Analysis of small-scale soil CO2 fluxes in an orange orchard under irrigation and soil conservative practices

The quantification of soil carbon dioxide (CO2) flux represents an indicator of the agro-ecosystems sustainability. However, the monitoring of these fluxes is quite challenging due to their high spatially-temporally variability and dependence on environmental variables and soil management practices.In this study, soil CO2 fluxes were measured using a low-cost accumulation chamber, that was realized ad hoc for the surveys, in an orange orchard managed under different soil management (SM, bare versus mulched soils) and water regime (WR, full irrigation versus regulated deficit irrigation) strategies. In particular, the soil CO2 flux measurements were acquired in discontinuous and continuous modes, together with ancillary agrometeorological and soil-related information, and then compared to the agrosystem scale CO2 fluxes measured by the eddy covariance (EC) technique.Overall significant differences were obtained for the soil CO2 discontinuous fluxes as function of the WR (0.16 ± 0.01 and 0.14 ± 0.01 mg m-2 s-1 under full irrigation and regulated deficit irrigation, respectively). For the continuous soil CO2 measurements, the response observed for the SM factor varied from year to year, indicating for the overall reference period 2022-23 higher soil CO2 flux under the mulched soils (0.24 ± 0.01 mg m-2 s-1) than under bare soil conditions (0.15 ± 0.00 mg m-2 s-1). Inter-annual variations were also observed as function of the day-of-year (DOY), the SM and their interactions, resulting in higher soil CO2 flux under the mulched soils (0.24 ± 0.02 mg m-2 s-1) than under bare soil (0.15 ± 0.01 mg m-2 s-1) in certain periods of the years, according to the environmental conditions.

Results

suggest the importance of integrating soil CO2 flux measurements with ancillary variables that explain the variability of the agrosystem and the need to conduct the measurements using different operational modalities, also providing for night-time monitoring of CO2. In addition, the study underlines that the small-scale chamber measurements can be used to estimate soil CO2 fluxes at orchard scale if fluxes are properly scaled.

phuEGO: A Network-Based Method to Reconstruct Active Signaling Pathways From Phosphoproteomics Datasets

Signaling networks are critical for virtually all cell functions. Our current knowledge of cell signaling has been summarized in signaling pathway databases, which, while useful, are highly biased toward well-studied processes, and do not capture context specific network wiring or pathway cross-talk. Mass spectrometry-based phosphoproteomics data can provide a more unbiased view of active cell signaling processes in a given context, however, it suffers from low signal-to-noise ratio and poor reproducibility across experiments. While progress in methods to extract active signaling signatures from such data has been made, there are still limitations with respect to balancing bias and interpretability. Here we present phuEGO, which combines up-to-three-layer network propagation with ego network decomposition to provide small networks comprising active functional signaling modules. PhuEGO boosts the signal-to-noise ratio from global phosphoproteomics datasets, enriches the resulting networks for functional phosphosites and allows the improved comparison and integration across datasets. We applied phuEGO to five phosphoproteomics data sets from cell lines collected upon infection with SARS CoV2. PhuEGO was better able to identify common active functions across datasets and to point to a subnetwork enriched for known COVID-19 targets. Overall, phuEGO provides a flexible tool to the community for the improved functional interpretation of global phosphoproteomics datasets.

Integrated systems biology approach identifies gene targets for endothelial dysfunction

Endothelial dysfunction (ED) is critical in the development and progression of cardiovascular (CV) disorders, yet effective therapeutic targets for ED remain elusive due to limited understanding of its underlying molecular mechanisms. To address this gap, we employed a systems biology approach to identify potential targets for ED. Our study combined multi omics data integration, with siRNA screening, high content imaging and network analysis to prioritise key ED genes and identify a pro- and anti-ED network. We found 26 genes that, upon silencing, exacerbated the ED phenotypes tested, and network propagation identified a pro-ED network enriched in functions associated with inflammatory responses. Conversely, 31 genes ameliorated ED phenotypes, pointing to potential ED targets, and the respective anti-ED network was enriched in hypoxia, angiogenesis and cancer-related processes. An independent screen with 17 drugs found general agreement with the trends from our siRNA screen and further highlighted DUSP1, IL6 and CCL2 as potential candidates for targeting ED. Overall, our results demonstrate the potential of integrated system biology approaches in discovering disease-specific candidate drug targets for endothelial dysfunction.

Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs

Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery of 1712 SLiM-based virus-host interactions using a phage peptidome tiling the intrinsically disordered protein regions of 229 RNA viruses. We find mimicry of host SLiMs to be a ubiquitous viral strategy, reveal novel host proteins hijacked by viruses, and identify cellular pathways frequently deregulated by viral motif mimicry. Using structural and biophysical analyses, we show that viral mimicry-based interactions have similar binding strength and bound conformations as endogenous interactions. Finally, we establish polyadenylate-binding protein 1 as a potential target for broad-spectrum antiviral agent development. Our platform enables rapid discovery of mechanisms of viral interference and the identification of potential therapeutic targets which can aid in combating future epidemics and pandemics.

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data

The morphology of breast cancer cells is often used as an indicator of tumor severity and prognosis. Additionally, morphology can be used to identify more fine-grained, molecular developments within a cancer cell, such as transcriptomic changes and signaling pathway activity. Delineating the interface between morphology and signaling is important to understand the mechanical cues that a cell processes in order to undergo epithelial-to-mesenchymal transition and consequently metastasize. However, the exact regulatory systems that define these changes remain poorly characterized. In this study, we used a network-systems approach to integrate imaging data and RNA-seq expression data. Our workflow allowed the discovery of unbiased and context-specific gene expression signatures and cell signaling subnetworks relevant to the regulation of cell shape, rather than focusing on the identification of previously known, but not always representative, pathways. By constructing a cell-shape signaling network from shape-correlated gene expression modules and their upstream regulators, we found central roles for developmental pathways such as WNT and Notch, as well as evidence for the fine control of NF-kB signaling by numerous kinase and transcriptional regulators. Further analysis of our network implicates a gene expression module enriched in the RAP1 signaling pathway as a mediator between the sensing of mechanical stimuli and regulation of NF-kB activity, with specific relevance to cell shape in breast cancer.

The Expander-Implant Breast Reconstruction in the COVID Era: Which is the "Unhappy" Tissue Expander Priority?

Breast surgeons seem to agree on the fact that a same-day surgery (mastectomy and breast reconstruction) protocol provides appropriate cancer treatment during times of unprecedented resource limitations, such as in the COVID era. In this scenario, pre-pectoral implant-based breast reconstruction can be definitively considered a sustainable technique. Nevertheless, the authors focus on the management of patients who had already undergone a same day procedure with two-stage breast reconstruction, implanting a breast tissue expander during the last two-year period and have been progressively delayed according to a surgical care based on priority. We coined the expression “unhappy tissue expander” to define all those symptomatic patients for which surgery should not be delayed even during an epidemic context.

Level of Evidence V This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.

LYMPHOVENOUS ANASTOMOSIS FOR THE TREATMENT OF LYMPHEDEMA: A SYSTEMATIC REVIEW OF THE LITERATURE AND META-ANALYSIS

Lymphovenous anastomosis (LVA) has been described as an effective treatment for early stages of lymphedema (LE). The aim of this study was to deepen the evaluation of the effectiveness of LVA by performing a meta-analysis to provide information about its utility in specific anatomical sites, clinical stages, duration of lymphedema, and surgical technique. A systematic literature search using PubMed/Medline, Google Scholar, and Cochrane Database was performed in November 2019. Only original studies in which exclusively LVA was performed for primary and/or secondary lymphedema in humans were eligible for data extraction. A meta-analysis was performed on articles with a well-defined endpoint and a subgroup analysis was conducted in relation to surgical technique, duration of lymphedema, stage of pathology. Forty-eight studies, including 6 clinical trials and 42 low-risk bias observational studies were included in our meta-analysis. 1,281 subjects were included and the majority of articles reported a pre-post analysis. Lymphaticovenular anastomosis appears to result effectively in treatment of lymphedema with an odds ratio of 0.07 (CI: 0.04, 0.13, p<0.001). All subgroup meta-analyses were statistically significant for LVAs specifically with regard to anatomical site, clinical stage, duration of LE, or type of microsurgical procedure (p<0.05). Our meta-analysis confirmed the efficacy of LVAs for the treatment of lymphedema, even when subgroup analysis was performed for clinical stage, duration of pathology, anatomical site of lymphedema, or type of microsurgical procedure. Further prospective trials with a common clearly defined outcome measure are warranted for an unbiased evaluation.

Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development

B lymphocyte development and selection are central to adaptive immunity and self-tolerance. These processes require B cell receptor (BCR) signaling and occur in bone marrow, an environment with variable hypoxia, but whether hypoxia-inducible factor (HIF) is involved is unknown. We show that HIF activity is high in human and murine bone marrow pro-B and pre-B cells and decreases at the immature B cell stage. This stage-specific HIF suppression is required for normal B cell development because genetic activation of HIF-1α in murine B cells led to reduced repertoire diversity, decreased BCR editing and developmental arrest of immature B cells, resulting in reduced peripheral B cell numbers. HIF-1α activation lowered surface BCR, CD19 and B cell-activating factor receptor and increased expression of proapoptotic BIM. BIM deletion rescued the developmental block. Administration of a HIF activator in clinical use markedly reduced bone marrow and transitional B cells, which has therapeutic implications. Together, our work demonstrates that dynamic regulation of HIF-1α is essential for normal B cell development.

Aerial strategies advance volcanic gas measurements at inaccessible, strongly degassing volcanoes

Volcanic emissions are a critical pathway in Earth's carbon cycle. Here, we show that aerial measurements of volcanic gases using unoccupied aerial systems (UAS) transform our ability to measure and monitor plumes remotely and to constrain global volatile fluxes from volcanoes. Combining multi-scale measurements from ground-based remote sensing, long-range aerial sampling, and satellites, we present comprehensive gas fluxes-3760 ± [600, 310] tons day^-1 CO₂ and 5150 ± [730, 340] tons day^-1 SO₂-for a strong yet previously uncharacterized volcanic emitter: Manam, Papua New Guinea. The CO₂/S_T ratio of 1.07 ± 0.06 suggests a modest slab sediment contribution to the sub-arc mantle. We find that aerial strategies reduce uncertainties associated with ground-based remote sensing of SO₂ flux and enable near-real-time measurements of plume chemistry and carbon isotope composition. Our data emphasize the need to account for time averaging of temporal variability in volcanic gas emissions in global flux estimates.

Breast surgeons updating on the thresholds of COVID-19 era: results of a multicenter collaborative study evaluating the role of online videos and multimedia sources on breast surgeons education and training

OBJECTIVE

Current trends show a rise of attention given to breast cancer patients' quality of life and the surgical reconstructive result. Along with this trend, surgical training quality and efficacy are gaining importance and innovative training methods such as online videos shared on social media portals, are becoming main updating tools. In hazardous times like COVID-19 pandemic nowadays, online communication becomes of vital importance and adaptation and innovation are fundamental to keep research and education alive. The authors aimed to investigate the role of video and multimedia sources on the daily activity and surgical training of a representative group of surgeons specifically dedicated to oncologic, oncoplastic and reconstructive breast surgeries.

MATERIALS AND METHODS

A survey was produced and administered to 20 major Italian Breast Centers. Collected data were analyzed with Fisher's Exact Test.

RESULTS

From October 2019 to March 2020, a total of 320 surveys were collected. Among the responders, there were 188 trainees (intern medical doctors and residents) and 110 faculty, 72% of them belonged to a plastic surgery environment, while 28% to general surgery environment. Almost all respondents have ever watched videos concerning breast surgery.

CONCLUSIONS

The results of the study show how breast surgeons rely on videos and web platforms, mostly YouTube, when searching for training info about surgical procedures. Social media offer great opportunities for sharing knowledge and diffusion of new ideas but greater attention to their reliability is mandatory.

Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions

Rho GTPases are central regulators of the cytoskeleton and, in humans, are controlled by 145 multidomain guanine nucleotide exchange factors (RhoGEFs) and GTPase-activating proteins (RhoGAPs). How Rho signalling patterns are established in dynamic cell spaces to control cellular morphogenesis is unclear. Through a family-wide characterization of substrate specificities, interactomes and localization, we reveal at the systems level how RhoGEFs and RhoGAPs contextualize and spatiotemporally control Rho signalling. These proteins are widely autoinhibited to allow local regulation, form complexes to jointly coordinate their networks and provide positional information for signalling. RhoGAPs are more promiscuous than RhoGEFs to confine Rho activity gradients. Our resource enabled us to uncover a multi-RhoGEF complex downstream of G-protein-coupled receptors controlling CDC42-RHOA crosstalk. Moreover, we show that integrin adhesions spatially segregate GEFs and GAPs to shape RAC1 activity zones in response to mechanical cues. This mechanism controls the protrusion and contraction dynamics fundamental to cell motility. Our systems analysis of Rho regulators is key to revealing emergent organization principles of Rho signalling.

Defective levels of both circulating dendritic cells and T-regulatory cells correlate with risk of recurrence in cutaneous melanoma

BACKGROUND

Immune markers in the peripheral blood of melanoma patients provide useful information for clinical management although there is poor consensus on circulating cells which could putatively reflect the disease activity and play a prognostic role. Here, we investigated both dendritic cells (DCs) and T-regulatory cells (Tregs).

METHODS

The number of DC subsets as myeloid (m) and plasmacytoid was measured by flowcytometry in 113 melanoma patients in different clinical stages and correlated with the disease activity to evaluate the recurrence free survival (RFS) calculated as difference between baseline and post-surgical values in relation to the criteria for the melanoma staging, as primary tumor removal, sentinel lymph node biopsy and completion of lymph node dissection.

RESULTS

Circulating mDC levels were significantly lower in metastatic melanoma than in other stages and inversely correlated to Treg values while both populations were similarly expressed in inactive disease at stage I-III. Furthermore, the levels of these cells after melanoma removal were apparently related to the disease activity since their persistent defect reflected high risk of recurrence and reduced the RFS.

CONCLUSIONS

This work highlighted the role of immune cell measurement for the management of melanoma activity and the identification of patients at potential risk of recurrence based on the mDC ratio.

Proteomics and phosphoproteomics in precision medicine: applications and challenges

Recent advances in proteomics allow the accurate measurement of abundances for thousands of proteins and phosphoproteins from multiple samples in parallel. Therefore, for the first time, we have the opportunity to measure the proteomic profiles of thousands of patient samples or disease model cell lines in a systematic way, to identify the precise underlying molecular mechanism and discover personalized biomarkers, networks and treatments. Here, we review examples of successful use of proteomics and phosphoproteomics data sets in as well as their integration other omics data sets with the aim of precision medicine. We will discuss the bioinformatics challenges posed by the generation, analysis and integration of such large data sets and present potential reasons why proteomics profiling and biomarkers are not currently widely used in the clinical setting. We will finally discuss ways to contribute to the better use of proteomics data in precision medicine and the clinical setting.

Postmastectomy upper limb lymphedema: Combined vascularized lymph node transfer and scar release with fat graft expedites surgical and patients' related outcomes. A retrospective comparative study

INTRODUCTION

Lymphedema resulting from breast cancer treatment is a chronic condition that can significantly compromise quality of life. Several works have documented the efficacy of vascularized lymph node flap transfer (VLNT) for the treatment of advanced-stage lymphedema. Given that the axillary scar may contribute to the patient's existing lymphedema, the authors assumed that combining VLNT and scar release with fat graft could be an effective strategy of treatment. The purpose of this study is to compare the efficacy in the reduction of limb circumference and health-related quality of life between a combined strategy, namely, VLN transfer (VLNT) and axillary scar release with fat grafting, and only VLNT for patients affected by postmastectomy upper limb lymphedema. The idea.

MATERIALS AND METHODS

All patients with stage II and III breast cancer-related lymphedema operated between January 2012 and January 2016 were retrospectively identified, and only those treated by combined VLNT and scar release (Group A) or only VLNT (Group B) were included. The outcomes were assessed clinically by limb circumference measurement and radiologically by lymphoscintigraphy. Lymphedema-related quality of life was evaluated preoperatively and at 1 year follow-up through the LYMQOL questionnaire.

RESULTS

Thirty-nine patients met inclusion criteria (Group A = 18; Group B = 21). Mean follow-up was 29 months for Group A and 32 months for Group B. Flap survival rate was 100%, with no donor site morbidity in all patients. A statistically significant difference between the circumference reduction rates (RR) at above elbow level was observed at 3 and 6 months of follow-up comparing the two groups (p<0.00001), with higher values in Group A than in Group B. No significant difference was detected comparing RR values at above and below elbow at 12 and 24 months postoperatively. LYMQOL metrics showed significantly better scores (p<0.0001) in all domains at all follow-up appointments in Group A.

CONCLUSIONS

Patients with postmastectomy upper limb lymphedema can benefit from combined lymph node transfer and axillary scar release with fat graft, as this approach seems to fasten the onset of improvement and to have a positive impact on patients' quality of life.

Why Choose the Septum-Supero-Medial (SSM)-Based Mammaplasty in Patients with Severe Breast Ptosis: An Anatomical Point of View

Nipple-areola complex (NAC) loss is one of the most devastating complications of mastopexy or breast reduction, and it requires revisional procedures with poor aesthetic outcome. In high-risk patients, a free nipple graft could be a choice, but it is associated with the same aesthetic concerns for both patients and surgeons. We report our experience with the septum-supero-medial-based mammaplasty to treat 22 patients with severe breast ptosis (nipple-to-sternal-notch distance > 40 cm). No NAC loss was observed. The study highlights surgical technical details and discusses anatomical considerations to justify the successful result. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

The use of Nexobridtm in debriding chronic ulcers: a preliminary observational study

Nexobrid is a highly selective enzymatic debriding agent used in the acute management of burns to perform escharectomy. From October 2016 to April 2017, we treated 6 patients affected with lower limb chronic ulcers of different etiologies with Nexobrid in order to perform eschar removal by enzymatic debridement. For all patients, a dosage of Nexobrid, calculated as 2gr per 1% TBSA, was applied in a 2-3 mm thick uniform layer on the ulcer eschar and fibrin tissue and left for 4 hours, covered with an occlusive dressing. Patients were assessed in terms of ulcer cleansing 24 hours and 7 days post Nexobrid debridement, by wound bed score (WBS) and % of remaining necrotic tissue. A patient pain VAS was also recorded at 24 hours and 7 days post debridement. Adverse events at these time points were also noted. The results documented a complete removal of necrotic tissue in a time frame of 4 hours. At 24 hours, all lesions were completely debrided. At 7 days, there was a partial recurrence of necrotic tissue, as also documented by decreased WBS. All patients reported none to mild pain, and no adverse events were noted, except for mild erythema along the edges of the lesion on healthy skin in one case. This is a preliminary observation. Optimal dosage and application of Nexobrid in this indication needs to be validated by further controlled data.

Validation of a novel Multi-Gas sensor for volcanic HCl alongside H2S and SO2 at Mt. Etna

Volcanic gas emission measurements inform predictions of hazard and atmospheric impacts. For these measurements, Multi-Gas sensors provide low-cost in situ monitoring of gas composition but to date have lacked the ability to detect halogens. Here, two Multi-Gas instruments characterized passive outgassing emissions from Mt. Etna's (Italy) three summit craters, Voragine (VOR), North-east Crater (NEC) and Bocca Nuova (BN) on 2 October 2013. Signal processing (Sensor Response Model, SRM) approaches are used to analyse H₂S/SO₂ and HCl/SO₂ ratios. A new ability to monitor volcanic HCl using miniature electrochemical sensors is here demonstrated. A "direct-exposure" Multi-Gas instrument contained SO₂, H₂S and HCl sensors, whose sensitivities, cross-sensitivities and response times were characterized by laboratory calibration. SRM analysis of the field data yields H₂S/SO₂ and HCl/SO₂ molar ratios, finding H₂S/SO₂ = 0.02 (0.01-0.03), with distinct HCl/SO₂ for the VOR, NEC and BN crater emissions of 0.41 (0.38-0.43), 0.58 (0.54-0.60) and 0.20 (0.17-0.33). A second Multi-Gas instrument provided CO₂/SO₂ and H₂O/SO₂ and enabled cross-comparison of SO₂. The Multi-Gas-measured SO₂-HCl-H₂S-CO₂-H₂O compositions provide insights into volcanic outgassing. H₂S/SO₂ ratios indicate gas equilibration at slightly below magmatic temperatures, assuming that the magmatic redox state is preserved. Low SO₂/HCl alongside low CO₂/SO₂ indicates a partially outgassed magma source. We highlight the potential for low-cost HCl sensing of H₂S-poor HCl-rich volcanic emissions elsewhere. Further tests are needed for H₂S-rich plumes and for long-term monitoring. Our study brings two new advances to volcano hazard monitoring: real-time in situ measurement of HCl and improved Multi-Gas SRM measurements of gas ratios.

Turmoil at Turrialba Volcano (Costa Rica): Degassing and eruptive processes inferred from high-frequency gas monitoring

Eruptive activity at Turrialba Volcano (Costa Rica) has escalated significantly since 2014, causing airport and school closures in the capital city of San José. Whether or not new magma is involved in the current unrest seems probable but remains a matter of debate as ash deposits are dominated by hydrothermal material. Here we use high-frequency gas monitoring to track the behavior of the volcano between 2014 and 2015 and to decipher magmatic versus hydrothermal contributions to the eruptions. Pulses of deeply derived CO₂-rich gas (CO₂/S_total > 4.5) precede explosive activity, providing a clear precursor to eruptive periods that occurs up to 2 weeks before eruptions, which are accompanied by shallowly derived sulfur-rich magmatic gas emissions. Degassing modeling suggests that the deep magmatic reservoir is ~8-10 km deep, whereas the shallow magmatic gas source is at ~3-5 km. Two cycles of degassing and eruption are observed, each attributed to pulses of magma ascending through the deep reservoir to shallow crustal levels. The magmatic degassing signals were overprinted by a fluid contribution from the shallow hydrothermal system, modifying the gas compositions, contributing volatiles to the emissions, and reflecting complex processes of scrubbing, displacement, and volatilization. H₂S/SO₂ varies over 2 orders of magnitude through the monitoring period and demonstrates that the first eruptive episode involved hydrothermal gases, whereas the second did not. Massive degassing (>3000 T/d SO₂ and H₂S/SO₂ > 1) followed, suggesting boiling off of the hydrothermal system. The gas emissions show a remarkable shift to purely magmatic composition (H₂S/SO₂ < 0.05) during the second eruptive period, reflecting the depletion of the hydrothermal system or the establishment of high-temperature conduits bypassing remnant hydrothermal reservoirs, and the transition from phreatic to phreatomagmatic eruptive activity.

Turmoil at Turrialba Volcano (Costa Rica): Degassing and eruptive processes inferred from high-frequency gas monitoring

Eruptive activity at Turrialba Volcano (Costa Rica) has escalated significantly since 2014, causing airport and school closures in the capital city of San José. Whether or not new magma is involved in the current unrest seems probable but remains a matter of debate as ash deposits are dominated by hydrothermal material. Here we use high-frequency gas monitoring to track the behavior of the volcano between 2014 and 2015 and to decipher magmatic versus hydrothermal contributions to the eruptions. Pulses of deeply derived CO₂-rich gas (CO₂/S_total > 4.5) precede explosive activity, providing a clear precursor to eruptive periods that occurs up to 2 weeks before eruptions, which are accompanied by shallowly derived sulfur-rich magmatic gas emissions. Degassing modeling suggests that the deep magmatic reservoir is ~8-10 km deep, whereas the shallow magmatic gas source is at ~3-5 km. Two cycles of degassing and eruption are observed, each attributed to pulses of magma ascending through the deep reservoir to shallow crustal levels. The magmatic degassing signals were overprinted by a fluid contribution from the shallow hydrothermal system, modifying the gas compositions, contributing volatiles to the emissions, and reflecting complex processes of scrubbing, displacement, and volatilization. H₂S/SO₂ varies over 2 orders of magnitude through the monitoring period and demonstrates that the first eruptive episode involved hydrothermal gases, whereas the second did not. Massive degassing (>3000 T/d SO₂ and H₂S/SO₂ > 1) followed, suggesting boiling off of the hydrothermal system. The gas emissions show a remarkable shift to purely magmatic composition (H₂S/SO₂ < 0.05) during the second eruptive period, reflecting the depletion of the hydrothermal system or the establishment of high-temperature conduits bypassing remnant hydrothermal reservoirs, and the transition from phreatic to phreatomagmatic eruptive activity.

ATtRACT-a database of RNA-binding proteins and associated motifs

RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available athttp://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discoveringde novomotifs enriched in a set of related sequences and compare them with the motifs included in the database.Database URL:http:// attract. cnic. es.

OPTIMIZING THE STAGING OF MELANOMA PATIENTS FOR THEIR BEST SURGICAL MANAGEMENT

Interval nodes (IN) are defined as lymph nodes that lie along the course of lymphatic collecting vessels between a primary tumor site and a draining node field. Sometimes INs contain metastases and a consensus on their surgical management is needed. Therefore, to optimize the surgical management of melanoma patients with metastatic lymphatic involvement, especially when the sentinel lymph node biopsy identifies an unusual drainage field, we identified patients treated at the Department of Plastic and Reconstruction Surgery of Bari between July 1994 and December 2012 identified with a primary-cutaneous melanoma who underwent lymphoscintigraphy and subsequent positive-IN the lymphadenectomy to evaluate the impact of this procedure on overall survival and disease-free-period. 51 patients presented INs, and lymphadenectomy (LA) of the subsequent lymphatic field was performed in 13 subjects with positive-IN. In 4 cases additional lymphatic metastases were detected in the usual basin beyond the IN+. Recurrence-free period and survival rate at 5 years were higher in patients with positive-IN who underwent LA than in subjects who underwent LA due to positive lymph nodes in the usual field. Immediate lymphadenectomy of the subsequent lymphatic field in patients with positive-INs may afford patients earlier stage treatment of their disease and improved prognosis.

Total (fumarolic + diffuse soil) CO2 output from Furnas volcano

Furnas volcano, in São Miguel island (Azores), being the surface expression of rising hydrothermal steam, is the site of intense carbon dioxide (CO₂) release by diffuse degassing and fumaroles. While the diffusive CO₂ output has long (since the early 1990s) been characterized by soil CO₂ surveys, no information is presently available on the fumarolic CO₂ output. Here, we performed (in August 2014) a study in which soil CO₂ degassing survey was combined for the first time with the measurement of the fumarolic CO₂ flux. The results were achieved by using a GasFinder 2.0 tunable diode laser. Our measurements were performed in two degassing sites at Furnas volcano (Furnas Lake and Furnas Village), with the aim of quantifying the total (fumarolic + soil diffuse) CO₂ output. We show that, within the main degassing (fumarolic) areas, the soil CO₂ flux contribution (9.2 t day^-1) represents a minor (~15 %) fraction of the total CO₂ output (59 t day^-1), which is dominated by the fumaroles (~50 t day^-1). The same fumaroles contribute to ~0.25 t day^-1 of H₂S, based on a fumarole CO₂/H₂S ratio of 150 to 353 (measured with a portable Multi-GAS). However, we also find that the soil CO₂ contribution from a more distal wider degassing structure dominates the total Furnas volcano CO₂ budget, which we evaluate (summing up the CO₂ flux contributions for degassing soils, fumarolic emissions and springs) at ~1030 t day^-1.

A knowledge base for Vitis vinifera functional analysis

Background

Vitis vinifera (Grapevine) is the most important fruit species in the modern world. Wine and table grapes sales contribute significantly to the economy of major wine producing countries. The most relevant goals in wine production concern quality and safety. In order to significantly improve the achievement of these objectives and to gain biological knowledge about cultivars, a genomic approach is the most reliable strategy. The recent grapevine genome sequencing offers the opportunity to study the potential roles of genes and microRNAs in fruit maturation and other physiological and pathological processes. Although several systems allowing the analysis of plant genomes have been reported, none of them has been designed specifically for the functional analysis of grapevine genomes of cultivars under environmental stress in connection with microRNA data.

Description

Here we introduce a novel knowledge base, called BIOWINE, designed for the functional analysis of Vitis vinifera genomes of cultivars present in Sicily. The system allows the analysis of RNA-seq experiments of two different cultivars, namely Nero d'Avola and Nerello Mascalese. Samples were taken under different climatic conditions of phenological phases, diseases, and geographic locations. The BIOWINE web interface is equipped with data analysis modules for grapevine genomes. In particular users may analyze the current genome assembly together with the RNA-seq data through a customized version of GBrowse. The web interface allows users to perform gene set enrichment by exploiting third-party databases.

Conclusions

BIOWINE is a knowledge base implementing a set of bioinformatics tools for the analysis of grapevine genomes. The system aims to increase our understanding of the grapevine varieties and species of Sicilian products focusing on adaptability to different climatic conditions, phenological phases, diseases, and geographic locations.

The number of excised lymph nodes is associated with survival of melanoma patients with lymph node metastasis

BACKGROUND

Although the number of excised LNs has been associated with patient prognosis in many solid tumors, this association has not been widely investigated in cutaneous melanoma. This study aims to evaluate the association between the number of excised regional lymph nodes (LNs) and melanoma-specific survival.

PATIENT AND METHODS

Clinico-pathological data from 2507 patients with LN metastasis treated at nine Italian centers were retrospectively collected.

RESULTS

The number of excised LNs correlated with younger age (P < 0.001), male sex (P < 0.001), neck LN field (P < 0.001), LN micrometastasis (P < 0.001) and number of positive LNs (P < 0.001). The number of excised LNs was an independent prognostic factor (HR = 0.85; P = 0.002) after adjustment for other staging features. Upon subgroup analysis, the number of excised LNs had a significant prognostic value in patients bearing 1.01-2.00 mm (HR = 0.79; P = 0.032) and 2.01-4.00 mm (HR = 0.71; P < 0.001) thick melanomas, primary tumors showing ulceration (HR = 0.86; P = 0.033) and Clark level V of invasion (HR = 0.86; P = 0.010), LN micrometastasis (HR = 0.83; P = 0.014) and two to three positive LNs (HR = 0.71; P = 0.001). Finally, this study investigated the influence of the number of excised LNs on patient staging: only when ≥11 nodes were excised the AJCC N stage could stratify prognosis (P < 0.001). Considering the number of excised LNs for each lymphatic field, at least 14, 11, 10 and 12 LNs were needed to stage patients according to the AJCC N stage after a lymphadenectomy of the neck, axilla, inguinal and ilioinguinal LN fields, respectively.

CONCLUSIONS

The number of excised LNs can be considered for risk stratification of patients with regional LN metastasis from cutaneous melanoma. We demonstrated that a minimum number of LNs is required for the correct staging of patients. Further research is needed to evaluate the effectiveness of the minimum number of LNs to be dissected.

The Marigliano–Cacciafesta polypathological scale: A tool for assessing fragility

The aim of our studies was to establish a standard method of assessment that allows an early identification of frailty in the elderly, i.e., to predict who are at risk of developing disabilities, in order to be able to intervene with preventive global and individualized measures. A new multidimensional scale called Marigliano-Cacciafesta polypathological scale (MCPS) was used on 180 elderly people, together with the Barthel index (BI), the global evaluation functional index (GEFI), the geriatric depression scale (GDS), the mini mental state examination (MMSE), the mini nutritional assessment (MNA), and the Tinetti test. A strongly significant statistical correlation was found between the MCPS and the nutritional state, mood level, motor functionality, level of disability and global functionality. As the fragile patients are at a risk to develop disabilities, we think that our scale can be a significant contribution to the multidimensional geriatric assessment (MGA), aimed at identifying and quantifying the parameter of fragility of each patient, an information which should be known, if we intend to introduce preventive measures.

Sperm activation and sperm-egg interaction

Different steps of sperm activation such as acrosomal reaction and capacitation are described in details. The molecules involved in sperm-egg interaction are also reported.

Stress response in mesoangioblast stem cells

Stem cells are presumed to survive various stresses, since they are recruited to areas of tissue damage and regeneration, where inflammatory cytokines and cytotoxic cells may result in severe cell injury. We explored the ability of mesoangioblasts to respond to different cell stresses such as heat, heavy metals and osmotic stress, by analyzing heat shock protein (HSP)70 synthesis as a stress indicator. We found that the A6 mesoangioblast stem cells constitutively synthesize HSP70 in a heat shock transcription factor (HSF)-independent way. However, A6 respond to heat shock and cadmium treatment by synthesizing HSP70 over the constitutive expression and this synthesis is HSF1 dependent. The exposure of A6 to copper or to a hypertonic medium does neither induce HSP70 synthesis nor activation of HSF1, while a constitutive binding of constitutive heat shock element binding factor was found. Together, these data suggest that mesoangioblasts constitutively express HSP70 as an 'a priori' activation mechanism, while they maintain the ability to respond to stress stimuli.

Factors which influence sperm ability to fertilize

Different factors influence animal sperm ability to fertilize. Some of them are reviewed here, sperm motility, block to polyspermy, chemioattraction, sperm competition for fertilization. Old and new data are reported, as for example the new notions on sperm motility derived from site directed mutagenesis in rodents, the new notions on the odour receptors in mammalian sperm attraction and new notions on sperm competition, which is variable in different species.

Surgical treatment of sequelae of fractures of the proximal third of the humerus. The role of osteotomies

Between 1996 and 2003 a total of 19 humeral head osteotomies were performed to treat post-traumatic malunion of the proximal humerus. Mean age was 46 years, ranging from 17 to 71 years. The period of time between traumas and surgeries ranged from 6 to 22 months. Osteotomy procedure was as follows: one after two-part fracture of the greater tuberosity, three after two-part fracture of the surgical neck, five after three-part fracture of the greater tuberosity, eight after four-part fracture, two after complex head splitting fracture, one after two-part fracture with anterior dislocation. Three different types of osteotomies were performed: osteotomy of the humeral neck for varus deformity, isolated osteotomy of the greater tuberosity, and a new osteotomy technique (two-plane and three-plane osteotomy) for three- and four-fragment fracture sequelae. At the time of follow-up evaluation, all 19 patients were questioned regarding pain and function. Excellent results in 14 patients and satisfactory results in 5 were obtained. None of the patients required revision surgery. Findings were recorded using the Constant rating scale. All patients had had significant pain relief after shoulder osteotomy. Range of motion was increased in all patients treated by osteotomy. The success of osteotomy in these cases was based on: patient selection, extensive preoperative evaluation, surgical technique and postoperative rehabilitation.

Anterior-inferior shoulder instability: treatment based on the Thal method

Purpose of this study is to analyze the results of a consecutive series of 139 patients affected with anterior-inferior shoulder instability and treated by arthroscopic capsuloplasty using the Thal method with absorbable and non-absorbable Mitek knotless anchors. Much attention was paid to the preoperative and intraoperative selection of patients, excluding from the arthroscopic procedure those with bony Bankart lesions measuring more than 25%, with an inverted-pear glenoid, with engaged Hill-Sachs lesions and patients with HAGL lesions. Pre- and postoperative clinical evaluation was carried out using the Rowe scale. Scores rose from 45-55 to 96 postoperatively. Intra-articular mobilization of the anchors did not occur and peri-metallic lysis was not manifested. Areas of bone resorption were observed in 7 cases (7/38, 18.4%) with the presence of peri-insertional geodes with biological anchors, but this had no effect on the clinical results.

The difficult approach to neoplastic superior vena cava syndrome: surgical option

AIM

Superior vena cava syndrome is a dramatic event that can be cured in specialized centers.

METHODS

Between 1989 and 1995 6 patients with superior vena cava syndrome underwent surgical treatment for thoracic tumors. In all cases the vena was restricted by a neoplastic sleeve. A median sternotomy was performed in all cases. Two patients received an associated right anterolateral thoracotomy to obtain good surgical exposure for tumor resection and grafting. A 12 mm diameter polytetrafluoroethylene graft was inserted in all cases. The tumor resection was radical in 4 cases (2 thymic carcinomas, 2 malignant germ cell tumors) and palliative in 2 (1 non-small cell lung cancer and 1 mediastinal fibrosis).

RESULTS

We had no in-hospital mortality. All patients had immediate relief of obstruction after by-pass. Three patients were alive without disease at the end of follow-up (40-96 mo), one patient died of postoperative complications after 4 mo, 2 patients died of disease after 4 and 12 mo.

CONCLUSION

PTFE by-pass graft for treatment of the obstructed SVC relieves SVC syndrome and has good medium term patency.

Master Amino acid Pattern as sole and total substitute for dietary proteins during a weight-loss diet to achieve the body's nitrogen balance equilibrium

Results of this multicentric study have shown that by giving Master Amino acid Pattern (MAP) as a sole and total substitute of dietary proteins to 500 overweight participants undergoing the American Nutrition Clinics/Overweight Management Program (ANC/OMP), the participants' body nitrogen balance could be maintained in equilibrium with essentially no calories (MAP 1 g=0.04 kcal), thereby preserving the body's structural and functional proteins, eliminating excessive water retention from the interstitial compartment, and preventing the sudden weight increase after study conclusion commonly known as the yo-yo effect. Study results have shown that the use of MAP, in conjunction with the ANC/OMP regimen, has proven to be safe and effective by preventing those adverse effects associated with a negative nitrogen balance, such as oversized or flabby tissue, stretch marks, the sagging of breast tissue, increased hair loss, faded hair color, and fragile or brittle nails. Also prevented were those anomalies commonly associated with weight-loss diets, such as hunger, weakness, headache caused by ketosis, constipation, and decreased libido. The use of MAP in conjunction with the ANC/OMP also allowed for mean weight loss of 2.5 kg (5.5 lb) per week, achieved through reduction of excessive fat tissue and elimination of excessive water retention from the interstitial compartment.

Master Amino acid Pattern as substitute for dietary proteins during a weight-loss diet to achieve the body's nitrogen balance equilibrium with essentially no calories

Results of this multicentric study have shown that by giving 10 g (10 tablets) of Master Amino acid Pattern (MAP) as a substitute for dietary proteins, once a day, to 114 overweight participants undergoing the American Nutrition Clinics/Overweight Management Program (ANC/OMP), the participants' nitrogen balance could be maintained in equilibrium with essentially no calories (MAP 1 g=0.04 kcal), thereby preserving the body's structural and functional proteins, eliminating excessive water retention from the interstitial compartment, and preventing the sudden weight increase after study conclusion commonly known as the yo-yo effect. Study results have shown that the use of MAP, in conjunction with the ANC/OMP, has proven to be safe and effective by preventing those adverse effects associated with a negative nitrogen balance, such as oversized or flabby tissue, stretch marks, sagging of breast tissue, increased hair loss, faded hair color, and fragile or brittle nails. Also preventing those anomalies commonly associated with weight-loss diets, such as hunger, weakness, headache caused by ketosis, constipation, or decreased libido, the use of MAP, in conjunction with the ANC/OMP, allowed for mean weight loss of 1.4 kg (3 lb) per week.

Unsuspected residual disease at the resection margin after surgery for lung cancer: fate of patients after long-term follow-up

OBJECTIVE

This retrospective study evaluates the survival impact of the residual margin disease after bronchial resection for cancer and suggests tactics in cases of microresidual disease.

METHODS

Between March 1988 and 1998, 4530 consecutive patients underwent surgery for non-small cell lung cancer at our institution. Only incomplete resections after microscopic evaluation (R1) were included in the study. Residual tumour cells were found on the bronchial resection margins of 39 lobectomies, 12 pneumonectomies, 4 segmental resections and one bilobectomy. Histological findings were: squamous cell carcinoma in 38 cases, adenocarcinoma in 15 and large cell carcinoma in three. In all 56 cases, invasive mucosal carcinoma was found exclusively on the bronchial resection margin. Nineteen tumours were stage I; 12, stage II; 17, stage IIIa; 5, stage IIIb; and three, stage IV. Nineteen patients (59.3%) with early stage tumours (I and II) received adjuvant radiation therapy and only three chemotherapy.

RESULTS

The prognosis in these cases was disease-stage related (21 and 38.4% of deaths due to the disease). Forty-one percent of the stage IIIa patients received radiation therapy and 17.6% chemotherapy: 70.6% died of tumour relapse. Forty percent of the stage IIIb patients received radiation therapy and 20% chemotherapy: 60% died of disease progression. All of the stage IV patients died within 3 months from surgical resection. At the end of the study, 21 patients were alive after an interval of 22-142 months (18 in stage I or II). The 10-year actuarial survival rate was 44%. The percentage survival for stage IIIa was 16.8, after 10 years, and fell to 45 months for stage IIIb.

CONCLUSIONS

The prognosis of our stage I or II patients with microresidual tumour on the bronchial resection margin (R1) was similar to that of the patients in the same disease stage, whose resection was microscopically radical (R0) and the same was true of the patients in stage III. In patients with residual tumour cells on the bronchial stump we did not observe worsened long-term survivals.

Lack of amplification phenomena of ribosomal RNA genes in sea urchin

Careful quantitative analyses by spot hybridization to homologous probes demonstrate that no rDNA amplification occurs during Paracentrotus lividus oogenesis. The same approach was used to measure the copy number of the genes involved in ribosome biogenesis. Surprisingly, differently from the organisms in which the lack of rDNA amplification phenomena was observed, a very low number of constitutive rDNA repeats was found in this organism.