Miracle-dz/UniFAR-FTUs huggingface dataset:
A multi-proxy assessment of dieback causes in a Mediterranean oak species

Drought stress causes forest dieback that is often explained by two interrelated mechanisms, namely hydraulic failure and carbon starvation. However, it is still unclear which functional and structural alterations, related to these mechanisms, predispose to dieback. Here we apply a multi-proxy approach for the characterization of tree structure (radial growth, wood anatomy) and functioning (δ13C, δ18O and non-structural carbohydrates (NSCs)) in tree rings before and after drought-induced dieback. We aim to discriminate which is the main mechanism and to assess which variables can act as early-warning proxies of drought-triggered damage. The study was tailored in southern Italy in two forests (i.e., San Paolo (SP) and Oriolo (OR)) where declining and non-declining trees of a ring-porous tree species (Quercus frainetto Ten.) showing anisohydric behavior coexist. Both stands showed growth decline in response to warm and dry spring conditions, although the onset of dieback was shifted between them (2002 in SP and 2009 in OR). Declining trees displayed a sharp growth drop after this onset with reductions of 49% and 44% at SP and OR sites, respectively. Further, contrary to what we expected, declining trees showed a lower intrinsic water-use efficiency compared with non-declining trees after the dieback onset (with reductions of 9.7% and 5.6% at sites SP and OR, respectively), due to enhanced water loss through transpiration, as indicated by the lower δ18O values. This was more noticeable at the most drought-affected SP stand. Sapwood NSCs did not differ between declining and non-declining trees, indicating no carbon starvation in affected trees. Thus, the characterized structural and functional alterations partially support the hydraulic failure mechanism of dieback. Finally, we show that growth data are reliable early-warning proxies of drought-triggered dieback.
Nanoscale view of assisted ion transport across the liquid–liquid interface

Significance The selective separation of targeted metal ions is utilized for environmental remediation, mining of rare earth and base metals, as well as the separation and isolation of long-lived radionuclides from nuclear waste. During the process of solvent extraction, organic extractant molecules complex with metal ions to assist their transfer from an aqueous to an organic phase. The structure of ion–extractant complexes at the interface, as well as the mechanism of ion transport across the interface, are generally unknown but are relevant for improving the kinetics and efficiency of this industrial process. Here, we describe experiments that reveal different ion–extractant complexes for divalent and trivalent ions, and discuss their consequences for the extraction process. During solvent extraction, amphiphilic extractants assist the transport of metal ions across the liquid–liquid interface between an aqueous ionic solution and an organic solvent. Investigations of the role of the interface in ion transport challenge our ability to probe fast molecular processes at liquid–liquid interfaces on nanometer-length scales. Recent development of a thermal switch for solvent extraction has addressed this challenge, which has led to the characterization by X-ray surface scattering of interfacial intermediate states in the extraction process. Here, we review and extend these earlier results. We find that trivalent rare earth ions, Y(III) and Er(III), combine with bis(hexadecyl) phosphoric acid (DHDP) extractants to form inverted bilayer structures at the interface; these appear to be condensed phases of small ion–extractant complexes. The stability of this unconventional interfacial structure is verified by molecular dynamics simulations. The ion–extractant complexes at the interface are an intermediate state in the extraction process, characterizing the moment at which ions have been transported across the aqueous–organic interface, but have not yet been dispersed in the organic phase. In contrast, divalent Sr(II) forms an ion–extractant complex with DHDP that leaves it exposed to the water phase; this result implies that a second process that transports Sr(II) across the interface has yet to be observed. Calculations demonstrate that the budding of reverse micelles formed from interfacial Sr(II) ion–extractant complexes could transport Sr(II) across the interface. Our results suggest a connection between the observed interfacial structures and the extraction mechanism, which ultimately affects the extraction selectivity and kinetics.
Groupwise Construction of Appearance Models using Piece-wise Affine Deformations

We describe an algorithm for obtaining correspondences across a group of imagesof deformable objects. The approach is to construct a statistical modelof appearance which can encode the training images as compactly as possible(a Minimum Description Length framework). Correspondences are defined bypiece-wise linear interpolation between a set of control points defined oneach image. Given such points a model can be constructed, which can approximateevery image in the set. The description length encodes the cost of the model,the parameters and most importantly, the residuals not explained by the model.By modifying the positions of the control points we can optimise the descriptionlength, leading to good correspondence. We describe the algorithm in detailand give examples of its application to MR brain images and to faces. We alsodescribe experiments which use a recently-introduced specificity measureto evaluate the performance of different components of the algorithm.
Unified Protocol Transdiagnostic Treatment in Group Format

Barlow et al. published the unified protocol (UP) for transdiagnostic treatment of emotional disorders, focusing on common pathological factors across a variety of diagnoses. The limited UP research to date suggests that this treatment may be particularly useful for anxiety disorders. However, it has largely been evaluated only in individual treatment format. The current study examined the effectiveness of the UP treatment in a group format, with individuals with comorbid anxiety disorder symptoms. Twenty-six individuals with clinically significant anxiety symptoms in at least two of the following areas, social anxiety, worry, or panic, participated in a 14-week manualized group treatment using the UP. Significant decreases were found on general anxiety, worry, social anxiety, panic, depression, and negative affect, and increases on positive affect. The UP may hold promise for a transdiagnostic group treatment of comorbid anxiety symptoms, but further examination of this treatment is warranted.
Towards a Formalism for Conservative Claims about the Dependability of Software-based Systems

In recent work we have argued for a formal treatment of confidence about the claims made in dependability cases for software-based systems. The key idea underlying this work is ‘the inevitability of uncertainty’: it is rarely possible to assert that a claim about safety or reliability is true with certainty. Much of this uncertainty is epistemic in nature, so it seems inevitable that expert judgment will continue to play an important role in dependability cases. Here we consider a simple case where an expert makes a claim about the probability of failure on demand (pfd) of a sub-system of a wider system, and is able to express his confidence about that claim probabilistically. An important, but difficult, problem then is how such sub-system (claim, confidence) pairs can be propagated through a dependability case for a wider system, of which the sub-systems are components. An informal way forward is to justify, at high confidence, a strong claim, and then conservatively only claim something much weaker: “I’m 99% confident that the pfd is less than 10, so it’s reasonable to be 100% confident that it is less than 10. ” These conservative pfds of sub-systems can then be propagated simply through the dependability case of the wider system. In this paper we provide formal support for such reasoning.
Comparison of graft-versus-host disease-free, relapse-free survival of transplantation using matched sibling donor, matched unrelated donor or unrelated cord blood after myeloablative conditioning for adult patients with hematological malignancies

Abstract The novel composite endpoint of graft-versus-host disease/relapse-free survival (GRFS) was proposed to evaluate ideal healthy recovery without ongoing morbidity in patients undergoing allogeneic hematopoietic cell transplantation (HCT). We herein analyzed long-term GRFS based on the data of 256 patients with hematological malignancies who underwent allogeneic HCT after myeloablative conditioning. The probabilities of GRFS in the entire cohort were 60.1% at 1 year, and 48.6% at 5 years. Compared with unrelated cord blood, the probability of treatment failure as defined by GRFS at 5 years was similar with matched sibling donor (hazard ratio [HR]: 1.33; p = 0.28), but was significantly higher with matched unrelated donor (HR: 1.96; p = 0.01) in multivariate analysis. Unrelated cord blood achieved the highest proportion of patients who had not experienced any GRFS events at 5 years. These data suggest that long-term GRFS after HCT was similar in matched sibling donor recipients to unrelated cord blood recipients.
Improvement of Proteinuria due to Combination Therapy with Daclatasvir and Asunaprevir in Hepatitis C Virus-associated Renal Disease without Cryoglobulinemia

We herein report a unique case of hepatitis C virus (HCV)-associated renal disease without cryoglobulinemia that showed proteinuria, hypoproteinemia, ascites, and edema. Due to combination therapy with daclatasvir and asunaprevir, the patient achieved sustained virological response at week 24 of the therapy. Furthermore, the therapy caused marked amelioration of her proteinuria, ascites, edema, and hypoalbuminemia, and finally improved her estimated glomerular filtration rate. There were no adverse events, and the combination therapy was well-tolerated. We recommend that HCV eradication with antiviral therapy using direct-acting antiviral agents be attempted first for all renal disease with HCV infection, regardless of cryoglobulinemia, considering the existence of resistance-associated variants.
Brain Network Alterations in Alzheimer's Disease Identified by Early-Phase PIB-PET

The aim of this study was to identify the brain networks from early-phase 11C-PIB (perfusion PIB, pPIB) data and to compare the brain networks of patients with differentiating Alzheimer's disease (AD) with cognitively normal subjects (CN) and of mild cognitively impaired patients (MCI) with CN. Forty participants (14 CN, 12 MCI, and 14 AD) underwent 11C-PIB and 18F-FDG PET/CT scans. Parallel independent component analysis (pICA) was used to identify correlated brain networks from the 11C-pPIB and 18F-FDG data, and a two-sample t-test was used to evaluate group differences in the corrected brain networks between AD and CN, and between MCI and CN. Our study identified a brain network of perfusion (early-phase 11C-PIB) that highly correlated with a glucose metabolism (18F-FDG) brain network and colocalized with the default mode network (DMN) in an AD-specific neurodegenerative cohort. Particularly, decreased 18F-FDG uptake correlated with a decreased regional cerebral blood flow in the frontal, parietal, and temporal regions of the DMN. The group comparisons revealed similar spatial patterns of the brain networks derived from the 11C-pPIB and 18F-FDG data. Our findings indicate that 11C-pPIB derived from the early-phase 11C-PIB could provide complementary information for 18F-FDG examination in AD.
Neuroanatomical correlates of grit: Growth mindset mediates the association between gray matter structure and trait grit in late adolescence

There is a long‐standing interest in exploring the factors related to student achievement. As a newly explored personality trait, grit is defined as a person's tendency to pursue long‐term goals with continual perseverance and passion, and grit plays a critical role in student achievement. Increasing evidence has shown that growth mindset, the belief that one's basic abilities are malleable and can be developed through effort, is a potential factor for cultivating grit. However, less is known about the association between grit and the brain and the role of growth mindset in this association. Here, we utilized voxel‐based morphometry to examine the neuroanatomical correlates of grit in 231 healthy adolescent students by performing structural magnetic resonance imaging. The whole‐brain regression analyses revealed that the regional gray matter volume (rGMV) in the left dorsolateral prefrontal cortex (DLPFC) negatively predicted grit. In contrast, the rGMV in the right putamen positively predicted grit. Furthermore, mediating analyses suggested that growth mindset served as a mediator in the association between left DLPFC volume and grit. Our results persisted even after controlling for the influences of self‐control and delayed gratification. Overall, our study presents novel evidence for the neuroanatomical basis of grit and highlights that growth mindset might play an essential role in cultivating a student's grit level.
Viruses Associated with Ovarian Degeneration in Apis mellifera L. Queens

Queen fecundity is a critical issue for the health of honeybee (Apis mellifera L.) colonies, as she is the only reproductive female in the colony and responsible for the constant renewal of the worker bee population. Any factor affecting the queen's fecundity will stagnate colony development, increasing its susceptibility to opportunistic pathogens. We discovered a pathology affecting the ovaries, characterized by a yellow discoloration concentrated in the apex of the ovaries resulting from degenerative lesions in the follicles. In extreme cases, marked by intense discoloration, the majority of the ovarioles were affected and these cases were universally associated with egg-laying deficiencies in the queens. Microscopic examination of the degenerated follicles showed extensive paracrystal lattices of 30 nm icosahedral viral particles. A cDNA library from degenerated ovaries contained a high frequency of deformed wing virus (DWV) and Varroa destructor virus 1 (VDV-1) sequences, two common and closely related honeybee Iflaviruses. These could also be identified by in situ hybridization in various parts of the ovary. A large-scale survey for 10 distinct honeybee viruses showed that DWV and VDV-1 were by far the most prevalent honeybee viruses in queen populations, with distinctly higher prevalence in mated queens (100% and 67%, respectively for DWV and VDV-1) than in virgin queens (37% and 0%, respectively). Since very high viral titres could be recorded in the ovaries and abdomens of both functional and deficient queens, no significant correlation could be made between viral titre and ovarian degeneration or egg-laying deficiency among the wider population of queens. Although our data suggest that DWV and VDV-1 have a role in extreme cases of ovarian degeneration, infection of the ovaries by these viruses does not necessarily result in ovarian degeneration, even at high titres, and additional factors are likely to be involved in this pathology.
Good correlation between the Afinion AS100 analyser and the ABX Pentra 400 analyser for the measurement of glycosylated haemoglobin and lipid levels in older adults in Durban, South Africa.

BACKGROUND The Afinion AS100 analyser is a small bench-top, multi-assay, point-of-care (POC) analyser that is able to measure glycated haemoglobin (HbA1c) and lipid levels. OBJECTIVE To assess performance of the Afinion analyser compared with a reference laboratory test for the measurement of HbA1c and lipid levels. METHOD The study involved men and women enrolled in a cross-sectional study, Sexual health, HIV infection and comorbidity with non-communicable diseases among Older Persons (SHIOP), which was conducted from February to May 2016. Whole blood was drawn aseptically by a trained study nurse into a serum separator gel tube and an ethylenediaminetetra-acetic acid (EDTA) tube. The EDTA whole blood was used to measure HbA1c levels, and serum to measure total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and triglyceride levels. Lin's correlation coefficient was used to assess the agreement between the Afinion and ABX Pentra 400 analysers for each marker. RESULTS A total of 435 older individuals were included in the study. The proportion of HbA1c results that were correctly classified by the Afinion analyser was 92.2%. Bland-Altman analysis and linear regression analysis showed a very good agreement (correlation concordance 0.89) between the two analysers for the measurement of HbA1c. The two-way scatter plot for TC showed a substantial correlation (0.80). However, a total of 69 cholesterol results that were within the normal range on the Pentra were misclassified as abnormal on the Afinion. The readings obtained for HDL-C levels with the Afinion were shown to be slightly overestimated when compared with the Pentra. However, correlation for HDL-C on the two analysers was 0.93, indicating an almost perfect agreement. Seventy-four LDL-C results were erroneously classified as abnormal on the Afinion but were within the normal range on the Pentra, resulting in a substantial correlation of 0.75. An excellent agreement was observed between triglyceride measurements (0.99). CONCLUSION This study supports the use of the Afinion AS100 analyser in POC testing for the measurement of HbA1c, triglycerides and HDL-C in a South African setting.
Separation of plasma‐derived exosomes into CD3(+) and CD3(–) fractions allows for association of immune cell and tumour cell markers with disease activity in HNSCC patients

Head and neck squamous cell carcinoma (HNSCC) is a highly immunosuppressive malignancy. Exosomes in HNSCC patients' plasma are enriched in inhibitory cargo and mediate immunosuppression. As these exosomes are products of various cells, the cellular origin of immunoregulatory proteins they carry is unknown. To test whether tumour‐ or T cell‐derived exosomes in patients' plasma are immunosuppressive and impact upon disease activity, we separated CD3(–) from CD3(+) exosomes by immunocapture using anti‐CD3 antibodies. The exosome protein cargo was evaluated for immunoregulatory proteins using on‐bead flow cytometry. Tumour protein‐enriched CD3(–) exosomes were CD44v3(+). Surprisingly, mean levels of programmed death ligand 1 (PD‐L1), cytotoxic T lymphocyte antigen 4 (CTLA‐4) and cyclooxygenase‐2 (COX‐2) were similar in CD3(+) and CD3(–) exosomes, although the latter induced higher (P < 0·0025) ex‐vivo apoptosis of CD8(+) T cells and greater (P < 0·005) conversion of CD4+ T cells to CD4(+)CD39(+) regulatory T cells (Treg). CD3(+) and CD3(–) exosomes carrying high levels of immunosuppressive proteins were highly effective in mediating these functions. Exosomes of patients with Union for International Cancer Control (UICC) stages III/IV disease had higher levels of PD‐L1 and COX‐2 than stages I/II patients (P < 0·005). Patients with nodal involvement had exosomes with the higher inhibitory protein content than N0 patients (P < 0·03). CD3(+) and CD3(–) exosomes of HNSCC patients had higher PD‐L1, COX‐2 and CD15s levels than healthy donors' exosomes (P < 0·009), although levels of immunostimulatory OX40 or OX40L were not different. By isolating CD3(–)/CD44v3‐enriched and CD3(+) exosomes from plasma, the cellular origins of immunoregulatory proteins they carry were identified. Association of exosome molecular profiles with disease progression supports the exosome potential as future cancer biomarkers.
Motivation but not valence modulates neuroticism‐dependent cingulate cortex and insula activity

Neuroticism has been found to specifically modulate amygdala activations during differential processing of valence and motivation while other brain networks yet are unexplored for associated effects. The main purpose of this study was to investigate whether neural mechanisms processing valence or motivation are prone to neuroticism in the salience network (SN), a network that is anchored in the anterior cingulate cortex (ACC) and the anterior insula. This study used functional magnetic resonance imaging (fMRI) and an approach/avoid emotional pictures task to investigate brain activations modulated by pictures’ valence or motivational status between high and low neurotic individuals. We found that neuroticism‐dependent SN and the parahippocampal‐fusiform area activations were modulated by motivation but not valence. Valence in contrast interacted with neuroticism in the lateral orbitofrontal cortex. We suggested that neuroticism modulated valence and motivation processing, however, under the influence of the two distinct networks. Neuroticism modulated the motivation through the SN while it modulated the valence through the orbitofrontal networks.
Characteristics of BCR-ABL kinase domain mutations in chronic myeloid leukemia from India: not just missense mutations but insertions and deletions are also associated with TKI resistance

Abstract We document the characteristics of BCR-ABL kinase domain mutations (KDM) in the largest study from India comprising of 385 patients and demonstrate that more than half (51.9%) of these patients have detectable abnormalities in the KD both in adult and in pediatric chronic myelogenous leukemia (CML). These comprise singly occurring missense mutations (25.5%), polyclonal/compound point mutations (4.9%), and insertions/deletions (29.6%). Missense mutations were most commonly seen in the imatinib-binding region followed by the P-loop. The commonest mutation in our dataset was T315I. Other common missense mutations were Y253H, M244V, and F317L. A high prevalence of BCR-ABL exon7 deletion (p.R362fs*) was also seen (25.5% of the entire cohort), whereas the 35bpintron-derived insertion/truncation mutation detected in 12 patients. In the pediatric age group, 58.8% of patients harbored missense mutations, polyclonal/compound mutations as well as insertions and deletions. We detected 11 novel mutations (seven missense mutations and four insertions/deletions).
Seen through the patients’ eyes: surgical safety and checklists

Objective We sought to explore the views patients have towards surgical safety and checklists. As a secondary aim, we explored if previous experience of error or other patient characteristics influence these views. Design A cross-sectional survey study design was applied. Participants The Flemish Patients' Platform network and social media were used to recruit participants. Main outcome measure(s) An 11-item questionnaire was designed to assess the following constructs: perception of surgical safety, attitudes towards the WHO surgical safety checklist and attitudes regarding checklist usage. Results Respondents' view (N = 444) on the risk of an adverse event showed considerable variation. Respondents were positive towards the checklist, strongly agreeing that it would impact positively on their safety. However, this positive perception did not translate into an attitude where patients will actively inform themselves whether a checklist is used. The majority of respondents have no difficulty with repetitive verification of identity, procedure and location of the surgery. Respondents with a clinical background were the least anxious. Views were divided regarding hearing discussions around blood loss or airway problems. Conclusions Patients perceive the checklist as a reliable safety tool. They do not mind repetitive verification of identity and procedure. However, hearing staff discussing specific, explicit, risks could cause anxiousness in some patients. Building a supportive and collaborative environment is needed to involve and empower patients to contribute in the realization of a safe hospital environment.