Miracle-dz/UniFAR-FTUs huggingface dataset:
Early Withdrawal of Axons from Higher Centers in Response to Peripheral Somatosensory Denervation

The mechanisms responsible for long-term, massive reorganization of representational maps in primate somatosensory cortex after deafferentation are poorly understood. Sprouting of cortical axons cannot account for the extent of reorganization, and withdrawal of axons of deafferented brainstem and thalamic neurons, permitting expression of previously silent synapses, has not been directly demonstrated. This study is focused on the second of these. In monkeys, deafferented for two years by section of the cuneate fasciculus at the C1 level, there was extensive withdrawal of axon terminals from thalamus and cortex, detectable a decade before visible atrophy of their parent neuronal somata in the cuneate nucleus or thalamus. Slow, inexorable progression of lemniscal and thalamocortical axonal withdrawal is a neurodegenerative phenomenon likely to be a powerful inducement to compensatory long-term plasticity, a mechanism that can explain the long-term evolution of cortical reorganization and, with it, phantom sensations in spinal patients and amputees.
Vision as an anticipatory process

Vision is a crucial sensor. It provides a very rich collection of information about our environment. The difficulty in vision arises, since this information is not obvious in the image, it has to be constructed. Wheres earlier approaches have favored a bottom-up approach, which maps the image onto an internal representation of the world, more recent approaches search for alternatives and develop frameworks which make use of top down connections. In these approaches vision is inherently a constructive process which makes use of a priory information. Following this line of research, a theory of anticipatory vision is outlined and demonstrated by a computational model of primate vision.
Eunicellin-Based Diterpenoids, Hirsutalins S–V, from the Formosan Soft Coral Cladiella hirsuta

Four new eunicellin-type hirsutalins S–V (1–4), along with a known compound (–)-6α-hydroxy polyanthellin A (5), were isolated from the soft coral Cladiella hirsuta. The structures of the metabolites were determined by extensive spectroscopic analysis. Cytotoxity of compounds 1–5 against the proliferation of a limited panel of cancer cell lines was measured. Anti-inflammatory activity of compounds 1–5 was evaluated by measuring their ability in suppressing superoxide anion generation and elastase release in fMLP/CB-induced human neutrophils.
Role of the Ca2+/Phosphatidylserine Binding Region of the C2 Domain in the Translocation of Protein Kinase Cα to the Plasma Membrane*

Signal transduction via protein kinase C (PKC) is closely regulated by its subcellular localization. To map the molecular determinants mediating the C2 domain-dependent translocation of PKCα to the plasma membrane, full-length native protein and several point mutants in the Ca2+/phosphatidylserine-binding site were tagged with green fluorescent protein and transiently expressed in rat basophilic leukemia cells (RBL-2H3). Substitution of several aspartate residues by asparagine completely abolished Ca2+-dependent membrane targeting of PKCα. Strikingly, these mutations enabled the mutant proteins to translocate in a diacylglycerol-dependent manner, suggesting that neutralization of charges in the Ca2+ binding region enables the C1 domain to bind diacylglycerol. In addition, it was demonstrated that the protein residues involved in direct interactions with acidic phospholipids play differential and pivotal roles in the membrane targeting of the enzyme. These findings provide new information on how the C2 domain-dependent membrane targeting of PKCα occurs in the presence of physiological stimuli.
Achieving High-Performance Blue GaN-Based Light-Emitting Diodes by Energy Band Modification on AlxInyGa1–x–yN Electron Blocking Layer

We have achieved high-performance blue GaN-based light-emitting diodes (LEDs) by energy band modification on an Al<sub><italic>x</italic></sub>In<sub><italic>y</italic></sub>Ga<sub>1–<italic>x</italic>–<italic>y</italic></sub>N electron blocking layer (EBL). It is demonstrated by simulation that the strategy using high In/Al ratio to decrease polarization charge density and to alleviate the negative effect from polarization electric fields is more favorable. Using the optimal In/Al ratio of 0.5, the LED with Al<sub>0.40</sub>In<sub>0.20</sub>Ga<sub>0.40</sub>N EBL shows a comprehensive performance improvement. With comparison to the LED with conventional Al<sub>0.15</sub>GaN<sub>0.85</sub>N EBL, such an LED owns a 270.15% improvement on the simulated luminous intensity and shows the smallest voltage of 3.34 V at 100 A/cm<sup>2</sup>. The subsequent experimental results provide the evidence to the superiority of Al<sub><italic>x</italic></sub>In<sub><italic>y</italic></sub>Ga<sub>1–<italic>x</italic>–<italic>y</italic></sub>N<sub>1–<italic>x</italic>–<italic>y</italic></sub>N EBL with a high In/Al ratio. Compared with the reference LED with Al<sub>0.15</sub>Ga<sub>0.85</sub>N EBL, the experimental light output power of the LED with Al<sub>0.35</sub>In<sub>0.18</sub>Ga<sub>0.47</sub>N EBL is 86.58 mW, achieving the best improvement by 31.38%. And the voltage of this LED at 14.4 A/cm<sup>2</sup> (20 mA) is 3.35 V, which is much smaller than the voltage of 3.45 V for the reference LED. Evidently, the Al<sub><italic>x</italic></sub>In<sub><italic>y</italic></sub>Ga<sub>1–<italic>x</italic>–<italic>y</italic></sub>N EBL with the In/Al ratio of 0.5 is very effective to promote the performance of LED, which is very promising to be applied in the further high-performance LED fabrication.
Predicting 30-Day Readmissions: Performance of the LACE Index Compared with a Regression Model among General Medicine Patients in Singapore

The LACE index (length of stay, acuity of admission, Charlson comorbidity index, CCI, and number of emergency department visits in preceding 6 months) derived in Canada is simple and may have clinical utility in Singapore to predict readmission risk. We compared the performance of the LACE index with a derived model in identifying 30-day readmissions from a population of general medicine patients in Singapore. Additional variables include patient demographics, comorbidities, clinical and laboratory variables during the index admission, and prior healthcare utilization in the preceding year. 5,862 patients were analysed and 572 patients (9.8%) were readmitted in the 30 days following discharge. Age, CCI, count of surgical procedures during index admission, white cell count, serum albumin, and number of emergency department visits in previous 6 months were significantly associated with 30-day readmission risk. The final logistic regression model had fair discriminative ability c-statistic of 0.650 while the LACE index achieved c-statistic of 0.628 in predicting 30-day readmissions. Our derived model has the advantage of being available early in the admission to identify patients at high risk of readmission for interventions. Additional factors predicting readmission risk and machine learning techniques should be considered to improve model performance.
Click‐iT™ assay with improved DNA distribution histograms

The Click‐iT™ Assay developed and commercialized by Invitrogen is based on incorporation of a new 5‐bromo‐2′‐deoxyuridine analog, 5‐ethynyl‐2′‐deoxyuridine (EdU) into newly synthesized DNA and its recognition by azide dyes via a copper mediated “click” reaction. This relatively convenient and useful procedure depends on fixation of cells with paraformaldehyde and staining of the DNA with 7‐aminoactinomycin‐D (7‐AAD). Both of these procedures result in DNA histograms with broad coefficients of variation (CV's). In this report, we have shown that after EdU incorporation, nuclei isolated by lysis can be incubated with the Click‐iT™ Assay and stained with propidium iodide for generation of DNA histograms with low CV's. This modified procedure results in better DNA histograms by replacing 7‐AAD with propidium iodide and also saves processing time by eliminating the fixation and permeabilization steps. © 2009 International Society for Advancement of Cytometry
Genetic engineering of baker's and wine yeasts using formaldehyde hyperresistance-mediating plasmids.

Yeast multi-copy vectors carrying the formaldehyde-resistance marker gene SFA have proved to be a valuable tool for research on industrially used strains of Saccharomyces cerevisiae. The genetics of these strains is often poorly understood, and for various reasons it is not possible to simply subject these strains to protocols of genetic engineering that have been established for laboratory strains of S. cerevisiae. We tested our vectors and protocols using 10 randomly picked baker's and wine yeasts all of which could be transformed by a simple protocol with vectors conferring hyperresistance to formaldehyde. The application of formaldehyde as a selecting agent also offers the advantage of its biodegradation to CO2 during fermentation, i.e., the selecting agent will be consumed and therefore its removal during down-stream processing is not necessary. Thus, this vector provides an expression system which is simple to apply and inexpensive to use.
Prognostic features in men who died of prostate cancer.

PURPOSE Since the advent of widespread prostate specific antigen (PSA) based screening in the United States, the risk of over diagnosis as well as delayed diagnosis due to existing PSA thresholds has become a concern. Treatment decision planning is generally linked to prognostic variables, most notably PSA, clinical stage and Gleason grade. We examined these and other prognostic variables in a cohort of men who ultimately died of prostate cancer. MATERIALS AND METHODS Of 413 men with prostate cancer in a cohort in San Antonio, Texas between 1993 and 2003 who died of disease we identified 211 who died as a direct result of prostate cancer. In these cases we assessed presenting symptoms, PSA history, tumor stage and Gleason score at diagnosis. RESULTS Of the 211 men 141 (67%) underwent screening for prostate cancer prior to diagnosis. Of 190 men with PSA data at diagnosis available 7 (3.7%) had PSA less than 4.0 ng/ml and 27 (14%) had PSA 4.0 to 10.0 ng/ml. Clinical stage distribution was cT1 in 21.1% of cases, cT2 in 50.7% and cT3 in 26.8%. Of 167 men for whom biopsy Gleason grade was available 16.8%, 16.2%, 24% and 43.1% had Gleason sum 5 or less, 6, 7 and 8 or higher, respectively. CONCLUSIONS While most men who ultimately die of prostate cancer have poor prognostic features, a substantial number have features associated with a potentially good prognosis, including low PSA and low Gleason grade. Many men who died of prostate cancer had undergone prior screening. These data demonstrate the need for improved markers of prognosis and continued assessment of the efficacy of screening with PSA.
Surfactants expressed by soil pseudomonads alter local soil-water distribution, suggesting a hydrological role for these compounds.

Several biological roles have been demonstrated for surfactants expressed by soil and rhizosphere Pseudomonas spp. , but the impact of these powerful surface-active agents on the local soil-water distribution within the partially saturated soil pore network has not been examined. To investigate this potential hydrological role, the liquid surface tension (γ)-reducing activities (LSTRA) of 72 pseudomonads isolated from a sandy loam soil by tensiometry of culture supernatants were characterized. Of these, 67% exhibited LSTRA, reducing γ to a minimum (γ(Min)) of 24 mN m(-1) established by individual distribution identification analysis. Soil microcosms were then used to examine the impact of surfactant expression on the local soil-water distribution. The volumetric water content (θ) of soil microcosms was significantly lowered (0.78 ×) by Pseudomonas fluorescens SBW25 expressing the surfactant viscosin compared with a surfactant-deficient mutant (P<0.002). Six of 15 soil pseudomonad isolates examined were found to have a similar impact on θ when compared with sterile microcosms (P<0.05). These findings indicate that surfactant-expressing pseudomonads could modify the local soil-water distributions and that surfactants may therefore play a significant hydrological role in soils, in addition to their recognized biological activities.
Separation of mouse spermatogenic cells by velocity sedimentation

Improvements have been made in methods of preparation of single cell suspensions from mouse testes for separation by sedimentation at unit gravity. Mechanical means of preparation specifically damage spermatogonia, young primary spermatocytes, and spermatids at various stages of development, resulting in apparent sedimentation velocities which correspond closely to those of free nuclei. Trypsin has been used to release these cells from the seminiferous tubules allowing measurement of the sedimentation properties of the intact cell. The exclusion of trypan blue from the cells, resistance to trypsin, and the persistence in vitro of the highly differentiated forms of macromolecular synthesis demonstrate the integrity of the cells in the suspensions prepared with trypsin. Differentiation pathways in terms of sedimentation velocities of the cells and nuclei have been constructed and are in agreement with morphological changes.
Conformational Nature of the Borrelia burgdorferi B31 Outer Surface Protein C Protective Epitope

ABSTRACT Active immunization with Escherichia coli-expressed recombinant outer surface protein C (OspC) of Borrelia burgdorferi has been demonstrated to confer protection against a tick-transmitted infection on laboratory animals. A previous study in this laboratory showed that OspC antibody raised against a denatured immunogen isolated from B. burgdorferi cells failed to provide protective immunity. Therefore, to determine whether the protective epitope of the recombinant antigen was sensitive to denaturation, recombinant OspC preparations were subjected to heat and chemical treatments prior to animal immunization. Following seroconversion to OspC, the animals were challenged with an infectious dose of B. burgdorferi B31 by tick bite. Whereas mice immunized with a soluble, nondenatured form continued to show protection rates close to 100%, mice that had been immunized with denatured antigen were not protected. Furthermore, mice that were immunized with an insoluble (rather than a soluble), nondenatured form of the recombinant OspC showed a protection rate of only 40%. Protective epitope localization experiments showed that either the amino or the carboxy end of the recombinant protein was required to react with a protective OspC-specific monoclonal antibody. The data from these experiments demonstrate that a conformational organization of the protein is essential for the protective capability of the strain B31 OspC immunogen.
Socio-economic factors in headwater land management

Headwaters are classified in different categories depending on geology, topography, and on climate. Socio-economic factors allow another classification, which is based on the use of, and the human interaction with, the headwater region. Because these regions are particularly vulnerable to human interference, a study of the development of headwater regions offers excellent demonstrations of the concept of sustainability and of sustainable development. Differences exist between mountainous areas with steep slopes, and gently sloping loess areas, such as found in southwest Germany. In the former, the opportunities offered to the inhabitants determine if the area is utilized in a sustainable manner, or whether economic forces and better opportunities elsewhere lead to neglect of headwaters, with resulting environmental degradation and high susceptibility to natural disasters. In the latter, a more gradual decline of the food-producing capacity of the head lands is generated by erosion, which, if the economic incentives are right, are compensated by capital or labour investments. For this, a decision support system is formulated, based on models developed in Karlsruhe.
Phospholipase PlaB of Legionella pneumophila Represents a Novel Lipase Family

Legionella pneumophila possesses several phospholipases capable of host cell manipulation and lung damage. Recently, we discovered that the major cell-associated hemolytic phospholipase A (PlaB) shares no homology to described phospholipases and is dispensable for intracellular replication in vitro. Nevertheless, here we show that PlaB is the major lipolytic activity in L. pneumophila cell infections and that PlaB utilizes a typical catalytic triad of Ser-Asp-His for effective hydrolysis of phospholipid substrates. Crucial residues were found to be located within the N-terminal half of the protein, and amino acids embedding these active sites were unique for PlaB and homologs. We further showed that catalytic activity toward phosphatidylcholine but not phosphatidylglycerol is directly linked to hemolytic potential of PlaB. Although the function of the prolonged PlaB C terminus remains to be elucidated, it is essential for lipolysis, since the removal of 15 amino acids already abolishes enzyme activity. Additionally, we determined that PlaB preferentially hydrolyzes long-chain fatty acid substrates containing 12 or more carbon atoms. Since phospholipases play an important role as bacterial virulence factors, we examined cell-associated enzymatic activities among L. pneumophila clinical isolates and non-pneumophila species. All tested clinical isolates showed comparable activities, whereas of the non-pneumophila species, only Legionella gormanii and Legionella spiritensis possessed lipolytic activities similar to those of L. pneumophila and comprised plaB-like genes. Interestingly, phosphatidylcholine-specific phospholipase A activity and hemolytic potential were more pronounced in L. pneumophila. Therefore, hydrolysis of the eukaryotic membrane constituent phosphatidylcholine triggered by PlaB could be an important virulence tool for Legionella pathogenicity.
Stochastic Optimization for CRF Autoencoders

The goal of this project is to implement existing stochastic optimization methods in the context of conditional random field (CRF) autoencoders [1]. CRF autoencoders are a class of probabilistic models which was designed to address unsupervised and semi-supervised problems in natural language processing. However, for concreteness, we will focus on a particular instantiation of CRF autoencoders for the classic problem of bitext word alignment [4]. In this milestone, we experimented with several variations of stochastic gradient descent (see §3.1 for details). By the end of the semester, we plan to also experiment with stochastic expectation maximization (see §3.1.1 for details).
Functional Piglet Model for the Clinical Syndrome and Postmortem Findings Induced by Staphylococcal Enterotoxin B

Staphylococcal enterotoxin (SE) B causes serious gastrointestinal illness, and intoxication with this exotoxin can lead to lethal toxic shock syndrome. In order to overcome significant shortcomings of current rodent and nonhuman primate models, we developed a piglet model of lethal SEB intoxication. Fourteen-day-old Yorkshire piglets were given intravenous SEB, observed clinically, and sacrificed at 4, 6, 24, 48, 72, or 96 hrs posttreatment. Clinical signs were biphasic with pyrexia, vomiting, and diarrhea within 4 hrs, followed by terminal hypotension and shock by 96 hrs. Mild lymphoid lesions were identified as early as 24 hrs, with severe lymphadenopathy, splenomegaly, and prominent Peyer's patches found by 72 hrs. Widespread edema—most prominent in the mesentery, between loops of spiral colon, and in retroperitoneal connective tissue—was found in animals at 72 hrs. Additional histologic changes included perivascular aggregates of large lymphocytes variably present in the lung and brain, circulating lymphoblasts, and lymphocytic portal hepatitis. Preliminary molecular investigation using gene array has uncovered several gene profile changes that may have implications in the pathophysiology leading to irreversible shock. Five genes were selected for further study, and all showed increased mRNA levels subsequent to SEB exposure. The use of this piglet model will continue to elucidate the pathogenesis of SEB intoxication and facilitate the testing of new therapeutic regimens that may better correlate with human lesions.
THE EFFICACY OF PSYCHOTHERAPY FOR BORDERLINE PERSONALITY DISORDER: A REVIEW

148 orderline Personality Disorder (BPD) involves considerable suffering both for the individuals who suffer from the disorder and the people around them, as well as a high consumption of healthcare resources (Bender et al., 2001; Zanarini, Frankenburg, Hennen, & Silk 2004), not only due to its prevalence of 12% in the general population (APA, 2000, Lieb, Zanarini, Schmahl, Linehan, & Bohus, 2004) and 10-20% in psychiatric patients (Torgersen, Kringlen, Cramer, 2001), but also due to its nature (Linehan, Heidi, Heard, Hubert, & Armstrong, 1993). The characteristics of borderline behavior and resistance to pharmacological treatments make psychotherapy the key element for the improvement of these patients. Currently there are multiple psychotherapies for the treatment of BPD with studies that support their effectiveness on the different conditions that make up the disorder. From here, one possible question to ask is what psychotherapy is most effective and why. The most studied and most empirically supported are: Dialectical Behavioral Therapy (DBT) (Linehan, Armstrong, Suarez, Allmon, & Heard, 1991), Mentalization-Based Therapy (MBT) (Bateman & Fonagy, 2004), Transference-Focused Therapy (TFT) (Clarkin, Kernberg, & Yeomans, 1999), Schema-Based Therapy (SBT) (Ball & Young, 1999), Cognitive Analytic Therapy (CAT) (Ryle, 1991), Hobson's Conversational Therapy (HCT) (Hobson, 1985) and Cognitive-Behavioral Therapy (CBT). DBT is a manualized psychotherapy, combining behavioral, cognitive and supportive strategies based on the duality of accepting the other in their present condition while promoting change (Heard & Linehan, 1994). On the contrary, MBT and TFT are psychoanalytic psychotherapies that focus on affect, comprehension, and interpretation, although there are also important differences between the two therapies. TFT pays special attention to transference and focuses its therapeutic action THE EFFICACY OF PSYCHOTHERAPY FOR BORDERLINE PERSONALITY DISORDER: A REVIEW