannathan, Priti Kumari, Ritika Kundra, Bryan Lai, Xiang Li, James Lindsay, Aaron Lisman, Divya Madala, Ramyasree Madupuri, Angelica Ochoa, Yusuf Ziya Özgül, Oleguer Plantalech, Sander Rodenburg, Baby Anusha Satravada, Robert Sheridan, Lucas Sikina, Jessica Singh, S Onur Sumer, Yichao Sun, Pim van Nierop, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Sjoerd van Hagen, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Jianjiong Gao, Nikolaus Schultz. cBioPortal for Cancer Genomics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4256.

Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Long-read whole genome sequencing is prohibitively expensive for mtDNA heteroplasmy detection and often does not recapitulate the full mtDNA length.Here we describe a method to target, multiplex and sequence full-length, native single-molecule the human mitochondrial genome utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks as barcodes with long-read sequencing, we implemented a protocol in an optimal setting for both high or low integrity genomic DNA to target the circular mitochondrial genome with extremely high coverage. Our analytical pipeline efficiently detects single nucleotide heteroplasmy, physically determines phase and can accurately disentangle complex deletion patterns. This workflow is a unique tool for studying mtDNA variation in health and disease, and will accelerate mitochondrial research.

Despite substantial development of production and purification protocols for heterologous recombinant proteins, some proteins are difficult to produce or, when produced, are accumulated in inclusion bodies (IBs). Nondenaturing protocols can be used to recover the entrapped protein from these protein aggregates. In this chapter, we provide a detailed procedure to analyze the physicochemical properties of one of those proteins produced in prokaryotic expression systems. Serum amyloid A3 (SAA3) was recovered from inclusion bodies (IBs) and its secondary structure associated to thermal stability and size was determined by circular dichroism (CD) and dynamic light scattering (DLS), respectively. These techniques were also applied to evaluate the SAA3 interaction with model membranes. These results show the importance of the structural analysis of proteins released from inclusion bodies under nondenaturing procedures, although similar approaches can be extended to any type of recombinant protein preparation.

Proteins are synthesized in heterologous systems because of the impossibility to obtain satisfactory yields from natural sources. The efficient production of soluble and functional recombinant proteins is among the main goals in the biotechnological field. In this context, it is important to point out that under stress conditions, protein folding machinery is saturated and this promotes protein misfolding and, consequently, protein aggregation. Thus, the selection of the optimal expression organism and its growth conditions to minimize the formation of insoluble protein aggregates should be done according to the protein characteristics and downstream requirements. Escherichia coli is the most popular recombinant protein expression system despite the great development achieved so far by eukaryotic expression systems. Besides, other prokaryotic expression systems, such as lactic acid bacteria and psychrophilic bacteria, are gaining interest in this field. However, it is worth mentioning that prokaryotic expression system poses, in many cases, severe restrictions for a successful heterologous protein production. Thus, eukaryotic systems such as mammalian cells, insect cells, yeast, filamentous fungus, and microalgae are an interesting alternative for the production of these difficult-to-express proteins.

Purification of inclusion bodies (IBs) is gaining importance due to the raising of novel applications for these submicron particulate protein clusters, with potential uses in the biomedical and biotechnological fields among others. Here, we present five optimized methods to purify IBs adapting classical procedures to the material nature, as well as the requirements of the producer cell (Gram-negative bacteria, Gram-positive bacteria, or yeast) and the IB final application.

Since inclusion bodies (IBs) contain an important amount of properly folded and active proteins, their solubilization using nondenaturing conditions to obtain aggregation-prone proteins has gained interest. Through these conditions, the refolding step is no longer required, which avoids the usual protein yield loss after this process. Here, we reveal a simple methodology to obtain pure and active difficult-to-produce proteins using two LPS-free expression systems: Lactococcus lactis and Lactobacillus plantarum. This protocol has proven to be successful to obtain proteins which are labile and prone-to-attach (difficult to be purified from other cytoplasmic proteins) and prone-to-aggregate (difficult to be obtained in their soluble form).