Getting Ready for Large-Scale Proteomics in Crop Plants

Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes

12th WINFOCUS world congress on ultrasound in emergency and critical care

Table of contents A1 Point-of-care ultrasound examination of cervical spine in emergency department Yahya Acar, Onur Tezel, Necati Salman A2 A new technique in verifying the placement of a nasogastric tube: obtaining the longitudinal view of nasogastric tube in addition to transverse view with ultrasound Yahya Acar, Necati Salman, Onur Tezel, Erdem Cevik A3 Pseudoaneurysm of the femoral artery after cannulation of a central venous line. Should we always use ultrasound in these procedures? Margarita Algaba-Montes, Alberto Oviedo-García, Mayra Patricio-Bordomás A4 Ultrasound-guided supraclavicular subclavian vein catheterization. A novel approach in emergency department Margarita Algaba-Montes, Alberto Oviedo-García, Mayra Patricio-Bordomás A5 Clinical ultrasound in a septic and jaundice patient in the emergency department Margarita Algaba-Montes, Alberto Oviedo-García, Mayra Patricio-Bordomás A6 Characterization of the eyes in preoperative cataract Saudi patients by using medical diagnostic ultrasound Mustafa Z. Mahmoud, Abdelmoneim Sulieman A7 High-frequency ultrasound in determining the causes of acute shoulder joint pain Mustafa Z. Mahmoud A8 Teaching WINFOCUS Ultrasound Life Support Basic Level 1 for Providers in resource-limited countries Abbas Ali, Alrayah Mustafa, Ihab Abdelrahman, Mustafa Bahar, Osama Ali, H. Lester Kirchner, Gregor Prosen A9 Changes of arterial stiffness and endothelial function during uncomplicated pregnancy Ajda Anzic, Paul Leeson A10 Cardiovascular haemodynamic properties before, during and after pregnancy Ajda Anzic, Paul Leeson A11 An old man with generalized weakness Maryam Bahreini, Fatemeh Rasooli A12 Ultrasonography for non-specific presentations of abdominal pain Maryam Bahreini, Houman Hosseinnejad A13 Introduction of a new imaging guideline for suspected renal colic in the emergency department: effect on CT Urogram utilisation Gabriel Blecher, Robert Meek, Diana Egerton-Warburton A14 Transabdominal ultrasound screening for pancreatic cancer in Croatian military veterans: a retrospective analysis from the first Croatian veteran’s hospital Edina Ćatić Ćuti, Stanko Belina, Tihomir Vančina, Idriz Kovačević A15 The challenge of AAA: unusual case of obstructive jaundice Edina Ćatić Ćuti, Nadan Rustemović A16 Educational effectiveness of easy-made new simulator model for ultrasound-guided procedures in pediatric patients: vascular access and foreign body management Ikwan Chang, Jin Hee Lee, Young Ho Kwak, Do Kyun Kim A17 Detection of uterine rupture by point-of-care ultrasound at emergency department: a case report Chi-Yung Cheng, Hsiu-Yung Pan, Chia-Te Kung A18 Abdominal probe in the hands of interns as a relevant diagnostic tool in revealing the cause of heart failure Ela Ćurčić, Ena Pritišanac, Ivo Planinc, Marijana Grgić Medić, Radovan Radonić A19 Needs assessment of the potential utility of point-of-care ultrasound within the Zanzibar health system Abiola Fasina, Anthony J. Dean, Nova L. Panebianco, Patricia S. Henwood A20 Ultrasonographic diagnosis of tracheal compression Oliviero Fochi, Moreno Favarato, Ezio Bonanomi A21 The role of ultrasound in the detection of lung infiltrates in critically ill patients: a pilot study Marijana Grgić Medić, Ivan Tomić, Radovan Radonić A22 The SAFER Lasso; a novel approach using point-of-care ultrasound to evaluate patients with abdominal complaints in the emergency department Youngrock Ha, Hongchuen Toh A23 Awareness and use of clinician-performed ultrasound among clinical clerkship faculty Elizabeth Harmon, Wilma Chan, Cameron Baston, Gail Morrison, Frances Shofer, Nova Panebianco, Anthony J. Dean A24 Clinical outcomes in the use of lung ultrasound for the diagnosis of pediatric pneumonias Angela Hua, Sharon Kim, James Tsung A25 Effectiveness of ultrasound in hypotensive patients Isa Gunaydin, Zeynep Kekec, Mehmet Oguzhan Ay A26 Moderate-to-severe left ventricular ejection fraction related to short-term mortality of patients with post-cardiac arrest syndrome after out-of-hospital cardiac arrest Jinjoo Kim, Jinhyun Kim, Gyoosung Choi, Dowon Shim A27 Usefulness of abdominal ultrasound for acute pyelonephritis diagnosis after kidney transplantation Ji-Han Lee A28 Lung ultrasound for assessing fluid tolerance in severe preeclampsia Jana Ambrozic, Katja Prokselj, Miha Lucovnik A29 Optic nerve sheath ultrasound in severe preeclampsia Gabrijela Brzan Simenc, Jana Ambrozic, Miha Lucovnik A30 Focused echocardiography monitoring in the postoperative period for non-cardiac patients Asta Mačiulienė, Almantas Maleckas, Algimantas Kriščiukaitis, Vytautas Mačiulis, Andrius Macas A31 POCUS-guided paediatric upper limb fracture reduction: algorithm, tricks, and tips Sharad Mohite A32 Point-of-care lung ultrasound: a good diagnostic tool for pneumonia in a septic patient Zoltan Narancsik, Hugon Možina A33 A case of undergraduate POCUS (r)evolution Sara Nikolić, Jan Hansel, Rok Petrovčič, Una Mršić, Gregor Prosen A34 The Graz Summer School for ultrasound: from first contact to bedside application: three-and-a-half-day undergraduate ultrasound training: résumé after two years of continuous development Simon Orlob, Markus Lerchbaumer, Niklas Schönegger, Reinhard Kaufmann A35 Usefulness of point-of-care ultrasound in the emergency room in a patient with acute abdominal pain Alberto Oviedo-García, Margarita Algaba-Montes, Mayra Patricio-Bordomás A36 Use of bedside ultrasound in a critically ill patient. A case report Alberto Oviedo-García, Margarita Algaba-Montes, Mayra Patricio-Bordomás A37 Diagnostic yield of clinical echocardiography for the emergency physician Alberto Oviedo-García, Margarita Algaba-Montes, Mayra Patricio-Bordomás A38 Focused cardiac ultrasound in early diagnosis of type A aortic dissection with atypical presentation Chun-I Pan, Hsiu-Yung Pan, Chien-Hung Wu A39 Detection of imperforated hymen by point-of-care ultrasound Hsiu-yung Pan, Chia-Te Kung A40 Developing a point-of-care ultrasound curriculum for pediatric nurse practitioners practicing in the pediatric emergency department Sarah Pasquale, Stephanie J. Doniger, Sharon Yellin, Gerardo Chiricolo A41 Use of transthoracic echocardiography in emergency setting: patient with mitral valve abscess Maja Potisek, Borut Drnovšek, Boštjan Leskovar A42 A young man with syncope Fatemeh Rasooli, Maryam Bahreini A43 Work-related repetitive use injuries in ultrasound fellows Kristine Robinson, Clara Kraft, Benjamin Moser, Stephen Davis, Shelley Layman, Yusef Sayeed, Joseph Minardi A44 Lung ultrasonography in the evaluation of pneumonia in children Irmina Sefic Pasic, Amra Dzananovic, Anes Pasic, Sandra Vegar Zubovic A45 Central venous catheter placement with the ultrasound aid: two years’ experience of the Interventional unit, Division of Intensive Care Medicine, KBC Zagreb Ana Godan Hauptman, Marijana Grgic Medic, Ivan Tomic, Ana Vujaklija Brajkovic, Jaksa Babel, Marina Peklic, Radovan Radonic A46 Duplicitas casui: two patients admitted due to acute liver failure Vedran Radonic, Ivan Tomic, Luka Bielen, Marijana Grgic Medic A47 A pilot survey on an understanding of Bedside Point-of-Care Ultrasound (POCUS) among medical doctors in internal medicine: exposure, perceptions, interest, and barriers to training Peh Wee Ming A48 Unusual case of defecation syncope Nur hafiza Yezid, Fatahul Laham Mohammed A49 A case report of massive pulmonary embolism; a multidisciplinary approach Zainal Abidin Huda, Wan Nasarudin Wan Ismail, W.Yus Haniff W.Isa, Hashairi Fauzi, Praveena Seeva, Mohd Zulfakar Mazla

12th WINFOCUS world congress on ultrasound in emergency and critical care.

10.1186/s13089-016-0046-8Crit Ultrasound J8Suppl 112-complete

Epidemiology and outcomes of hospital-acquired bloodstream infections in intensive care unit patients: the EUROBACT-2 international cohort study

Purpose In the critically ill, hospital-acquired bloodstream infections (HA-BSI) are associated with significant mortality. Granular data are required for optimizing management, and developing guidelines and clinical trials. Methods We carried out a prospective international cohort study of adult patients (≥ 18 years of age) with HA-BSI treated in intensive care units (ICUs) between June 2019 and February 2021. Results 2600 patients from 333 ICUs in 52 countries were included. 78% HA-BSI were ICU-acquired. Median Sequential Organ Failure Assessment (SOFA) score was 8 [IQR 5; 11] at HA-BSI diagnosis. Most frequent sources of infection included pneumonia (26.7%) and intravascular catheters (26.4%). Most frequent pathogens were Gram-negative bacteria (59.0%), predominantly Klebsiella spp. (27.9%), Acinetobacter spp. (20.3%), Escherichia coli (15.8%), and Pseudomonas spp. (14.3%). Carbapenem resistance was present in 37.8%, 84.6%, 7.4%, and 33.2%, respectively. Difficult-to-treat resistance (DTR) was present in 23.5% and pan-drug resistance in 1.5%. Antimicrobial therapy was deemed adequate within 24 h for 51.5%. Antimicrobial resistance was associated with longer delays to adequate antimicrobial therapy. Source control was needed in 52.5% but not achieved in 18.2%. Mortality was 37.1%, and only 16.1% had been discharged alive from hospital by day-28. Conclusions HA-BSI was frequently caused by Gram-negative, carbapenem-resistant and DTR pathogens. Antimicrobial resistance led to delays in adequate antimicrobial therapy. Mortality was high, and at day-28 only a minority of the patients were discharged alive from the hospital. Prevention of antimicrobial resistance and focusing on adequate antimicrobial therapy and source control are important to optimize patient management and outcomes

The role of centre and country factors on process and outcome indicators in critically ill patients with hospital-acquired bloodstream infections

Purpose: The primary objective of this study was to evaluate the associations between centre/country-based factors and two important process and outcome indicators in patients with hospital-acquired bloodstream infections (HABSI). Methods: We used data on HABSI from the prospective EUROBACT-2 study to evaluate the associations between centre/country factors on a process or an outcome indicator: adequacy of antimicrobial therapy within the first 24 h or 28-day mortality, respectively. Mixed logistical models with clustering by centre identified factors associated with both indicators. Results: Two thousand two hundred nine patients from two hundred one intensive care units (ICUs) were included in forty-seven countries. Overall, 51% (n = 1128) of patients received an adequate antimicrobial therapy and the 28-day mortality was 38% (n = 839). The availability of therapeutic drug monitoring (TDM) for aminoglycosides everyday [odds ratio (OR) 1.48, 95% confidence interval (CI) 1.03-2.14] or within a few hours (OR 1.79, 95% CI 1.34-2.38), surveillance cultures for multidrug-resistant organism carriage performed weekly (OR 1.45, 95% CI 1.09-1.93), and increasing Human Development Index (HDI) values were associated with adequate antimicrobial therapy. The presence of intermediate care beds (OR 0.63, 95% CI 0.47-0.84), TDM for aminoglycoside available everyday (OR 0.66, 95% CI 0.44-1.00) or within a few hours (OR 0.51, 95% CI 0.37-0.70), 24/7 consultation of clinical pharmacists (OR 0.67, 95% CI 0.47-0.95), percentage of vancomycin-resistant enterococci (VRE) between 10% and 25% in the ICU (OR 1.67, 95% CI 1.00-2.80), and decreasing HDI values were associated with 28-day mortality. Conclusion: Centre/country factors should be targeted for future interventions to improve management strategies and outcome of HABSI in ICU patients

Presentation, management, and outcomes of older compared to younger adults with hospital-acquired bloodstream infections in the intensive care unit: a multicenter cohort study

Purpose: Older adults admitted to the intensive care unit (ICU) usually have fair baseline functional capacity, yet their age and frailty may compromise their management. We compared the characteristics and management of older (≥ 75 years) versus younger adults hospitalized in ICU with hospital-acquired bloodstream infection (HA-BSI). Methods: Nested cohort study within the EUROBACT-2 database, a multinational prospective cohort study including adults (≥ 18 years) hospitalized in the ICU during 2019-2021. We compared older versus younger adults in terms of infection characteristics (clinical signs and symptoms, source, and microbiological data), management (imaging, source control, antimicrobial therapy), and outcomes (28-day mortality and hospital discharge). Results: Among 2111 individuals hospitalized in 219 ICUs with HA-BSI, 563 (27%) were ≥ 75 years old. Compared to younger patients, these individuals had higher comorbidity score and lower functional capacity; presented more often with a pulmonary, urinary, or unknown HA-BSI source; and had lower heart rate, blood pressure and temperature at presentation. Pathogens and resistance rates were similar in both groups. Differences in management included mainly lower rates of effective source control achievement among aged individuals. Older adults also had significantly higher day-28 mortality (50% versus 34%, p < 0.001), and lower rates of discharge from hospital (12% versus 20%, p < 0.001) by this time. Conclusions: Older adults with HA-BSI hospitalized in ICU have different baseline characteristics and source of infection compared to younger patients. Management of older adults differs mainly by lower probability to achieve source control. This should be targeted to improve outcomes among older ICU patients