Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic variation in drought hardiness of coastal Douglas-fir seedlings from British Columbia

1716 Abstract: Genetic variation in drought hardiness traits and their genetic correlations with growth potential and recovery traits were investigated in 39 full-sib families of coastal Douglas-fir ( Pseudotsuga menziesii var. menziesii (Mirb.) Franco) from southwestern British Columbia. Seedlings of these families were grown in raised nursery beds and sub- jected to three moisture regimes each in the second (well-watered or control, mild, and moderate drought) and third (control, severe drought, and recovery from second-year moderate drought) seasons. Traits assessed included drought hardiness (foliage damage, cavitation of xylem tracheids, xylem hydraulic conductivity, and height and diameter growth increment) in the drought treatments, growth potential (total height and diameter) in the control treatment, and height and diameter growth increments in the recovery treatment. Xylem cavitation in the growth ring produced in a particular year was nearly three times greater under the moderate drought and four times greater under the severe drought than in the control treatment. Xylem hydraulic conductivity of seedlings in the severe drought treatment was 40% lower than conductivity of seedlings under the control treatment. Mean foliage damage in seedlings subjected to severe drought (third season) was much greater (33%) than in seedlings subjected to mild or moderate drought (second season). Fam- ilies differed significantly in most drought hardiness traits, with individual tree heritabilities averaging 0.19. Thus, much potential exists for identifying drought-hardy families at the seedling stage and using this information for deploy - ment or breeding purposes. In addition, most hardiness traits were strongly intercorrelated (genetic correlations often exceeded |0.80|) indicating that these traits are controlled largely by the same set of genes and that selection for hardi- ness based on one trait will increase hardiness as reflected in the other traits as well. Genetic correlations were only moderate (0.49) between hardiness traits measured in different years, perhaps due to the large difference in severity of the drought applied in the two seasons. Although injury to seedlings, as reflected in foliage damage and xylem cavita- tion, was relatively low under the moderate drought of the second season, it did result in reduced growth increment the following (recovery) year. Growth potential under favorable moisture regimes was nearly uncorrelated with drought har- diness, suggesting that drought hardiness could be improved in this southwestern British Columbia breeding population
Intermediate Susceptibility to Ciprofloxacin among Salmonella enterica Serovar Typhi Isolates in Lima, Peru

ABSTRACT Thirty-three Salmonella enterica serovar Typhi blood isolates from Lima, Peru (2008 to 2012), were fully susceptible to trimethoprim-sulfamethoxazole, chloramphenicol, ceftriaxone, and tetracycline; 8/33 (24.2%) showed intermediate susceptibility to ciprofloxacin carrying mutations in the quinolone resistance-determining region of the gyrA gene (Ser83-Phe and Asp87-Asn) and in the gyrB gene (Ser464-Phe).
‘Coexisting pituitary adenoma and suprasellar meningioma—a coincidence or causation effect: report of two cases and review of the literature’

Abstract Coexistence of pituitary adenoma (PA) and another type of brain tumor is a very rare clinical scenario. Even though such a presentation can be an incidental event but a thorough review of the literature will be made to elucidate the possible mechanisms and treatment options in similar cases. Two cases of concomitant sellar and suprasellar/diaphragmatic tumors are reported. A 37-year-old lady with prolactinoma and a suprasellar diaphragmatic meningioma and a 42-year-old acromegalic man with suprasellar/diaphragmatic meningioma and a PA. Both meningiomas were removed transcranially. The prolactinoma could be managed medically and the growth hormone secreting adenoma was removed trans-sphenoidally. The visual problems and hormonal imbalances of both patients improved postoperatively. The literature is reviewed on this topic and the possible pathogenesis and management protocol of similar lesions are discussed.
Double Sequential Defibrillation for Refractory Ventricular Fibrillation: A Case Report

Abstract A 40-year-old male struck his chest against a pole during a basketball game and had sudden out-of-hospital cardiac arrest. After bystander cardiopulmonary resuscitation, fire and emergency medical services personnel provided six defibrillation attempts prior to emergency department arrival. A 7th attempt in the emergency department using a different vector was unsuccessful. On the 8th attempt, using a second defibrillator with defibrillator pads placed adjacent to the primary set of defibrillator pads, two shocks were administered in near simultaneous fashion. The double sequential defibrillation was successful and the patient had return of spontaneous circulation at the next pulse check. He recovered in the intensive care unit, was discharged home 1 month later, and continues to follow up in clinic over 1 year later with a Cerebral Performance Category score of 1 (short-term memory deficits).
A gene at 59 minutes on the Escherichia coli chromosome encodes a lipoprotein with unusual amino acid repeat sequences

We report a 1.432-kb DNA sequence at 59 min on the Escherichia coli chromosome that connects the published sequences of the pcm gene for the isoaspartyl protein methyltransferase and that of the katF or rpoS (katF/rpoS) gene for a sigma factor involved in stationary-phase gene expression. Analysis of the DNA sequence reveals an open reading frame potentially encoding a polypeptide of 379 amino acids. The polypeptide sequence includes a consensus bacterial lipidation sequence present at residues 23 to 26 (Leu-Ala-Gly-Cys), four octapeptide proline- and glutamine-rich repeats of consensus sequence QQPQIQPV, and four heptapeptide threonine- and serine-rich repeats of consensus sequence PTA(S,T)TTE. The deduced amino acid sequence, especially in the C-terminal region, is similar to that of the Haemophilus somnus LppB lipoprotein outer membrane antigen (40% overall sequence identity; 77% identity in last 95 residues). The LppB lipoprotein binds Congo red dye and has been proposed to be a virulence determinant in H. somnus. Utilizing a plasmid construct with the E. coli gene under the control of a phage T7 promoter, we demonstrate the lipidation of this gene product by the incorporation of [3H]palmitic acid into a 42-kDa polypeptide. We also show that treatment of E. coli cells with globomycin, an inhibitor of the lipoprotein signal peptidase, results in the accumulation of a 46-kDa precursor. We thus designate the protein NlpD (new lipoprotein D). E. coli cells overexpressing NlpD bind Congo red dye, suggesting a common function with the H. somnus LppB protein. Disruption of the chromosomal E. coli nlpD gene by insertional mutagenesis results in decreased stationary-phase survival after 7 days.
Approche déterministe du séchage des avivés de résineux de fortes épaisseurs pour proposer des conduites industrielles adaptées

Les secheurs connaissent des difficultes pour secher les avives d'epicea de fortes epaisseurs avec les sechoirs industriels classiques. Notre etude a pour ambition d'ameliorer les connaissances sur le sechage des avives de resineux de fortes epaisseurs par une approche deterministe. Le code numerique TransPore, developpe par Patrick Perre, de part sa capacite a simuler les transferts couples de chaleur et de masse dans une planche de bois, est place au cœur de notre approche. Notre demarche scientifique a necessite la mise en place de deux outils : - un dispositif experimental a ete mis en place pour obtenir des informations descriptives sur les transferts de masse s'effectuant dans la planche au cours de son sechage, et sur les contraintes mecaniques engendrees par le sechage. Ce dispositif mesure en continu l'epaisseur des avives, les fentes de surface, et le champ de teneur en eau dans la planche par attenuation de rayons X ; - une unite de calcul des contraintes de sechage a ete developpee et greffee a TransPore (version 1D) pour aborder l'aspect qualitatif du sechage. La formulation mecanique adoptee est monodimensionnelle, et elle prend en compte la courbure eventuelle de la planche pour, par exemple, simuler un sechage dissymetrique. Les resultats experimentaux ont ensuite ete confrontes aux resultats theoriques pour confirmer et valider les resultats predits par la simulation numerique. La comparaison s'est averee souvent tres probante, tant au niveau des transferts couples de chaleur et de masse qu'au niveau de l'evaluation des contraintes de sechage. Ce travail se termine par l'utilisation du code TransPore comme outil d'aide a la comprehension des mecanismes couples qui rendent le sechage des fortes epaisseurs particulierement difficile. Cet outil a montre egalement sa capacite a guider ses utilisateurs dans le developpement de nouvelles conduites de sechage. Cette derniere application ouvre une voie prometteuse vers l'optimisation des tables de sechage.
Adaptive aneuploidy protects against thiol peroxidase deficiency by increasing respiration via key mitochondrial proteins

Significance Aneuploidy, a condition of abnormal chromosomal content, can support adaptive mechanisms in response to environmental cues but comes at the expense of decreased proliferation and dysfunction of cellular processes. Here we show that the gain of an extra copy of chromosome XI in yeast is an adaptive mechanism to deal with oxidative stress under conditions of antioxidant deficiency. We narrowed down the effect of adaptive aneuploidy to two genes on chromosome XI, which supported increased mitochondrial abundance and respiration, which in turn provided reducing equivalents for hydroperoxide removal. Forced expression of these genes eliminated aneuploidy, improved cell growth, and was sufficient for protection against oxidative stress. Thus, aneuploidy can adaptively reprogram cellular metabolism, protecting against oxidative stress by upregulating respiration. Aerobic respiration is a fundamental energy-generating process; however, there is cost associated with living in an oxygen-rich environment, because partially reduced oxygen species can damage cellular components. Organisms evolved enzymes that alleviate this damage and protect the intracellular milieu, most notably thiol peroxidases, which are abundant and conserved enzymes that mediate hydrogen peroxide signaling and act as the first line of defense against oxidants in nearly all living organisms. Deletion of all eight thiol peroxidase genes in yeast (∆8 strain) is not lethal, but results in slow growth and a high mutation rate. Here we characterized mechanisms that allow yeast cells to survive under conditions of thiol peroxidase deficiency. Two independent ∆8 strains increased mitochondrial content, altered mitochondrial distribution, and became dependent on respiration for growth but they were not hypersensitive to H2O2. In addition, both strains independently acquired a second copy of chromosome XI and increased expression of genes encoded by it. Survival of ∆8 cells was dependent on mitochondrial cytochrome-c peroxidase (CCP1) and UTH1, present on chromosome XI. Coexpression of these genes in ∆8 cells led to the elimination of the extra copy of chromosome XI and improved cell growth, whereas deletion of either gene was lethal. Thus, thiol peroxidase deficiency requires dosage compensation of CCP1 and UTH1 via chromosome XI aneuploidy, wherein these proteins support hydroperoxide removal with the reducing equivalents generated by the electron transport chain. To our knowledge, this is the first evidence of adaptive aneuploidy counteracting oxidative stress.
“Diastolic heart failure” or heart failure caused by subtle left ventricular systolic dysfunction?

Objectives: To determine whether patients with suspected heart failure but preserved systolic function, as determined by conventional echocardiographic measures (often said to have “diastolic heart failure), might have subtle left ventricular systolic dysfunction detectable by a new measure of left ventricular systolic function—left ventricular systolic atrioventricular plane displacement. Design: Observational study. Setting: Direct access echocardiography. Patients: 147 patients with suspected heart failure referred by general practitioners. Measurements: Echocardiographic assessment of conventional measures of left ventricular systolic function (fractional shortening, ejection fraction (by Simpson's biplane method) and “eyeball” assessment) and measurement of left ventricular systolic atrioventricular plane displacement. Results: Between 21% and 33% of patients with “normal” left ventricular systolic function by conventional methods were found to have abnormal left ventricular systolic atrioventricular plane displacement. Conclusions: Approximately one quarter of patients with suspected heart failure but preserved systolic function by conventional methods have abnormal atrioventricular plane displacement. These patients with suspected heart failure but preserved systolic function by conventional echocardiographic measures may have heart failure caused by subtle systolic dysfunction rather than isolated “diastolic heart failure”.
Relationship Banking, Fragility and the Asset-Liability Matching Problem

We address a fundamental question in relationship banking: why do banks that make relationship loans finance themselves primarily with core deposits and when would it be optimal to finance such loans with purchased money? We show that not only are relationship loans informationally opaque and illiquid, but they also require the relationship between the bank and the borrower to endure in order for the bank to add value. However, the informational opacity of relationship loans gives rise to endogenous withdrawal risk that makes the bank fragile. Core deposits are an attractive funding source for such loans because the bank provides liquidity services to core depositors and this diminishes the likelihood of premature deposit withdrawal, thereby facilitating the continuity of relationship loans. That is, we show that banks will wish to match the highest value-added liabilities with the highest value-added loans and that doing so simultaneously minimizes the bank's fragility owing to withdrawal risk and maximizes the value the bank adds in relationship lending. We also examine the impact of interbank competition on the bank's asset-liability matching and extract numerous testable predictions. , Oxford University Press.
Substance P receptor expression by inhibitory interneurons of the rat hippocampus: Enhanced detection using improved immunocytochemical methods for the preservation and colocalization of GABA and other neuronal markers

Two unresolved issues regarding the identification and characterization of hippocampal interneurons were addressed in this study. One issue was the longstanding inability to detect γ–aminobutyric acid (GABA) in the somata of several hippocampal interneuron subpopulations, which has prevented the unequivocal identification of all hippocampal interneurons as GABA neurons. The second issue was related to the identification of the hippocampal interneurons that constitutively express substance P (neurokinin‐1) receptors (SPRs). The recent development of neurotoxins that specifically target SPR‐expressing cells suggests that it may be possible to destroy hippocampal inhibitory interneurons selectively for experimental purposes. Although SPRs are apparently expressed in the hippocampus only by interneurons, colocalization studies have found that most interneurons of several subtypes and hippocampal subregions appear SPR‐negative. Thus, the identities and locations of the inhibitory interneurons that are potential targets of an SPR‐directed neurotoxin remain in doubt. Using newly developed methods designed to copreserve and colocalize GABA and polypeptide immunoreactivities with increased sensitivity, the authors report that virtually all hippocampal interneuron somata that are immunoreactive for parvalbumin (PV), calbindin, calretinin, somatostatin (SS), neuropeptide Y, cholecystokinin, and vasoactive intestinal peptide exhibited clearly detectable, somal, GABA‐like immunoreactivity (LI). Hippocampal SPR‐LI was detected only on the somata and dendrites of GABA‐immunopositive interneurons. All glutamate receptor subunit 2‐immunoreactive principal cells, including dentate granule cells, hilar mossy cells, and hippocampal pyramidal cells, were devoid of detectable SPR‐LI, even after prolonged electrical stimulation of the perforant pathway that induced the expression of other neuronal proteins in principal cells. Thus, hippocampal interneurons of all subtypes and subregions were found to be SPR‐immunoreactive, including the PV‐positive interneurons of the dentate hilus and hippocampus, and the SS‐positive cells of area CA1, both of which were previously reported to lack SPR‐LI. Only minor proportions of hippocampal interneurons appeared clearly devoid of detectable SPR‐LI. These results demonstrate for the first time that all identified interneuron subpopulations of the rat hippocampus are GABA‐immunoreactive, and that many inhibitory interneurons of all subtypes in all subregions of the rat hippocampus express SPRs constitutively. J. Comp. Neurol. 430:283–305, 2001. © 2001 Wiley‐Liss, Inc.
Quantitative analysis of Langerhans' cells in oral chronic graft-vs.-host disease.

BACKGROUND The Langerhans cells (LCs) are scattered throughout the epithelium of skin and mucosa and have been associated with the graft-vs.-host disease (GVHD), which is the highest cause of morbidity and mortality in patients who underwent bone marrow transplant (BMT). This study aims at quantifying the LCs in the oral chronic GVHD (cGVHD). METHODS Microscopic sections from biopsies carried out in the buccal mucosa of 40 patients who underwent allogenic BMT and developed (20) or not (20) oral cGVHD (Groups 1 and 2, respectively) were utilised. For the control group, free surgical margins of 20 biopsies of non-inflammatory lesions in the buccal mucosa (Group 3) were used. The sections were studied in routine colouration and immunostained for CD1a. RESULTS Group 1 (with cGVHD) presented a greater number of Langerhans' cells/mm(2) (50.6 +/- 37.2) when compared with the other groups (Group 2, 23.11 +/- 19.7; Group 3, 16.6 +/- 17.3). CONCLUSION Our results suggest a greater recruitment of LCs in patients transplanted with cGVHD, probably as a result of cytokines secreted by the inflammatory cells.
Lipopolysaccharide induces fever and depresses locomotor activity in unrestrained mice.

The purpose of this study was to characterize the basic biology of fever to lipopolysaccharide (LPS) in unrestrained mice. Although LPS has been shown to induce fevers in many laboratory animals (e.g., rats, guinea pigs, rabbits), there is some question of whether LPS causes a fall or rise in body temperature (Tb) in mice. Tb was measured by biotelemetry in unrestrained mice maintained at an ambient temperature of 30 degrees C. Intraperitoneal injections of LPS at doses of 1.0, 2.5, and 3.0 mg/kg induced dose-independent prompt decreases of Tb for 5.7 h. After this postinjection reduction, Tb increased and reached a peak at approximately 24 h postinjection. The peak rises in Tb were dose dependent. Changes in Tb due to LPS were accompanied by suppression of locomotor activity. Indomethacin, at a dose that did not affect normal Tb, enhanced the temperature-lowering effect of LPS as well as inhibited the febrile rise of Tb after LPS. Indomethacin did not modify the reduction in activity caused by the injections of LPS. Food intake of the mice was decreased by LPS in a dose-dependent manner, and tolerance developed to a second injection of LPS. We conclude that freely moving mice can develop pronounced and reproducible fevers in response to LPS, which is different in time course, dose-dependent profile, induction of pyrogenic tolerance profile, and mode of inhibition by indomethacin from those responses that have been observed in other species studied so far.
SE3-Pose-Nets: Structured Deep Dynamics Models for Visuomotor Planning and Control

In this work, we present an approach to deep visuomotor control using structured deep dynamics models. Our deep dynamics model, a variant of SE3-Nets, learns a low-dimensional pose embedding for visuomotor control via an encoder-decoder structure. Unlike prior work, our dynamics model is structured: given an input scene, our network explicitly learns to segment salient parts and predict their pose-embedding along with their motion modeled as a change in the pose space due to the applied actions. We train our model using a pair of point clouds separated by an action and show that given supervision only in the form of point-wise data associations between the frames our network is able to learn a meaningful segmentation of the scene along with consistent poses. We further show that our model can be used for closed-loop control directly in the learned low-dimensional pose space, where the actions are computed by minimizing error in the pose space using gradient-based methods, similar to traditional model-based control. We present results on controlling a Baxter robot from raw depth data in simulation and in the real world and compare against two baseline deep networks. Our method runs in real-time, achieves good prediction of scene dynamics and outperforms the baseline methods on multiple control runs. Video results can be found at: this https URL
DNA Methylation Profiling Defines Clinically Relevant Biological Subsets of Non–Small Cell Lung Cancer

Purpose: Non–small cell lung cancers (NSCLC) comprise multiple distinct biologic groups with different prognoses. For example, patients with epithelial-like tumors have a better prognosis and exhibit greater sensitivity to inhibitors of the epidermal growth factor receptor (EGFR) pathway than patients with mesenchymal-like tumors. Here, we test the hypothesis that epithelial-like NSCLCs can be distinguished from mesenchymal-like NSCLCs on the basis of global DNA methylation patterns. Experimental Design: To determine whether phenotypic subsets of NSCLCs can be defined on the basis of their DNA methylation patterns, we combined microfluidics-based gene expression analysis and genome-wide methylation profiling. We derived robust classifiers for both gene expression and methylation in cell lines and tested these classifiers in surgically resected NSCLC tumors. We validate our approach using quantitative reverse transcriptase PCR and methylation-specific PCR in formalin-fixed biopsies from patients with NSCLC who went on to fail front-line chemotherapy. Results: We show that patterns of methylation divide NSCLCs into epithelial-like and mesenchymal-like subsets as defined by gene expression and that these signatures are similarly correlated in NSCLC cell lines and tumors. We identify multiple differentially methylated regions, including one in ERBB2 and one in ZEB2, whose methylation status is strongly associated with an epithelial phenotype in NSCLC cell lines, surgically resected tumors, and formalin-fixed biopsies from patients with NSCLC who went on to fail front-line chemotherapy. Conclusions: Our data show that patterns of DNA methylation can divide NSCLCs into two phenotypically distinct subtypes of tumors and provide proof of principle that differences in DNA methylation can be used as a platform for predictive biomarker discovery and development. Clin Cancer Res; 18(8); 2360–73. ©2012 AACR.