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Contains fulltext : 282509.pdf (Publisher’s version ) (Open Access) Although the genomic and immune microenvironmental landscape of follicular lymphoma (FL) has been extensively investigated, little is known about the potential biological differences between stage I and stage III/IV disease. Using next-generation sequencing and immunohistochemistry, 82 FL nodal stage I cases were analyzed and compared with 139 FL stage III/IV nodal cases. Many similarities in mutations, chromosomal copy number aberrations, and microenvironmental cell populations were detected. However, there were also significant differences in microenvironmental and genomic features. CD8+ T cells (P = .02) and STAT6 mutations (false discovery rate [FDR]

Large B-cell lymphoma of immune-privileged sites (LBCL-IP) arise in immune sanctuaries including the testis and central nervous system (CNS). After initially reaching complete response, relapses occur in almost 50% of patients, typically at other immune-privileged sites. Resolution of the clonal relationships and evolutionary patterns of LBCL-IP is required to understand the unique clinical behavior. We collected a unique set of 33 primary–relapse LBCL-IP sample pairs and performed next-generation sequencing for copy number, mutation, translocation, and immunoglobulin clonality analysis. All LBCL-IP sample pairs were clonally related, and both tumors developed from a common progenitor cell (CPC) with MYD88 and TBL1XR1 mutations and/or BCL6 translocations in 30/33 cases, indicating that these are early genetic events. This was succeeded by intermediate genetic events including shared, as well as unique alterations in targets of aberrant somatic hypermutation (aSHM), CD79B mutations, and 9p21.3/CDKN2A loss. Genetic alterations in genes involved in immune escape (HLA, CD274/PDCD1LG2) were predominantly unique in primary and relapse samples and thus considered late genetic events. Together, this study indicates that primary and relapsed LBCL-IP follow an early parallel evolutionary pattern where the CPC contains genetic alterations that support prolonged survival/proliferation and retention in a memory B-cell state, followed by germinal center reentry, aSHM and immune escape. Significance: Genomic analyses reveal that primary and relapse LBCL-IP originate from a common progenitor cell with a small set of genetic alterations, followed by extensive parallel diversification, elucidating the clonal evolution of LBCL-IP.

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Large B-cell lymphoma of immune-privileged sites (LBCL-IP) arise in immune sanctuaries including the testis and central nervous system (CNS). After initially reaching complete response, relapses occur in almost 50% of patients, typically at other immune-privileged sites. Resolution of the clonal relationships and evolutionary patterns of LBCL-IP is required to understand the unique clinical behavior. We collected a unique set of 33 primary–relapse LBCL-IP sample pairs and performed next-generation sequencing for copy number, mutation, translocation, and immunoglobulin clonality analysis. All LBCL-IP sample pairs were clonally related, and both tumors developed from a common progenitor cell (CPC) with MYD88 and TBL1XR1 mutations and/or BCL6 translocations in 30/33 cases, indicating that these are early genetic events. This was succeeded by intermediate genetic events including shared, as well as unique alterations in targets of aberrant somatic hypermutation (aSHM), CD79B mutations, and 9p21.3/CDKN2A loss. Genetic alterations in genes involved in immune escape (HLA, CD274/PDCD1LG2) were predominantly unique in primary and relapse samples and thus considered late genetic events. Together, this study indicates that primary and relapsed LBCL-IP follow an early parallel evolutionary pattern where the CPC contains genetic alterations that support prolonged survival/proliferation and retention in a memory B-cell state, followed by germinal center reentry, aSHM and immune escape.Significance:Genomic analyses reveal that primary and relapse LBCL-IP originate from a common progenitor cell with a small set of genetic alterations, followed by extensive parallel diversification, elucidating the clonal evolution of LBCL-IP.

In routine diagnostic pathology, cancer biopsies are preserved by formalin-fixed, paraffin-embedding (FFPE) procedures for examination of (intra-) cellular morphology. Such procedures inadvertently induce DNA fragmentation, which compromises sequencing-based analyses of chromosomal rearrangements. Yet, rearrangements drive many types of hematolymphoid malignancies and solid tumors, and their manifestation is instructive for diagnosis, prognosis, and treatment. Here, we present FFPE-targeted locus capture (FFPE-TLC) for targeted sequencing of proximity-ligation products formed in FFPE tissue blocks, and PLIER, a computational framework that allows automated identification and characterization of rearrangements involving selected, clinically relevant, loci. FFPE-TLC, blindly applied to 149 lymphoma and control FFPE samples, identifies the known and previously uncharacterized rearrangement partners. It outperforms fluorescence in situ hybridization (FISH) in sensitivity and specificity, and shows clear advantages over standard capture-NGS methods, finding rearrangements involving repetitive sequences which they typically miss. FFPE-TLC is therefore a powerful clinical diagnostics tool for accurate targeted rearrangement detection in FFPE specimens., Preservation of cancer biopsies by FFPE introduces DNA fragmentation, hindering analysis of rearrangements. Here the authors introduce FFPE Targeted Locus Capture for identification of translocations in preserved samples.

Breast implant–associated anaplastic large cell lymphoma (BIA-ALCL) is a very rare type of T-cell lymphoma that is uniquely caused by a single environmental stimulus. Here, we present a comprehensive genetic analysis of a relatively large series of BIA-ALCL (n = 29), for which genome-wide chromosomal copy number aberrations (CNAs) and mutational profiles for a subset (n = 7) were determined. For comparison, CNAs for anaplastic lymphoma kinase (ALK)− nodal anaplastic large cell lymphomas (ALCLs; n = 24) were obtained. CNAs were detected in 94% of BIA-ALCLs, with losses at chromosome 20q13.13 in 66% of the samples. Loss of 20q13.13 is characteristic of BIA-ALCL compared with other classes of ALCL, such as primary cutaneous ALCL and systemic type ALK+ and ALK− ALCL. Mutational patterns confirm that the interleukin-6–JAK1–STAT3 pathway is deregulated. Although this is commonly observed across various types of T-cell lymphomas, the extent of deregulation is significantly higher in BIA-ALCL, as indicated by phosphorylated STAT3 immunohistochemistry. The characteristic loss of chromosome 20 in BIA-ALCL provides further justification to recognize BIA-ALCL as a separate disease entity. Moreover, CNA analysis may serve as a parameter for future diagnostic assays for women with breast implants to distinguish seroma caused by BIA-ALCL from other causes of seroma accumulation, such as infection or trauma.

El presente documento aborda la contextualización del proyecto ALFENIC, comprendido en la producción y comercialización de caramelos de alfeñique el cual se fundamentó esta idea creativa en la imagen e innovación justificada por medio de las metodologías como el Desing Thinking, Modelo Canvas y el método del embudo siendo las herramientas fundamentales que permitiendo el desarrollo del producto con la incursión de soluciones innovadores y valor agregado. Por consiguiente, este proyecto se fundamentó por medio del Estudio de mercado en donde se recopilo la información necesaria para la selección del segmento, apoyado por investigación y sondeos de mercado que facilito información para las combinaciones de las estrategias competitivas de acuerdo al tipo de segmento seleccionado. Es por eso, que la realización del plan de producción en combinación con los resultados de dicho estudio de mercado permitió la planificación adecuada en cuanto al número de productos y de maquinaria. Igualmente, la estructura del plan de organización y gestión se detalló las principales leyes, reglamentos y requisitos que benefician la integración de la organización de ALFENIC y la importancia del bienestar de los colaboradores los cuales son el pilar fundamental de esta microempresa. Finalmente se realizó un plan financiero donde se proyectó una rentabilidad del 133% sobre el proyecto, cifra que se obtuvo de la división de la utilidad neta del ejercicio al primer año de operaciones entre la inversión inicial requerida para dar marcha al funcionamiento productivo de la organización.

TO THE EDITOR: In rare instances, malignant lymphomas present as a body cavity–based effusion, without an identifiable tumor mass. Most frequently, this concerns primary effusion lymphoma (PEL), a human herpes virus-8 (HHV8)-positive B-cell lymphoma that typically occurs in HIV-positive patients

Chromosomal translocations with immunoglobin (IG) loci are the classic drivers in a large subset of B-cell lymphomas. Detection of these translocations is important for confirmation of diagnosis and for prognosis and therapy decisions. Currently, molecular diagnosis of translocations in lymphomas is not addressed well by next-generation sequencing (NGS). The standard method for detection of translocations is fluorescence in situ hybridization (FISH), which is labor intensive and can be difficult to interpret. There is a need for a robust technology that can be standardized. Targeted Locus Capture (TLC) selectively enriches and sequences entire genes based on the crosslinking of physically proximal sequences, and thereby enables complete sequencing of genes of interest, including detection of large structural variants. Because the technology is based on the crosslinking and fragmenting of DNA, it has particular advantages in the analysis of formalin-fixed, paraffin-embedded (FFPE) samples in which DNA is inherently crosslinked and fragmented. In order to validate the FFPE-TLC technology as a novel approach for translocation detection in lymphoma samples, we have developed a panel assay containing genes with frequent translocations (MYC, BCL2, BCL6, IG loci). With this assay we have analyzed >140 lymphoma and control FFPE samples of variable input amounts and qualities that had previously been analyzed with FISH, and a subset also with standard targeted NGS. Good concordance with FISH results was observed for both translocation-positive and -negative samples. In 10 cases for which FFPE-TLC analysis resulted in a different finding than FISH, discordance could be explained by higher sensitivity of FFPE-TLC or by inconclusive FISH results. In a specific case, FFPE-TLC detected a small-distance rearrangement on chromosome 3 that caused a BCL6 fusion but led to insufficient and therefore undetectable break-apart with FISH. Secondly, the FFPE-TLC approach was tested on a set of 19 B-cell lymphoma FFPE samples that had previously been analyzed using standard targeted NGS and FISH and was enriched for discordant results between these methods. FFPE-TLC-based NGS enables more robust translocation calling as the detection relies on broad sequencing coverage across the translocation partner rather than on breakpoint sequences only. In 3 cases, FFPE-TLC could proof false negative calls in standard targeted NGS due to breakpoints located in regions difficult to capture or to sequence. In 1 case, standard targeted NGS had made a false positive call on a breakpoint sequence that was shown to be caused by a small insertion rather than a genuine translocation. This study shows that FFPE-TLC promises to be a robust alternative for FISH analysis and standard targeted NGS procedures in lymphoma diagnostics and in other cancers with frequent structural variants. The FFPE-TLC approach enables a single, DNA-based NGS test detecting both small mutations and translocations. Citation Format: Amin Allahyar, Mark Pieterse, Joost Swennenhuis, Tjitske Los-de Vries, Mehmet Yilmaz, Roos Leguit, Ruud Meijers, Nathalie Hijmering, Daphne de Jong, Bauke Ylstra, Robert van der Geize, Joost Vermaat, Arjen Cleven, Tom van Wezel, Arjan Diepstra, Leon van Kempen, Karima Hajo, Harma Feitsma, Marieke Simonis, Max van Min, Erik Splinter, Wouter de Laat. Robust detection of translocations in lymphoma FFPE samples using Targeted Locus Capture-based sequencing [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-45.

Atmospheric concentrations of Botrytis cinerea conidia were monitored for two seasons in a strawberry crop in Moguer (Huelva, southwestern Spain). Concentrations of conidia were estimated using a Burkard volumetric spore sampler. A diurnal pattern of conidial release was observed. Airborne conidial concentration was significantly and positively correlated with the average solar radiation and mean temperature, and negatively with rainfall and relative humidity. Among the weather variables considered, solar radiation showed the most consistent results in the regression analysis, explaining over 40% of airborne conidial concentration variability. Correlation between Botrytis fruit rot incidence and accumulated number of conidia over seven days was significant and positive. Two regression models containing three variables explained over 62 and 52% of the fruit rot incidence variability. A positive but non-significant correlation was established between B. cinerea incidence in flowers and airborne conidial concentration. It was not possible to fit a consistent regression model to relate flower infection incidence to conidial concentration or weather variables.

[The calanoid copepod, Boeckella poopoensis Marsh, 1906 inhabits shallow saline ponds located in the Andes mountains in Argentina, Bolivia, Chile, and Peru, as well as in the plains of southern Argentina. The species is halophilic and can tolerate salinity levels of 1 to 90 ppt. This paper describes the relative abundance of the species in shallow mountain ponds in northern Chile from 23° to 27° S. A direct correlation was observed between salinity and the relative abundance of B. poopoensis (r2 = 0.4139), and between 45 and 90 ppt S the species was found to be dominant in zooplankton assemblages. Crustacean species richness at the sites studied showed a significant, inverse trend with salinity (r2 = 0.7329), and this trend became even stronger (r2 = 0.7681) when data previously published for the Bolivian Andean plateau were included. Ecological and biogeographical issues related with these results are discussed. El copepodo calanoideo Boeckella poopoensis Marsh, 1906 vive en lagunas salinas poco profundas localizadas en el altiplano Andino de Argentina, Bolivia, Chile y Peru, y en el sur de Argentina. Esta especie es marcadamente halofilica, y tolera salinidades entre 1 y 90 g/l, estos habitats tienen una pobre riqueza especifica de crustaceos zooplanctonicos. Este estudio describe la abundancia relativa de esta especie en lagunas poco profundas de montana en el norte de Chile, entre los 23 y 27 grados sur de latitud. Se observo una relacion directa notoria entre la salinidad y la abundancia relativa de B. poopoensis (r2 = 0.4139), encontrandose practicamente esta especie como habitante exclusivo a salinidades superiores entre 45 g/l y 90 g/l, lo que coincide con las descripciones de la literatura. La riqueza especifica de especies de crustaceos presento una relacion inversa notoria con la salinidad en los sitios estudiados (r2 = 0.7329), lo cual fue mas robusto al incorporar informacion publicada para el Altiplano de Bolivia (r2 = 0.7681). En este estudio se discutieron implicancias ecologicas y biogeograficas relacionadas con los resultados observados., The calanoid copepod, Boeckella poopoensis Marsh, 1906 inhabits shallow saline ponds located in the Andes mountains in Argentina, Bolivia, Chile, and Peru, as well as in the plains of southern Argentina. The species is halophilic and can tolerate salinity levels of 1 to 90 ppt. This paper describes the relative abundance of the species in shallow mountain ponds in northern Chile from 23° to 27° S. A direct correlation was observed between salinity and the relative abundance of B. poopoensis (r2 = 0.4139), and between 45 and 90 ppt S the species was found to be dominant in zooplankton assemblages. Crustacean species richness at the sites studied showed a significant, inverse trend with salinity (r2 = 0.7329), and this trend became even stronger (r2 = 0.7681) when data previously published for the Bolivian Andean plateau were included. Ecological and biogeographical issues related with these results are discussed. El copepodo calanoideo Boeckella poopoensis Marsh, 1906 vive en lagunas salinas poco profundas localizadas en el altiplano Andino de Argentina, Bolivia, Chile y Peru, y en el sur de Argentina. Esta especie es marcadamente halofilica, y tolera salinidades entre 1 y 90 g/l, estos habitats tienen una pobre riqueza especifica de crustaceos zooplanctonicos. Este estudio describe la abundancia relativa de esta especie en lagunas poco profundas de montana en el norte de Chile, entre los 23 y 27 grados sur de latitud. Se observo una relacion directa notoria entre la salinidad y la abundancia relativa de B. poopoensis (r2 = 0.4139), encontrandose practicamente esta especie como habitante exclusivo a salinidades superiores entre 45 g/l y 90 g/l, lo que coincide con las descripciones de la literatura. La riqueza especifica de especies de crustaceos presento una relacion inversa notoria con la salinidad en los sitios estudiados (r2 = 0.7329), lo cual fue mas robusto al incorporar informacion publicada para el Altiplano de Bolivia (r2 = 0.7681). En este estudio se discutieron implicancias ecologicas y biogeograficas relacionadas con los resultados observados.]

Amino acid Asp-351 in the ligand binding domain of estrogen receptor alpha (ERalpha) plays an important role in regulating the estrogen-like activity of selective estrogen receptor modulator-ERalpha complexes. 4-Hydroxytamoxifen is a full agonist at a transforming growth factor alpha target gene in situ in MDA-MB-231 human breast cancer cells stably transfected with the wild-type ERalpha. In contrast, raloxifene (Ral), which is also a selective estrogen receptor modulator, is a complete antiestrogen in this system. Because D351G ERalpha allosterically silences activation function-1 activity in the 4-hydroxytamoxifen-ERalpha complex with the complete loss of estrogen-like activity, we examined the converse interaction of amino acid 351 and the piperidine ring of the antiestrogen side chain of raloxifene to enhance estrogen-like action. MDA-MB-231 cells were either transiently or stably transfected with Asp-351 (the wild type), D351E, D351Y, or D351F ERalpha expression vectors. Profound differences in the agonist and antagonist actions of Ralcenter dotERalpha complexes were noted only in stable transfectants. The agonist activity of the Ralcenter dotERalpha complex was enhanced with D351E and D351Y ERalpha, but raloxifene lost its agonist activity with D351F ERalpha. The distance between the piperidine nitrogen of raloxifene and the negative charge of amino acid 351 was critical for estrogen-like actions. The role of the piperidine ring in neutralizing Asp-351 was addressed using compound R1h, a raloxifene derivative replacing the nitrogen on its piperidine ring with a carbon to form cyclohexane. The derivative was a potent agonist with wild type ERalpha. These results support the concept that the side chain of raloxifene shields and neutralizes the Asp-351 to produce an antiestrogenic ERalpha complex. Alteration of either the side chain or its relationship with the negative charge at amino acid 351 controls the estrogen-like action at activating function 2b of the selective estrogen receptor modulator ERalpha complex.

We report on a search for extremely-high energy neutrinos with energies greater than $10^6$ GeV using the data taken with the IceCube detector at the South Pole. The data was collected between April 2008 and May 2009 with the half completed IceCube array. The absence of signal candidate events in the sample of 333.5 days of livetime significantly improves model independent limit from previous searches and allows to place a limit on the diffuse flux of cosmic neutrinos with an $E^{-2}$ spectrum in the energy range $2.0 \times 10^{6}$ $-$ $6.3 \times 10^{9}$ GeV to a level of $E^2 \phi \leq 3.6 \times 10^{-8}$ ${\rm GeV cm^{-2} sec^{-1}sr^{-1}}$., Comment: 9 pages, 4 figures. This corresponds to the paper Phys.Rev.D 83, 092003(2011), and its erratum Phys.Rev.D 84, 079902(2011)

Laparoscopic radical cystectomy has been developed after the expansion of laparoscopic radical prostatectomy. This technique makes possible a minimally invasive approach to muscle-invasive bladder cancer with less blood loss and faster postoperative recovery.From September 2004 to January 2007, 54 laparoscopic radical cystectomies were performed, 48 of them in stage T2, from which 43 (90%) were male and 5 (10%) female patients. Mean age was 64 years (27-881. Lymphadenectomy was carried out by laparoscopic approach in all cases, with a mean of 13 nodes obtained (4-24). Urinary diversion was done through the incision needed to extract the specimen in all cases but one that was completed completely intracorporeally; constructing a Bricker-type ureteroileostomy in 30 (62%) cases, orthotopic neobladder (Vesica Ileale Padovana) in 17 cases (35%), and cutaneous ureterostomy in 1 case (2%).Mean surgical time for the whole procedure was 287 minutes (180-480), 270 minutes for Bricker-type derivation cases and 316 minutes for neobladder cases. Blood transfusion rate was 25%. Mean ileal paralysis was 5 days (2-10) with a mean hospital stay of 13 days (6-34) for Bricker cases and 16 days (8-30) for neobladder cases. Oncological control, after a mean follow-up of 10,8 months (0,4-30), showed a cancer-specific survival of 90% with a mean survival time of 28 months (95% CI 26-30). Global mean survival was 79% with a mean survival of 26 months (95% CI 23-29).Laparoscopic radical cystectomy is a feasible technique that offers some advantages. It allows excision with less blood loss and an easier postoperative period. Randomized studies should demonstrate these advantages to confirm this approach as the technique of choice. Urinary diversion performed through the laparotomy incision, necessary to extract the specimen, optimizes derivation results and whole surgical time without reducing the beneficial effects of the laparoscopic exeresis.

We present a new case of splenogonadal fusion in a 27 years old male. This anomaly is the result of an embryological fusion between gonad and spleen. Occasionally there is an association with other congenital alterations (peromelia). Usually it occurs in the left scrotum and, although described in both sexes, it is more frequent in males. Its only symptom is palpable tumor and this makes the surgical approach the only way to make the diagnosis. A frozen section study can avoid unnecessary radical surgery.

To evaluate the differences between laparoscopic (LRP) and open radical prostatectomy (ORP).From 2004 to 2005 180 Radical prostatectomies (RP) were performed, 105 laparoscopical and 75 by an open approach. Different urologists have acted as first surgeon; 51% of them, fully experienced ones in OPR, and 56% in LRP. Differences in operative time, estimated blood loss (difference of pre and post operative hematocrite), and duration of hospitalization were compared. Additionally, we have also analysed surgical and oncologic control of the specimen defined by the following variables: Malignant margins (MM) (positive margin in a pT3 specimen), and benign/malign surgical incision (BSI/MSI).Groups were similar concerning age, clinical stage and Gleason score, and there are only differences in PSA. Mean operative time was significantly higher in LRP (172 minutes) versus ORP (145 minutes) (p0.001). Difference of pre and post operative hematocrite was also higher in the open group (10.7 vs 9.2) (p = 0.03), together with hospital stay, which was one day longer in the ORP group (p = 0.001). ORP group had a higher rate of benign surgical incisions (48.7% vs 26.7%) (p = 0.001). Regarding oncologic results, LRP presented a 5.4% of positive margins, which compared significantly with a 16.9% rate in the open group (p = 0.023). However, no differences concerning malignant surgical incisions were observed.With no differences in clinical and pathological stage, LRP offers a significant reduction of surgical aggressiveness on the specimen, together with a better MM control. We also observe a clear decrease in blood loss and hospital stay. Therefore, we conclude that LRP in our environment is a valid approach of surgical prostate cancer treatment in spite of a longer operative time (27 minutes) and a steep learning curve.

To determine the epidemiological situation of Chronic Hepatitis C (CHC) in our country.Chronic Hepatitis C affects 170 million people worldwide, and about 0.7% of Mexican population. There is no enough epidemiological information about CHC in our country, and it is very probable that some cases are not even detected.An investigation poll was performed. Age, gender, birthday, weight, race, residence and birth place, routes of transmission, ALT levels, histological, serological and molecular diagnosis, evidence of complications and previous treatments were recorded. A data recollection sheet was dispatched to different country provinces; they had 6 months to answer it, in order to recollect all information.831 patients were analized (58.6% female and 41.4% male) with the following distribution in our country provinces: Aguascalientes 15, Chihuahua 12, Distrito Federal 495, Durango 10, Jalisco 89, Guanajuato 78, Yucatán 8, Querétaro 11, Sonora 40, Tabasco 15, Baja California 5, Veracruz 13, Tamaulipas 2 and 38 patients of Nuevo León. The highest incidence of CHC was found at fifth and sixth decade of life (28.5% y 26.7% respectively. The weight distribution was 36.2%65kg, 34.6% 65-75 kg and 29.2%75 kg. 86.5% had chronic hepatitis and 13.2% cirrhosis. The risk factors for HCV infection analysis showed that the main route of transmission was via contaminated blood (64.2%); when we excluded the patients that were exposed before 1995, the incidence was lowered to 4.5%. The higher incidence was showed between 1970 and 1990 (68%). The intravenous drug users were predominantly male and on those patients in the provinces near the north border line of our country. The predominant genotype was gen- 1 no matter the province (72.2%), in the intravenous drug users genotype 3 was found in 25%. The viral load was similar in all the provinces. 75% of the patients had have treatment and 22.5% had have two cycles, 50% of cirrhotic patients had have treatment whereas only 28% of the patients with late complications had have it. The most common treatment was pegylated alpha-2a interferon plus ribavirine.1. The main route of transmission was blood transfusion. There is a marked decrease in the incidence of post-transfusional hepatitis since the introduction of anti-VHC antibody screening of blood donors (4.5%). 2. The time between the infection and diagnosis was 23 years for chronic hepatitis and 26 years for cirrhosis. 3. Intravenous drugs use was an important route of transmission in the north of our country. 4. The predominant genotype was gen-1. 5. Almost all the patients with chronic hepatitis received treatment, the most common used was pegylated interferon alpha-2a and ribavirin. 6.50% of the patients with CHC have late complications.