Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparative study of two polymorphs of bis(1-hydroxy-2-methylpropan-2-aminium) carbonate.

Alkanolamines have been known for their high CO2 absorption for over 60 years and are used widely in the natural gas industry for reversible CO2 capture. In an attempt to crystallize a salt of (RS)-2-(3-benzoylphenyl)propionic acid with 2-amino-2-methylpropan-1-ol, we obtained instead a polymorph (denoted polymorph II) of bis(1-hydroxy-2-methylpropan-2-aminium) carbonate, 2C4H12NO(+)·CO3(2-), (I), suggesting that the amine group of the former compound captured CO2 from the atmosphere forming the aminium carbonate salt. This new polymorph was characterized by single-crystal X-ray diffraction analysis at low temperature (100 K). The salt crystallizes in the monoclinic system (space group C2/c, Z = 4), while a previously reported form of the same salt (denoted polymorph I) crystallizes in the triclinic system (space group P-1, Z = 2) [Barzagli et al. (2012). ChemSusChem, 5, 1724-1731]. The asymmetric unit of polymorph II contains one 1-hydroxy-2-methylpropan-2-aminium cation and half a carbonate anion, located on a twofold axis, while the asymmetric unit of polymorph I contains two cations and one anion. These polymorphs exhibit similar structural features in their three-dimensional packing. Indeed, similar layers of an alternating cation-anion-cation neutral structure are observed in their molecular arrangements. Within each layer, carbonate anions and 1-hydroxy-2-methylpropan-2-aminium cations form planes bound to each other through N-H.O and O-H.O hydrogen bonds. In both polymorphs, the layers are linked to each other via van der Waals interactions and C-H.O contacts. In polymorph II, a highly directional C-H.O contact (C-H.O = 156°) shows as a hydrogen-bonding interaction. Periodic theoretical density functional theory (DFT) calculations indicate that both polymorphs present very similar stabilities.
The elderly offender: an 11-year survey of referrals to a regional forensic psychiatric service

The elderly offender remains under-researched, with few or no published data on elderly referrals to the medium secure forensic service in the UK. Our aim was to generate data describing the characteristics of elderly offenders, to review whether the complex needs of such patients were being suitably assessed from an holistic perspective and to produce assessment guidelines for elderly forensic referrals. We identified elderly referrals retrospectively and scrutinized their medical notes. We found that 66% of referrals came from solicitors, with sexual offending being the most common offence in 56% of cases. There was no diagnosis of mental disorder in 56%, dementia being the most common diagnosis in 19%. There was poor use of diagnostic tools and investigations in the assessment process. An integrated approach to assessment and management between the forensic and old age psychiatric services is advocated. We have no declaration of interest to make.
Proteomic analysis of heterosis during maize seed germination

Heterosis is observed for most phenotypic traits and developmental stages in many plants. In this study, the embryos, from germinating seeds after 24 h of soaking, for five elite maize hybrids and their parents were selected to unravel the genetic basis of heterosis using 2‐D proteomic method. In total, 257 (80.06%), 363 (58.74%), 351 (79.95%), 242 (54.50%), and 244 (46.30%) nonadditively expressed proteins were identified in hybrids Zhengdan 958, Nongda 108, Yuyu 22, Xundan 20, and Xundan 18, respectively. The nonadditive proteins were divided into above high‐parent (++; 811, 55.66%), high‐parent (+; 121, 8.30%), partial dominance (+−; 249, 17.09%), low‐parent (−; 30, 2.06%), below low‐parent (− −; 62, 4.26%), and D (different; 184, 12.63%) expression patterns. The observed patterns indicate the important roles of dominance, partial dominance, and overdominance in regulating seed germination in maize. Additionally, 54 different proteins were identified by mass spectrometry and classified into nine functional groups: metabolism (9), cell detoxification (8), unknown functional proteins (8), chaperones (7), signal transduction (6), development process (5), other (5), transporter (3), and stress response (3). Of these, the most interesting are those involved with germination‐related hormone signal transduction and the abscisic acid and gibberellin regulation networks.
Proteomic profiling of birch (Betula verrucosa) pollen extracts from different origins

Pollen of the European white birch is a major source of spring pollinosis in Europe. Pollen‐allergy diagnosis and treatment by specific immunotherapy commonly rely on extracts of natural origin. To gain insight into the protein content and its variability, we evaluated the profile of allergenic and non‐allergenic proteins in extracts of pollen from different origins by MS‐based proteomics. Aqueous extracts prepared from commercially available Swedish birch pollen, pollen collected from Austrian trees and a commercial skin prick extract were analyzed by 1‐DE, 2‐DE, immunoblotting and mass spectrometry, resulting in a complete inventory of extractable, disease‐relevant pollen proteins. A main focus of this study was on the isoform distribution of Bet v 1, the major allergen of birch pollen. Using a combination of intact mass determination and peptide sequencing, five isoforms (a, b, d, f and j) were unequivocally identified in Swedish and Austrian birch pollen extracts, while the skin prick extract contained only isoforms a, b and d. Using the same methods as for Bet v 1, divergencies in the sequence of birch profilin (Bet v 2), a plant panallergen, were solved. The molecular characterization of pollen extracts is relevant for standardization and development of new reagents for specific immunotherapy.
iTRAQ protein quantification: A quality‐controlled workflow

Reporter ion‐based methods are among the major techniques to quantify peptides and proteins. Two main labels, tandem mass tag (TMT) and iTRAQ, are widely used by the proteomics community. They are, however, often applied as out‐of‐the‐box methods, without thorough quality control. Thus, due to undiscovered limitations of the technique, irrelevant results might be trusted. To address this issue, we here propose a step‐by‐step quality control of the iTRAQ workflow. From sample preparation to final ratio calculation we provide metrics and techniques assessing the actual effectiveness of iTRAQ quantification as well as a novel method for more reliable protein ratio estimation.
The extracellular proteome of Bifidobacterium animalis subsp. lactis BB‐12 reveals proteins with putative roles in probiotic effects

Probiotics are live microorganisms that exert health‐promoting effects on the human host, as demonstrated for numerous strains of the genus Bifidobacterium. To unravel the proteins involved in the interactions between the host and the extensively used and well‐studied probiotic strain Bifidobacterium animalis subsp. lactis BB‐12, proteins secreted by the bacterium, i.e. belonging to the extracellular proteome present in the culture medium, were identified by 2‐DE coupled with MALDI‐TOF MS. Among the 74 distinct proteins identified, 31 are predicted to carry out their physiological role either outside the cell or on its surface. These proteins include solute‐binding proteins for oligosaccharides, amino acids and manganese, cell wall‐metabolizing proteins, and 18 proteins that have been described to interact with human host epithelial cells or extracellular matrix proteins. The potential functions include binding of plasminogen, formation of fimbriae, adhesion to collagen, attachment to mucin and intestinal cells as well as induction of immunomodulative response. These findings suggest a role of the proteins in colonization of the gastrointestinal tract, adhesion to host tissues, or immunomodulation of the host immune system. The identification of proteins predicted to be involved in such interactions can pave the way towards well targeted studies of the protein‐mediated contacts between bacteria and the host, with the goal to enhance the understanding of the mode of action of probiotic bacteria.
Learning From Different Lenses: Reports of Medical Errors in Primary Care by Clinicians, Staff, and Patients: A Project of the American Academy of Family Physicians National Research Network

Objectives: To test whether family doctors, office staff, and patients will report medical errors and to investigate differences in how and what they report. Methods: Clinicians, staff, and patients in 10 family medicine clinics of the American Academy of Family Physicians National Research Network representing a diversity of clinical and community settings were invited to report errors they observed. They were asked to report routinely during 10 weeks and to report every error on 5 specific days. They submitted anonymous reports via a Web site, paper forms, and a voice-activated phone system. Results: Four hundred one clinicians and staff reported 935 errors within 717 events, 37% (265) of which came from the 5 intensive reporting days and 61% (440) from routine reports. Staff made 384 (53%) reports, and clinicians, 342 (47%) reports. Most (96%) errors reported were process errors, not related to knowledge or skill. Staff reported more errors in patient flow and communication; clinicians reported more medication and laboratory errors. Reports suggest that patients with complex health issues (31% versus 20%, P = 0.013) are vulnerable to more severe outcomes. Patients submitted 126 reports, 18 of which included errors. Conclusions: Clinicians and staff offer different and independently valuable lenses for understanding errors and their outcomes in primary care, but both predominantly reported process- or system-related errors. There is a clear need to find more effective ways to invite patients to report on errors or adverse events. These findings suggest that patient safety organizations authorized by recent legislation should invite reports from a variety of health care workers and staff.
Two novel ficolin‐like proteins act as pattern recognition receptors for invading pathogens in the freshwater crayfish Pacifastacus leniusculus

To isolate pathogen‐associated molecular patterns (PAMPs)‐binding molecules, the bacterium, Staphylococcus aureus was used as an affinity matrix to find bacteria‐binding proteins in the plasma of the freshwater crayfish, Pacifastacus leniusculus. Two new bacteria‐binding ficolin‐like proteins (FLPs) were identified by 2‐DE and MS analysis. The FLPs have a fibrinogen‐related domain (FReD) in their C‐terminal and a repeat region in their N‐terminal regions with putative structural similarities to the collagen‐like domain of vertebrate ficolins and mannose binding lectins (MBLs). Phylogenetic analysis shows that the newly isolated crayfish FLP1 and FLP2 cluster separately from other FReD‐containing proteins. A tissue distribution study showed that the mRNA expression of FLP occurred mainly in the hematopoietic tissue (Hpt) and in the hepatopancreas. Recombinant FLPs exhibited agglutination activity of Gram‐negative bacteria Escherichia coli and Aeromonas hydrophila in the presence of Ca2+. The FLPs could bind to A. hydrophila, E. coli as well as S. aureus as judged by bacteria adsorption. Moreover, the FLPs may help crayfish to clear Gram‐negative bacteria, but not Gram‐positive bacteria which had been injected into the hemolymph. When Gram‐negative bacteria coated with FLPs were incubated with Hpt cells, a lower death rate of the cells was found compared with control treatment. Our results suggest that FLPs function as pattern recognition receptors in the immune response of crayfish.
The ABRF Proteomics Research Group Studies: Educational exercises for qualitative and quantitative proteomic analyses

Resource (core) facilities have played an ever‐increasing role in furnishing the scientific community with specialized instrumentation and expertise for proteomics experiments in a cost‐effective manner. The Proteomics Research Group (PRG) of the Association of Biomolecular Resource Facilities (ABRF) has sponsored a number of research studies designed to enable participants to try new techniques and assess their capabilities relative to other laboratories analyzing the same samples. Presented here are results from three PRG studies representing different samples that are typically analyzed in a core facility, ranging from simple protein identification to targeted analyses, and include intentional challenges to reflect realistic studies. The PRG2008 study compares different strategies for the qualitative characterization of proteins, particularly the utility of complementary methods for characterizing truncated protein forms. The use of different approaches for determining quantitative differences for several target proteins in human plasma was the focus of the PRG2009 study. The PRG2010 study explored different methods for determining specific constituents while identifying unforeseen problems that could account for unanticipated results associated with the different samples, and included 15N‐labeled proteins as an additional challenge. These studies provide a valuable educational resource to research laboratories and core facilities, as well as a mechanism for establishing good laboratory practices.
A proteomic view of the host–pathogen interaction: The host perspective

The host–pathogen interaction represents a complex and dynamic biological system. The outcome of this interaction is dependent on the microbial pathogen properties to establish infection and the ability of the host to control infection. Although bacterial pathogens have evolved a variety of strategies to subvert host defense functions, several general mechanisms have been shown to be shared among these pathogens. As a result, host effectors that are critical for pathogen entry, survival and replication inside the host cells have become a new paradigm for antimicrobial targeting. This review focuses on the potential utility of a proteomics approach in defining the host–pathogen interaction from the host's perspective.
The effect of sex and prematurity on the cardiovascular baroreflex response in sheep

What is the central question of this study? Late preterm infants are often assumed to escape long‐term morbidities known to impact earlier preterm offspring. Is this true for the cardiovascular system? What is the main finding and its importance? We show that late preterm birth is a risk factor for cardiovascular dysfunction in early adulthood and is influenced by sex. Early signs of cardiovascular dysfunction might predispose to heart disease in adulthood.
Successful Treatment of 1-34 Parathyroid Hormone (PTH) after Failure of Bisphosphonate Therapy in a Complex Case of Pregnancy Associated Osteoporosis and Multiple Fractures

Abstract Introduction: Pregnancy associated osteoporosis (PAO) was first reported almost half a century ago. The most common symptom is acute lower back pain due to vertebral fractures in the last trimester or immediately after birth. Patient: We present a case involving a female patient born in 1971 (gravida II, para I) with a history of PAO. In April 2000 at the age of 28 years, she delivered a son and breastfed him for 4 months. A first magnetic resonance tomography (MRT) screening in June 2000 showed osteoporotic fractures at lumbar vertebra 1–4. Therefore, the patient received oral alendronate therapy. In May 2001, a second MRT exhibited burst fracture of thoracic 8, end-plate fracture of thoracic 11, 12, lumbar 2–5 and compression fracture of lumbar 1. The oral therapy was switched to ibandronate (3 mg) intravenously every 3 months. An X-ray in December 2002 showed 3 new additional end-plate fractures at thoracic 4, 6 and 7. Ibandronate was discontinued in September 2004 and the patient received daily subcutaneous (s. c.) injections of 1-34 PTH in September 2005. Results: After starting 1-34 PTH treatment for 18 months, a further increase in bone mineral density (BMD) was achieved without any further fracture. Conclusion: We presented for the first time a case of severe PAO with 11 spine fractures. We observed an unsatisfactory effect of oral and i. v. bisphosphonates in combination with adequate calcium and vitamin D supplementation. The treatment with 1-34 PTH showed an increase in BMD with no further fractures.
Mitoprotection preserves the renal vasculature in porcine metabolic syndrome

What is the central question of this study? We hypothesized that chronic mitoprotection would decrease renal vascular remodelling and dysfunction in swine metabolic syndrome. What is the main finding and its importance? This study shows that experimental metabolic syndrome exerts renal microvascular and endothelial cell mitochondrial injury, which were attenuated by mitoprotection, underscoring the contribution of mitochondrial injury to the pathogenesis of metabolic syndrome‐induced vascular damage.
Proteome analysis of host–pathogen interactions: Investigation of pathogen responses to the host cell environment

Infectious diseases are still a major health risk, and thus a better understanding of the interaction between human host cells and pathogenic microbes is urgently required. Since the interplay between both partners is highly complex, genome‐wide analysis by OMICs approaches will likely make a major contribution to the elucidation of the pathophysiology of infection processes. In the concert of OMICs technologies, proteomics is particularly important because it reveals changes in the active players of the cell and has thus a close relationship to the phenotypic changes observed. While proteomic studies of in vitro‐grown microbial pathogens are routinely established in many labs, in vivo proteomic approaches are still rare. Here, we will review the challenges and recent developments of proteomic analysis of microbial pathogens derived from cell culture or in vivo infection settings and summarize some lessons that have been learned from these studies.
Bothrops jararaca venom proteome rearrangement upon neonate to adult transition

The pharmacological activities displayed by Bothrops jararaca venom undergo a significant ontogenetic shift. Similarly, the diet of this species changes from ectothermic prey in early life to endothermic prey in adulthood. In this study we used large and representative newborn and adult venom samples consisting of pools from 694 and 110 specimens, respectively, and demonstrate a significant ontogenetic shift in the venom proteome complexity of B. jararaca. 2‐DE coupled to MS protein identification showed a clear rearrangement of the toxin arsenal both in terms of the total proteome, as of the glycoproteome. N‐glycosylation seems to play a key role in venom protein variability between newborn and adult specimens. Upon the snake development, the subproteome of metalloproteinases undergoes a shift from a P‐III‐rich to a P‐I‐rich profile while the serine proteinase profile does not vary significantly. We also used isobaric tag labeling (iTRAQ) of venom tryptic peptides for the first time to examine the quantitative changes in the venom toxins of B. jararaca upon neonate to adult transition. The iTRAQ analysis showed changes in various toxin classes, especially the proteinases. Our study expands the in‐depth understanding of venom complexity variation particularly with regard to toxin families that have been associated with envenomation pathogenesis.
3. Skin tests for diagnosis of IgE‐mediated allergy

Skin testing means introduction into the superficial layer of (application on) the skin of allergenic material. Provided IgE-antibodies, with an idiotype corresponding to the allergen introduced, are attached to skin mast cells, mast cell mediators are released, causing an early (immediate)(EPR) and under certain circumstances also a late phase reaction (LPR)(l)(See Chapter 1). The latter is more often found when high concentrations of allergen are used for testing in highly sensitive individuals (3). In this chapter, emphasis will be put on EPR, since LPR is seen in only 8 % of adults using a concentration suitable for routine diagnosis by SPT (16). However, LPR is more easily induced by ICT then by SPT, since ICT is "̂ 30 000 times more sensitive then SPT (3). This fact should be kept in mind in scientific studies, evaluating the influence of therapeutic measures on LPR.
Theorising equipment-sharing in a cohort of Scottish drug users

Findings are reported from a cohort of 1007 Scottish drug users entering treatment, including prison-based treatment, in 2001/2002. At follow-up, 33 months later, 14.4% of the sample had shared needles and/or syringes in the 3 months prior to interview; if the definition of equipment-sharing is extended to sharing filters, spoons or flush water, then 21.8% had shared in the same period. Logistic regression analyses were performed to establish the co-variables associated with equipment-sharing for those of the study population who were injectors at baseline and who had been interviewed at all four sweeps; separate additional analyses were performed for those receiving baseline treatment inside prison and for those receiving treatment outside prison. Variables occurring in the models independently associated with equipment-sharing included severity of drug dependence, poorer mental health and whether or not the interviewee's partner had a drug problem, with the last co-variable indicating the continuing importance of the social patterning of equipment sharing. Further, a very strong independent association was found between frequency of injecting and recent equipment-sharing: other things being equal, those injecting drugs most often are those who are most likely to share injecting equipment. This is not simply self-evidential; it also speaks to the importance of ‘accidental’ sharing. Theorising of this risk behaviour must not just emphasise the situated rationality of sharing, but must also embrace contingency.
Chamber‐specific effects of hypokalaemia on ventricular arrhythmogenicity in isolated, perfused guinea‐pig heart

Diuretic‐induced hypokalaemia has been shown to promote cardiac arrhythmias in hypertensive patients. The present study was designed to determine whether hypokalaemia increases arrhythmic susceptibility of the left ventricle (LV) or the right ventricle (RV), or both. Proarrhythmic effects of hypokalaemic perfusion (2.5 mm K+ for 30 min) were assessed in isolated guinea‐pig heart preparations using simultaneous recordings of volume‐conducted electrocardiogram and monophasic action potentials from six ventricular epicardial sites. Effective refractory periods, ventricular fibrillation thresholds and inducibility of tachyarrhythmias by programmed electrical stimulation and tachypacing were determined at the LV and the RV epicardial stimulation sites. Hypokalaemia promoted spontaneous ventricular ectopic activity, an effect attributed to non‐uniform prolongation of ventricular repolarization resulting in increased RV‐to‐LV transepicardial dispersion of refractoriness and action potential duration. Furthermore, hypokalaemic perfusion was associated with reduced ventricular fibrillation threshold and increased inducibility of tachyarrhythmias by programmed electrical stimulation and tachypacing as determined at the LV stimulation site. In contrast, the RV stimulation revealed no change in arrhythmic susceptibility of the RV chamber. Consistently, hypokalaemia reduced the LV effective refractory period but had no effect on the RV refractoriness. This change enabled generation of premature propagating responses by extrastimulus application at earlier time points during LV repolarization. Increased prematurity of extrastimulus‐evoked propagating responses was associated with exaggerated local inhomogeneities in intraventricular conduction and action potential duration in hypokalaemic LV, thus creating a favourable stage for re‐entrant tachyarrhythmias. Taken together, these findings suggest that proarrhythmic effects of hypokalaemia are mostly attributed to increased LV arrhythmogenicity in the guinea‐pig heart.