gebhart/patrepeval huggingface dataset:
Androgen receptors and growth fraction in metastatic prostate cancer as predictors of time to tumour progression after hormonal therapy. (1991)

Reliable predictors of response for prostate cancer patients undergoing hormone therapy are lacking. Since 80-90% of such patients do respond but the time between therapy and relapse (progression) is variable, our goal has been to predict the time to tumour progression after therapy rather than merely to predict whether a patient would respond. We investigated AR positivity and Ki-67 growth fraction of malignant epithelial cells as potential predictors of the time to progression; these studies are summarized in this chapter. The percentage of AR positive nuclei has no predictive value; however, the variance of AR immunostaining intensity within a certain specimen is an important discriminator between good responders (patients with a prolonged interval between initiation of therapy and relapse) and poor responders (short time to relapse). There is a trend towards a higher growth fraction in poor responders, but statistical significance is borderline at best. Growth fraction measurement might be more useful as a predictor if the rate of cell death could also be evaluated or if analysis could be limited to the androgen independent cells that continue to proliferate after hormone therapy and that ultimately are responsible for the clinical manifestation of tumour progression and relapse.
Tacks: A New Technique for Craniofacial Fixation (2001)

Biodegradable fixation in craniofacial surgery provides secure fixation while eliminating much of the concern over intracranial migration of metallic plates and screws. One limitation of present biodegradable systems, however, is the need for tapping the drill hole before screw insertion. Herein, a new method of rigid, biodegradable fixation with tacks (Macrapore, Inc., San Diego, CA) is described. The tacks are made of a 70:30 ratio of the L and DL form of polylactic acid (L,DL-PLA). Degradation times range from 18 to 36 months. Newer prototypes are nearly developed for more rapid dissolution times. From April 1999 to February 2000, tack fixation has been applied in 100 patients (51 males, 49 females aged 3 months to 61 years). Indications for operation were craniosynostosis (n = 33); craniofacial trauma or post-traumatic deformities (n = 11); cleft lip and palate (n = 13); craniofacial syndromes (n = 18); other diagnoses (n = 11). Patients underwent fronto-orbital advancement with cranial reshaping; monobloc osteotomy, open reduction-internal fixation of fractures; hypertelorbitism repair; cranioplasty; stabilization of grafts; major cranial reconstruction; zygomatic advancement; alveolar cleft repair; and iliac bone graft donor site protection. Tacks were also used for temporalis muscle and lateral canthal suspension. Follow-up ranged from 16 to 28 months. Complications occurred in 7 patients, 4 of whom had infections and during debridement had biodegradable implants removed. None of the complications appeared to be related to the use of tacks. The tacks are carried in a specially designed holder and may be placed by hand or with the light tap of a mallet on the tack driver. An automatic driver has been developed. Overall, the performance of the tacks has been excellent. They are easily handled by the nursing personnel and rapidly inserted by the surgeon. Stability appears to be excellent. At this time, it is probably preferable to employ tap and screws for orthognathic surgery or other osteotomies with substantial load bearing.
Nerve Growth Factor in CNS Repair (1994)

The hypothesis that neurotrophic factors play important roles in the adult central nervous system (CNS) has been successfully investigated in the past decade with regard to experimental and pathologic situations. Trophic roles in adult CNS axonal regeneration, on the other hand, have received much less attention. We review three groups of recent studies that demonstrate the relevance of nerve growth factor (NGF) for the regeneration of selected axons into adult central nervous tissue. The first group concerns a septohippocampal model where transected septal cholinergic axons are allowed to regrow into the hippocampal formation through a peripheral nerve bridge implanted into the transection lesion gap. NGF is required in the bridge, enhances penetration of the hippocampal tissue when infused there, and both attracts and promotes sprouting within the septum when infused in the lateral ventricle or the septal tissue itself. The second group of studies concerns the development of a spinal cord sensory regeneration model, where dorsal root ganglionic axons regrow into a nerve bridge placed within the dorsal spinal cord. Preliminary data indicate that NGF infusion rostral to the bridge once again promotes substantial penetration of the adult cord tissue by the regenerating NGF-sensitive fibers. In the third group of studies, attention has been shifted to the location of endogenous NGF in the adult rat hippocampal formation and the normal or lesion-induced occurrence of extrasomal NGF immunoreactivity. These regions of anchored NGF have the ability to attract NGF-sensitive growing axons and may provide opportunities to investigate local cues for final definition of terminal fields.
Two different phosphorylation-dephosphorylation cycles of Na,K-ATPase proteoliposomes accompanying Na+ transport in the absence of K+. (1987)

The phosphorylated intermediate (EP) of the Na,K-ATPase proteoliposomes (PL) prepared from the electric eel enzyme is composed of an ADP-sensitive K+-insensitive form (E1P), an ADP- and K+-sensitive form (E*P), and a K+-sensitive ADP-insensitive form (E2P). The composition of the intermediate varied with the cholesterol content of the lipid bilayer. The PL containing less than 30 mol % cholesterol (LCPL) formed E2P-rich EP in the presence of 10 mM Na+ on both sides at 15 degrees C, while the PL containing more than 35 mol % cholesterol (HCPL) formed E*P-rich EP under the same condition. In the presence of ionophore (monensin, nigericin, A23187), the HCPL formed E2P-rich EP as reported in the preceding paper. The turnover rate of Na-ATPase activity (the ratio of Na-ATPase to the EP level) in the LCPL was lower than that in the HCPL, and the addition of 20 microM monensin or A23187 to the HCPL reduced the Na-ATPase activity. The coupling ratio of Na+ influx (cellular efflux):Na+ efflux (cellular influx):ATP hydrolysis was 2.8:1.8:1 in the LCPL, although 1.6:0.6:1 in the HCPL. The coupling ratio of Na+ influx:ATP hydrolysis in the HCPL increased to 2.8:1 in the presence of A23187. Moreover, the increase of ATP concentration enhanced not only the Na-ATPase activity in the LCPL and HCPL with monensin but also the Na+ influx in the LCPL. This ATP enhancement was not found, however, in the HCPL without ionophores. The ADP enhancement of the Na+ influx was not observed in either the HCPL or the LCPL. We conclude from these observations that there are at least two different phosphorylation-dephosphorylation cycles (an E2P cycle and an E*P cycle) in the PL in the absence of K+. The E2P cycle transports three Na+ from the extravesicular (cytoplasmic) to the intravesicular (extracellular) side and two Na+ in the opposite direction per cycle and is similar to the ATP-dependent Na+-Na+ exchange system already reported (Blostein, R. (1983) J. Biol. Chem. 258, 7948-7953; Cornelius, F., and Skou, J. C. (1985) Biochim. Biophys. Acta 818, 211-221). However, the E*P cycle transports one Na+ from the extravesicular to the intravesicular side/cycle and has not yet been previously reported.
Failure to Phosphorylate the Retinoblastoma Gene Product in Senescent Human Fibroblasts (1990)

Heterokaryon studies suggest that senescent and quiescent human diploid fibroblasts (HDF) contain a common inhibitor of entry into S phase. DNA synthesis can be induced in senescent and quiescent HDF by fusing them with cells containing DNA viral oncogenes such as SV40 T antigen, adenovirus E1A, or human papillomavirus E7. Both senescent and quiescent HDF contained the unphosphorylated form (p110Rb) of the retinoblastoma protein, a putative inhibitor of proliferation. After serum stimulation, senescent HDF did not phosphorylate p110Rb and did not enter S phase, whereas quiescent HDF phosphorylated p110Rb and entered S phase. These findings, combined with the observations that T antigen, E1A, and E7 form complexes with, and presumably inactivate, unphosphorylated p110Rb, suggest that failure to phosphorylate p110Rb may be an immediate cause of failure to enter S phase in senescent HDF.
Yeast microarrays for genome wide parallel genetic and gene expression analysis (1997)

We have developed high-density DNA microarrays of yeast ORFs. These microarrays can monitor hybridization to ORFs for applications such as quantitative differential gene expression analysis and screening for sequence polymorphisms. Automated scripts retrieved sequence information from public databases to locate predicted ORFs and select appropriate primers for amplification. The primers were used to amplify yeast ORFs in 96-well plates, and the resulting products were arrayed using an automated micro arraying device. Arrays containing up to 2,479 yeast ORFs were printed on a single slide. The hybridization of fluorescently labeled samples to the array were detected and quantitated with a laser confocal scanning microscope. Applications of the microarrays are shown for genetic and gene expression analysis at the whole genome level.
Maturation of embryonic tissues in a lymph node: a new approach for bioengineering complex organs (2014)

Given our recent finding that the lymph node (LN) can serve as an in vivo factory to generate complex structures like liver, pancreas, and thymus, we investigated whether LN could also support early development and maturation from several mid-embryonic (E14.5/15.5) mouse tissues including brain, thymus, lung, stomach, and intestine. Here we observed brain maturation in LN by showing the emergence of astrocytes with well-developed branching processes. Thymus maturation in LN was monitored by changes in host immune cells. Finally, newly terminally differentiated mucus-producing cells were identified in ectopic tissues generated by transplantation of lung, stomach and intestine in LN. Thus, we speculate the LN offers a unique approach to study the intrinsic and extrinsic differentiation potential of cells and tissues during early development, and provides a new site for bioengineering complex body parts.
Abnormal development of dendritic spines in FMR1 knock-out mice. (2001)

Fragile X syndrome is caused by a mutation in the FMR1 gene leading to absence of the fragile X mental retardation protein (FMRP). Reports that patients and adult FMR1 knock-out mice have abnormally long dendritic spines of increased density suggested that the disorder might involve abnormal spine development. Because spine length, density, and motility change dramatically in the first postnatal weeks, we analyzed these properties in mutant mice and littermate controls at 1, 2, and 4 weeks of age. To label neurons, a viral vector carrying the enhanced green fluorescent protein gene was injected into the barrel cortex. Layer V neurons were imaged on a two-photon laser scanning microscope in fixed tissue sections. Analysis of >16,000 spines showed clear developmental patterns. Between 1 and 4 weeks of age, spine density increased 2.5-fold, and mean spine length decreased by 17% in normal animals. Early during cortical synaptogenesis, pyramidal cells in mutant mice had longer spines than controls. At 1 week, spine length was 28% greater in mutants than in controls. At 2 weeks, this difference was 10%, and at 4 weeks only 3%. Similarly, spine density was 33% greater in mutants than in controls at 1 week of age. At 2 or 4 weeks of age, differences were not detectable. The spine abnormality was not detected in neocortical organotypic cultures. The transient nature of the spine abnormality in the intact animal suggests that FMRP might play a role in the normal process of dendritic spine growth in coordination with the experience-dependent development of cortical circuits.
Lymphokine-activated killer cells. VII. IL-4 induces an NK1.1+CD8 alpha+beta- TCR-alpha beta B220+ lymphokine-activated killer subset (1993)

Murine IL-2-induced lymphokine-activated killers (LAK) can be divided into two mutually exclusive subsets: NK1.1+CD8- and NK1.1-CD8+. We have previously established that the lytically active subset of each of these two populations expressed B220, as determined by the mAb 6B2, on its surface. In this study, we examined the lytically active subsets induced by IL-4. We found that, similar to IL-2, the lytically active IL-4-LAK expressed B220 on their surface. Similar to IL-2-LAK, IL-4-LAK cultures also contained NK1.1+CD8- B220+, and NK1.1-CD8+B220+ subsets. IL-4-LAK cultures, however, contained two novel and unexpected lymphocyte subsets determined by their surface markers to be either: i) NK1.1+CD8 alpha+beta-B220+, or ii) NK1.1-CD8 alpha+beta-B220+. These subsets were not derived from NK1.1+ or CD8+ precursors but were induced from a CD4-CD8-NK1.1-Slg- splenocyte subpopulation. Most of the CD8 alpha+beta- cells seen in the IL-4 cultures expressed TCR-alpha beta with little or no TCR-gamma delta detected on their surface. Similar to IL-2-LAK, the IL-4-LAK subsets appeared to display a bias as to their susceptible target cells with the NK1.1-CD8 alpha+beta+ subset being most potent against trinitrophenyl-modified autologous lymphoblasts (2,4,6-trinitrobenzene sulfonic acid (TNBS)-self). The NK1.1+CD8 alpha-beta- effectors were most potent against YAC-1 and CL27A with little activity against TNBS-self. All three targets were susceptible to lysis by the NK1.1+CD8 alpha+beta- subset. These findings document the characteristics of a novel lymphocyte subset, derived from splenic precursors, which shares certain features with cells previously thought to be present exclusively in intraepithelial lymphocytes.
Detection of Symptomatic Carotid Plaque Using Source Data from MR and CT Angiography: A Correlative Study (2015)

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Carotid plaque MRI has been a useful method to characterize vulnerable atherosclerotic plaque elements. Recent investigations have suggested that source images from CT angiography (CTA) and MR angiography (MRA) can identify the simple high-risk features of symptom-producing carotid artery plaque. We studied the correlation and relative diagnostic accuracies of CTA and MRA source images in detecting symptomatic carotid artery plaque. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; Subjects were eligible if they had carotid stenosis between 50 and 99% and had MRA and CTA exams performed within 10 days of one another. We measured the soft (non-calcified) plaque and hard (calcified) plaque thickness on CTA axial source images and intraplaque high-intensity signal (IHIS) on 3D-time-of-flight MRA source images in subjects. We assessed whether a correlation existed between increasing CTA soft plaque thicknesses and the presence of MRA IHIS using the Student's t-test. We calculated the differences in sensitivity and specificity measures of CTA and MRA source-imaging data with the occurrence of recent ipsilateral stroke or transient ischemic attack (TIA) as the reference standard. We also performed logistic regression analyses to evaluate the predictive strength of plaque showing both IHIS and increased CTA soft plaque thickness in predicting symptomatic disease status. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; Of 1994 screened patients, 48 arteries met the final inclusion criteria with MRA and CTA performed within 10 days of one another. The mean and median time between CTA and MRA exams were 2.0 days and 1 day, respectively. A total of 34 of 48 stenotic vessels (70.8%) were responsible for giving rise to ipsilateral stroke or TIA. CTA mean soft plaque thickness was significantly greater (4.47 vs. 2.30 mm, p &lt; 0.0001) in patients with MRA-defined IHIS, while CTA hard plaque thickness was significantly greater (2.09 vs. 1.16 mm, p = 0.0134) in patients without MRA evidence of IHIS. CTA soft plaque thickness measurements were more sensitive than MRA IHIS (91.2 vs. 67.6%, p = 0.011) in detecting symptomatic plaque, while differences in specificity were not significantly different (p = 0.1573). In the subset of patients with both IHIS on MRA and plaque thickness &gt;2.4 mm on CTA, the odds ratio of detecting symptomatic plaque, corrected for stenosis severity, was 45.3 (p &lt; 0.0005). &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; Unprocessed source images from CTA and MRA, which are routinely evaluated for clinical studies demonstrate the highly correlated presence of IHIS and increasing soft plaque thickness. In particular, plaque that shows high-risk features on both MRA and CTA are very strongly associated with symptom-producing carotid plaque. With further validation, such techniques are promising practical methods of extracting risk information from routine neck angiographic imaging.
Effect of colchicine on the uptake of prolactin and insulin into Golgi fractions of rat liver. (1982)

In previous studies we have shown that 125I-labeled prolactin is taken up by a receptor-dependent process and concentrated in an intact form in Golgi elements from female rat liver (J. Biol. Chem., 1979, 254:209-214). In this study we have examined the effect of colchicine on this uptake process into Golgi elements. Colchicine [25 mumol (10 mg)/100 gm body wt] was injected intraperitoneally in adult female rats, and hepatic Golgi fractions were prepared at 1, 2, and 3 h postinjection. The enzyme recoveries and morphological appearance of fractions from colchicine-treated and control (alcohol alone) animals were similar. At times greater than 1 h after colchicine there was a marked (greater than 60%) inhibition of uptake of 125I-ovine prolactin (125I-oPRL) into Golgi light and intermediate fractions but no inhibition of uptake into Golgi heavy and plasmalemma elements. At times from 2 to 45 min postinjection, 125I-oPRL was extracted from Golgi elements and found to be largely intact as judged by rebinding to receptors. The inhibitory effect of colchicine was seen at doses ranging from 0.25 mumol to 25 mumol/100 g body wt. Vincristine also inhibited 125I-oPRL uptake into the Golgi light and intermediate fractions but lumicolchicine had no inhibitory effect. There was a smaller effect of colchicine both at early (1 h) and later (3 h) times on the extent and pattern of 125I-insulin uptake. Colchicine treatment did not produce a significant change in lactogen receptor levels in the Golgi fractions. These results demonstrate that colchicine treatment inhibited the transfer of prolactin into Golgi vesicular elements. The much smaller effect on insulin uptake suggests that there may be differences in the manner in which the two hormones are handled in the course of internalization.
Biochemical and molecular characterization of hepatocyte‐like cells derived from human bone marrow mesenchymal stem cells on a novel three‐dimensional biocompatible nanofibrous scaffold (2008)

The data presented in this study show that the engineered nanofibrous scaffold is a conductive matrix which supports and enhances MSC development into functional hepatocyte-like cells.
Animal Models of Huntington's Disease (2003)

Huntington’s disease (HD) is an inherited, progressive neurodegenerative disorder transmitted by a single autosomal dominant gene. The symptomology of the disease was first described by George Huntington in 1872 as consisting of a progressive dementia coupled with bizarre uncontrollable movements and abnormal postures. HD is found in nearly all ethnic and racial groups with slight variations in prevalence rates. Overall, the prevalence rate of HD in the US is approx 50/1,000,000 (; ). Although HD may occur during the juvenile years (); the manifestation of the disorder typically occurs in middle life, about 35–45 years of age. From the time of onset, an intractable course of mental deterioration and progressive motor abnormalities begins with death usually occurring within 15 years.
PROTDES: CHARMM toolbox for computational protein design (2008)

We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html .
Site-specifically labeled CA19.9-targeted immunoconjugates for the PET, NIRF, and multimodal PET/NIRF imaging of pancreatic cancer (2015)

Molecular imaging agents for preoperative positron emission tomography (PET) and near-infrared fluorescent (NIRF)-guided delineation of surgical margins could greatly enhance the diagnosis, staging, and resection of pancreatic cancer. PET and NIRF optical imaging offer complementary clinical applications, enabling the noninvasive whole-body imaging to localize disease and identification of tumor margins during surgery, respectively. We report the development of PET, NIRF, and dual-modal (PET/NIRF) imaging agents, using 5B1, a fully human monoclonal antibody that targets CA19.9, a well-established pancreatic cancer biomarker. Desferrioxamine (DFO) and/or a NIRF dye (FL) were conjugated to the heavy-chain glycans of 5B1, using a robust and reproducible site-specific (ss) labeling methodology to generate three constructs ((ss)DFO-5B1, (ss)FL-5B1, and (ss)dual-5B1) in which the immunoreactivity was not affected by the conjugation of either label. Each construct was evaluated in a s.c. xenograft model, using CA19.9-positive (BxPC3) and -negative (MIAPaCa-2) human pancreatic cancer cell lines. Each construct showed exceptional uptake and contrast in antigen-positive tumors with negligible nonspecific uptake in antigen-negative tumors. Additionally, the dual-modal construct was evaluated in an orthotopic murine pancreatic cancer model, using the human pancreatic cancer cell line, Suit-2. The (ss)dual-5B1 demonstrated a remarkable capacity to delineate metastases and to map the sentinel lymph nodes via tandem PET-computed tomography (PET/CT) and NIRF imaging. Fluorescence microscopy, histopathology, and autoradiography were performed on representative sections of excised tumors to visualize the distribution of the constructs within the tumors. These imaging tools have tremendous potential for further preclinical research and for clinical translation.
Integrated Microdevice for DNA Restriction Fragment Analysis (1996)

An integrated monolithic device (8 mm × 10 mm) that performs an automated biochemical procedure is demonstrated. The device mixes a DNA sample with a restriction enzyme in a 0.7-nL reaction chamber and after a digestion period injects the fragments onto a 67-mm-long capillary electrophoresis channel for sizing. Materials are precisely manipulated under computer control within the channel structure using electrokinetic transport. Digestion of the plasmid pBR322 by the enzyme HinfI and fragment analysis are completed in 5 min using 30 amol of DNA and 2.8 × 10(-3) unit of enzyme per run.