Miracle-dz/UniFAR-FTUs huggingface dataset:
Saturation labeling with cysteine‐reactive cyanine fluorescent dyes provides increased sensitivity for protein expression profiling of laser‐microdissected clinical specimens

Laser capture microdissection (LCM) provides the capability to isolate and analyze small numbers of cells from a specific area of a histologic section. LCM has particular value for analysis of early stage tumors, which are often small and intermixed with non‐tumor tissue. It has previously been shown that a new generation of cysteine‐reactive cyanine dyes can, in principle, provide increased sensitivity for two‐dimensional fluorescence difference gel electrophoresis (2‐D DIGE) profiling when sample quantitities are limiting. However, the comparative advantage of the new dyes in a clinical setting has not been established. Here, we report that cysteine‐reactive dyes allowed the identification of more features than established, lysine‐reactive dyes with a given number of cells. This was true both with extracts prepared from human papillomavirus E6 and E7‐transduced human keratinocytes, a model for early‐stage cervical cancer, and with LCM samples. In an experiment comparing LCM clinical samples of gastric adenocarcinoma versus precancerous, spasmolytic polypeptide expressing metaplasia (SPEM) from the same patient, cysteine labeling allowed the identification of more than 1000 discrete protein spots in samples containing 5000 cells. This is a 5‐ to 50‐fold smaller sample than used in previous studies. Both labeling methods had a comparable success rate for protein identification by mass spectrometry (MS). The proteins associated with more than 40 differentially abundant spots in the clinical samples were identified by MS. In this exploratory analysis, changes in expression levels of cytoskeletal proteins, molecular chaperones, and cell‐signaling proteins were seen. The identification of a number of proteins that are potentially relevant to tumor progression suggests that the method holds promise for biomarker discovery.
Molecular cloning and analysis of the Catsper 1 gene promoter

CatSper channels are essential for hyperactivity of sperm flagellum, progesterone-mediated chemotaxis and oocyte fertilization. Catsper genes are exclusively expressed in the testis during spermatogenesis, but the function and regulation of the corresponding promoter regions are unknown. Here, we report the cloning and characterization of the promoter regions in the human and murine Catsper1 genes. These promoter regions were identified and isolated from genomic DNA, and transcriptional activities were tested in vitro after transfection into human embryonic kidney 293, mouse Sertoli cells 1 and GC-1spg cell lines as well as by injecting plasmids directly into mouse testes. Although the human and murine Catsper1 promoters lacked a TATA box, a well-conserved CRE site was identified. Both sequences may be considered as TATAless promoters because their transcriptional activity was not affected after deletion of TATA box-like sites. Several transcription initiation sites were revealed by RNA ligase-mediated rapid amplification of the cDNA 5′-ends. We also found that the immediate upstream region and the first exon in the human CATSPER1 gene negatively regulate transcriptional activity. In the murine Catsper1 promoter, binding sites for transcription factors SRY, SOX9 and CREB were protected by the presence of nuclear testis proteins in DNAse degradation assays. Likewise, the mouse Catsper1 promoter exhibited transcriptional activity in both orientations and displayed significant expression levels in mouse testis in vivo, whereas the suppression of transcription signals in the promoter resulted in low expression levels. This study, thus, represents the first identification of the transcriptional control regions in the genes encoding the human and murine CatSper channels.
Paracellular Permeability Restricts Airway Epithelial Responses to Selectively Allow Activation by Mediators at the Basolateral Surface1

Respiratory pathogens and toxins often assault the lung from the airway lumen. Airway epithelia may initiate and amplify inflammation in response to these attacks, but under certain conditions confinement of inflammation to the airway lumen may be beneficial to the host. Accordingly, we hypothesized that airway epithelial polarity allows different responses to basolateral vs apical stimuli that may modulate inflammation. Using primary human airway epithelial cells differentiated at an air-liquid interface in culture, we found that responses to several cytokines required basolateral mediator application. In contrast, responses to Haemophilus influenzae occurred after either basolateral or apical interaction with airway epithelia. Experiments focused on IFN-γ receptor polarity confirmed its predominant basolateral location in cultured airway epithelia as well as in normal human airway tissue. Furthermore, physical and pharmacologic disruption of barrier function in airway epithelia allowed responses to apical application of IFN-γ and other cytokines. These in vitro studies directly correlated with experiments in mice in which an airway epithelial response to IFN-γ injected into the airway lumen was seen only after disruption of barrier function. The results indicate that airway epithelia with intact barrier function restrict inflammatory responses by limitation of cell activation through requiring interaction of selected mediators with the basolateral surface. However, loss of barrier integrity allows epithelial responses to these mediators if located in the airway lumen to amplify airway defenses.
Multicenter closed-loop/hybrid meal bolus insulin delivery with type 1 diabetes.

BACKGROUND This study evaluated meal bolus insulin delivery strategies and associated postprandial glucose control while using an artificial pancreas (AP) system. SUBJECTS AND METHODS This study was a multicenter trial in 53 patients, 12-65 years of age, with type 1 diabetes for at least 1 year and use of continuous subcutaneous insulin infusion for at least 6 months. Four different insulin bolus strategies were assessed: standard bolus delivered with meal (n=51), standard bolus delivered 15 min prior to meal (n=40), over-bolus of 30% delivered with meal (n=40), and bolus purposely omitted (n=46). Meal carbohydrate (CHO) intake was 1 g of CHO/kg of body weight up to a maximum of 100 g for the first three strategies or up to a maximum of 50 g for strategy 4. RESULTS Only three of 177 meals (two with over-bolus and one with standard bolus 15 min prior to meal) had postprandial blood glucose values of <60 mg/dL. Postprandial hyperglycemia (blood glucose level >180 mg/dL) was prolonged for all four bolus strategies but was shorter for the over-bolus (41% of the 4-h period) than the two standard bolus strategies (73% for each). Mean postprandial blood glucose level was 15.9 mg/dL higher for the standard bolus with meal compared with the prebolus (baseline-adjusted, P=0.07 for treatment effect over the 4-h period). CONCLUSIONS The AP handled the four bolus situations safely, but at the expense of having elevated postprandial glucose levels in most subjects. This was most likely secondary to suboptimal performance of the algorithm.
Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators.

Members of the SOX family of transcription factors are found throughout the animal kingdom, are characterized by the presence of a DNA-binding HMG domain, and are involved in a diverse range of developmental processes. Previous attempts to group SOX genes and deduce their structural, functional, and evolutionary relationships have relied largely on complete or partial HMG box sequence of a limited number of genes. In this study, we have used complete HMG domain sequence, full-length protein structure, and gene organization data to study the pattern of evolution within the family. For the first time, a substantial number of invertebrate SOX sequences have been included in the analysis. We find support for subdivision of the family into groups A-H, as has been suggested in some previous studies, and for the assignment of two new groups, I and J. For vertebrate genes, it appears that relatedness as suggested by HMG domain sequence is congruent with relatedness as indicated by overall structure of the full-length protein and intron-exon structure of the genes. Most of the SOX groups identified in vertebrates were represented by a single SOX sequence in each invertebrate species studied. We have named anonymous sequences and, where appropriate, have suggested systematic names for some previously identified sequences. In addition, we identify an HMG domain signature motif which may be considered representative of the SOX family. Based on our data, we propose a robust phylogeny of SOX genes that reflects their evolutionary history in metazoans.
Combination of QuEChERS and DLLME for GC-MS determination of pesticide residues in orange samples

A new method combining QuEChERS (quick, easy, cheap, effective, rugged and safe) and DLLME (dispersive liquid–liquid microextraction) followed by gas chromatography-mass spectrometry with selected ion monitoring (SIM) was developed for the simultaneous determination of 19 pesticides from nine chemical groups exhibiting or suspected to exhibit endocrine-disrupting properties in orange samples. Acetonitrile extract obtained from QuEChERS extraction was used for DLLME as dispersive solvent and carbon tetrachloride as extractive solvent to increase the enrichment factor of the extraction procedure. The effect of several extraction parameters, such as volume extract achieved by the QuEChERS method and subsequently used for DLLME, selection of extractive solvent and its volume, was tested. Under optimum conditions, good linearity, satisfactory recoveries and repeatability were obtained. Limits of quantification (LOQs) achieved (ranging from 0.02 to 47 ng/g) were below the maximum residue limits established by the European Union. The proposed method was applied to the monitoring of pesticide residue levels in oranges commercialised in Portugal.
Lactate Production in Pancreatic Islets

Lactate production, glucose utilization, glucose oxidation, and insulin release were studied in islets from rat and ob/ob mice. Lactate was determined with a highly sensitive method, based on esterification, subsequent separation, and quantitation with high-performance liquid chromatography. There was a significant lactate production in the absence of glucose, which increased with glucose concentrations up to 3 mmol/l, reaching its half-maximal rate in the presence of 0.2–1.0 mmol/l glucose in both species. Glucose utilization displayed a wider glucose concentration dependence, with a KQ 5 value between 3 and 10 mmol/l glucose. The rates of glucose utilization and lactate production were similar at 3 mmol/l glucose in rat islets and at about 6 mmol/l glucose in ob/ob mice islets. Saturation of lactate production at low glucose concentrations is probably contributing to the observed preferential stimulation of oxidative metabolism at higher concentrations. D-Mannoheptulose caused a marked inhibition of glucose utilization and glucose oxidation at 20 mmol/l glucose in islets from rat or ob/ob mice, as would be expected from a competitive inhibition of glucokinase. By contrast, D-mannoheptulose reduced only marginally the islet metabolism at 3 mmol/l glucose, which is consistent with an effective mannoheptulose-induced inhibition of the glucokinase-dependent, minor part of glucose phosphorylation at this low glucose concentration.
Review of Imprinted Polymer Microrings as Ultrasound Detectors: Design, Fabrication, and Characterization

Detectors play a vital role in ultrasound sensing and imaging applications. With the rapid development of photoacoustic imaging technology in recent years, novel ultrasound detectors based on optical methods have gained increased attention, among which the imprinted polymer microring is a representative one. This review covers the device design, fabrication, and characterization, with an emphasis on how the imprinting-based fabrication methodology benefits the device performance, which further facilitates photoacoustic imaging and sensing applications. By carefully designing and fabricating the imprint mold, the imprinted polymer microring has a quality factor on the order of $10^{5}$ at 780 nm. The device has advantages such as wide acoustic bandwidth response from dc to 350 MHz at -3 dB, low noise equivalent detectable pressure, wide acceptance angle, and so on. The polymer microring has been successfully employed in applications such as photoacoustic imaging and real-time terahertz pulse detection.
Unequal and Genotype-Dependent Expression of Mitochondrial Genes in Larvae of the Pacific Oyster Crassostrea gigas

Mitochondria are essential for regulation of energy metabolism, but little is known about patterns of mitochondrial genome expression in invertebrates. To explore the association of mitochondrial expression with differential growth of Crassostrea gigas, the Pacific oyster, we crossed two inbred lines to produce inbred and hybrid larvae, which grew at different rates under the same environmental conditions. Using high-throughput cloning and sequencing methods, we identified 1.1 million expressed sequence tags from the mitochondrial genome, 96.7% of which were perfect matches to genes targeted by the method. Expression varied significantly among genes, ranging over nearly four orders of magnitude, from mt:lRNA, which constituted 21% of all transcripts, to mt:CoII, which constituted less than 0.02% of all transcripts. Variable expression of genes coding for subunits of macromolecular complexes (e.g., mt:CoI and mt:CoII) implies that stoichiometry in these complexes must be regulated post-transcriptionally. Surprisingly, the mitochondrial transcriptome contained non-coding transcripts, which may play a role in the regulation of mitochondrial function. Finally, mitochondrial expression depended strongly on maternal factors and nuclear-cytoplasmic interactions, which may explain previously observed growth differences between reciprocal hybrids. Differences in mitochondrial gene expression could provide a biochemical index for the metabolic basis of genetically determined differences in larval growth.
A micromachined WR-3 band waveguide diplexer based on coupled resonator structures

A novel micromachined coupled-resonator waveguide diplexer operating in frequency range 220–325 GHz is presented. The diplexer has been synthesised using coupling matrix optimization of multiple coupled resonators, and constructed with innovative structure using micromachining technology. The diplexer structure consists of waveguide cavity resonators, waveguide extensions, and embedded bends, and it has been made of four layers of metal coated SU-8. The diplexer structure allows accurate alignment and secure connection with the flanges of waveguide test ports and matched loads.
Clonal boundary analysis in the developing retina using X-inactivation transgenic mosaic mice.

Transgenic mice harboring the lacZ reporter gene on one X chromosome have been used to mark 50% of all retinal progenitors. The distribution of clones arising from this population of marked progenitors reveals a conspicuous columnar segregation of clonally related cells, indicating that most retinal neuroblasts migrate exclusively radially. Against this columnar background of the transgenic retina, single cone, horizontal, amacrine and ganglion cells are observed to transgress clonal borders, mixing freely with cells derived from different precursors. This tangential dispersion is due to the lateral movement of postmitotic neuroblasts around the time of their differentiation, rather than to the dispersion of a proliferative sibling at the time of cell birth. Tangential dispersion is suggested to play a significant role in creating the functional architecture of the mature retina, being the means by which the orderly spacing, or regularity, of retinal mosaics is established during development.
Isoflurane Posttreatment Reduces Brain Injury After an Intracerebral Hemorrhagic Stroke in Mice

BACKGROUND: Intracerebral hemorrhage (ICH) is a devastating stroke subtype affecting 120,000 Americans annually. Of those affected, 40%to 50% will die within the first 30 days, whereas the survivors are left with a lifetime of neurobehavioral disabilities. Recently, it has been shown that volatile anesthetics such as isoflurane can reduce brain injury after an ischemic stroke. As a result, in this study, we investigated the effects of isoflurane as a posttreatment therapeutic modality in ICH-injured mice. Specifically, we investigated whether isoflurane posttreatment can preserve the structural integrity of the brain by reducing apoptotic damage and, in turn, improve functional outcome by amelioration of brain edema and neurobehavioral deficits. METHODS: Male CD1 mice (n = 53) were divided into the following groups: sham (n = 14), ICH (n = 14), ICH treated with 1.5% isoflurane posttreatment for 1 hour (n = 15), and ICH treated with 1.5% isoflurane posttreatment for 2 hours (n = 10). The blood injection ICH model was adapted; this involved extracting autologous blood from the mouse tail and injecting it directly into the right basal ganglia. One hour after surgery, treated mice were placed in a glass chamber maintained at 37°C and infused with 1.5% isoflurane for 1 or 2 hours. At 24 hours postinjury, mice were assessed for neurobehavioral deficits using the Modified Garcia Score and then killed and assessed for brain water content. Double immunofluorescent staining was performed using neuronal marker MAP-2 and TUNEL under a fluorescent microscope to assess for apoptosis. RESULTS: Our results indicated that after 1-hour 1.5% isoflurane posttreatment, there was a significant reduction in brain edema, a decrease in apoptotic cell death, and a significant improvement in neurobehavioral deficits. CONCLUSIONS: Our results suggest that isoflurane may be an effective posttreatment therapeutic option for ICH because of its ability to reduce structural damage and subsequently preserve functional integrity.
Adjuvant intraoperative post-dissectional tumor bed chemotherapy-A novel approach in treating midgut neuroendocrine tumors.

BACKGROUND Midgut neuroendocrine tumor (NET) patients are often diagnosed at an advanced stage with extensive mesenteric lymph node and liver metastasis. Even with skillful surgical dissection, macro and microscopic residual disease at the dissection site remains a possibility. We hypothesize these potential tumor residuals in mesenteric lymph node dissection beds can be eliminated safely by a local application of 5-fluorouracil (5-FU). We describe a novel technique invented by the author to treat these micro and macro residuals. METHODS Retrospectively, charts of 62 consecutive midgut NET patients with boggy mesenteric lymphadenopathy who underwent cytoreductive debulking surgeries from 1/2007 to 12/2009 were reviewed. A total of 32 patients received an intraoperative application of 5-FU saturated gelfoam strips secured into the mesenteric defect following the extensive lymphadenectomy. A total of 30 untreated patients served as a control. RESULTS The 5-year survival after cytoreductive surgeries was 22/32 (68.8%) for the treated group, vs. 20/30 (66.7%) for the control. Six patients (6/32, 18.8%) among the study group required additional debulking surgeries, vs. 16 patients (16/30, 53.3%) in the control group. Upon reoperation, loco-regional recurrence was noted in 9 of the 16 patients (56.3%) in the control group, vs. only 2/6 (33.3%) of treated patients. Overall, local recurrence rate is 6.25% (2/32) in the treated group vs. 30% (9/30) in the control group. Post-op complication rates are similar in the two arms. CONCLUSIONS Intraoperative application of chemotherapy is a safe and effective adjuvant to reduce local recurrence and the need of reoperation by the tumoricidal or tumorstatic effects of 5-FU on any potential microscopic residual disease after extensive cytoreductive surgeries in advanced stage NET patients with mesenteric lymph node metastasis. It provides patients with sustained, slow releasing, high dose of 5-FU within the surgical bed with a negligible side effect profile. Further studies are required to evaluate its effect on long term survival.
Symptom perception and asthma control

Abstract Objectives: Asthma control is the goal of asthma management. The perception of asthma symptoms represents a cornerstone aspect in this issue. The visual analogue scale (VAS) has been proposed as a useful tool for assessing respiratory symptoms perception. The present cross-sectional real-life study investigated whether VAS assessment of asthma symptoms perception could predict asthma control level. Methods: This cross-sectional study included a total of 370 (153 males, mean age 39.9 years) patients with asthma. Perception of asthma symptoms was assessed by VAS; clinical examination, lung function, fraction of exhaled nitric oxide (FeNO) measurement, Asthma Control Test (ACT) and Hospital Anxiety Depression Scale questionnaires were also evaluated. Results: Asthma was well controlled in 47% of patients. Considering most of the evaluated parameters, there were significant differences among patients with well-controlled, partly controlled and uncontrolled asthma. VAS values were significantly (p < 0.001) different considering the asthma control level. VAS score were significantly related with ACT scores (p < 0.001). A VAS <6 was able to reliably predict uncontrolled asthma (area under the curve: 0.74; odds ratio: 5.16). Conclusion: The present real-life study demonstrates that asthma symptoms assessment by VAS might be useful for approximately predicting uncontrolled asthma in particular conditions, such as at home or at the general practitioner’s office.
Lower rhombic lip‐derived cells undergo transmedian tangential migration followed by radial migration in the chick embryo brainstem

Migration behaviour and fate of cells originated from the lower rhombic lip (LRL) was examined in the chick embryo hindbrain. LRL‐derived cells tangentially migrate along the pial surface of the brainstem and form a transient subpial migratory stream. In the initial stages of migration, LRL‐derived cells appose each other or axon‐like processes, which is indicative of mode of homophilic chain migration and/or axophilic migration. Some LRL‐derived cells relocate rostroventrally towards the pontine region, although the majority of them migrate circumferentially to the ventral medulla oblongata. Depending on the stage of generation, LRL‐derived cells undergo transmedian migration; late‐generated LRL‐derived cells preferentially colonize the contralateral brainstem compared with early generated cells. Thus, latecomer neuron precursors may migrate past their predecessors in the migratory stream. When LRL‐derived cells leave the subpial migratory stream, they change their migratory direction to a radial one and relocate inwardly, with a profile that resembles a tangential‐to‐radial change seen in cerebellar granule cell precursors. After they enter the parenchymal region of the brainstem, they exhibited morphological differentiation, and some differentiate into excitatory neurons. The present results suggest that LRL‐derived cells migrate across boundaries such as midline or rhombomere, which may facilitate to build up cellular and functional architectures of the hindbrain.