Miracle-dz/UniFAR-FTUs huggingface dataset:
Receptive fields of barrels in the somatosensory neocortex of the rat

Peripheral receptive fields of “barrels” in the somatosensory neocortex (SmI) of rats were determined with microelectrode recording and anatomical techniques. A method of flattening each hemisphere prior to embedding was devised so that the organization of layer IV could be seen through the full extent of SmI on a single section. All of the barrels in the rat are located within layer IV of SmI. Sinus hairs on the lateral and rostral face and furry buccal pad project to a continuous sheet of barrels in the head area of the contralateral SmI. The pattern of projections in this area indicates that each barrel receives information from one sinus hair. Large whisking vibrissae project to the largest celldense barrels and smaller non‐whisking sinus hairs project to smaller barrels that are relatively cell‐sparse. Barrels were also found outside of the head area in regions that receive projections from the forepaw and hindfoot. Receptive fields of these barrels are located on glabrous and hairy surfaces of the appendages that do not include any sinus hairs. Other parts of the body project to celldense areas of SmI that do not appear to contain barrels. Barrel subgroups and other somatotopic areas are separated by narrow barrel‐free zones. As a result of this pattern of contrasting cell densities, an outline of the rat's body is delneated within layer IV.
Neural Correlate of Spatial Presence in an Arousing and Noninteractive Virtual Reality: An EEG and Psychophysiology Study

Using electroencephalography (EEG), psychophysiology, and psychometric measures, this is the first study which investigated the neurophysiological underpinnings of spatial presence. Spatial presence is considered a sense of being physically situated within a spatial environment portrayed by a medium (e.g., television, virtual reality). Twelve healthy children and 11 healthy adolescents were watching different virtual roller coaster scenarios. During a control session, the roller coaster cab drove through a horizontal roundabout track. The following realistic roller coaster rides consisted of spectacular ups, downs, and loops. Low-resolution brain electromagnetic tomography (LORETA) and event-related desynchronization (ERD) were used to analyze the EEG data. As expected, we found that, compared to the control condition, experiencing a virtual roller coaster ride evoked in both groups strong SP experiences, increased electrodermal reactions, and activations in parietal brain areas known to be involved in spatial navigation. In addition, brain areas that receive homeostatic afferents from somatic and visceral sensations of the body were strongly activated. Most interesting, children (as compared to adolescents) reported higher spatial presence experiences and demonstrated a different frontal activation pattern. While adolescents showed increased activation in prefrontal areas known to be involved in the control of executive functions, children demonstrated a decreased activity in these brain regions. Interestingly, recent neuroanatomical and neurophysiological studies have shown that the frontal brain continues to develop to adult status well into adolescence. Thus, the result of our study implies that the increased spatial presence experience in children may result from the not fully developed control functions of the frontal cortex.
Native low density lipoprotein promotes lipid raft formation in macrophages

Oxidized low-density lipoprotein (LDL) has an important role in atherogenesis; however, the mechanisms underlying cell-mediated LDL oxidation remain to be elucidated. The present study investigated whether native-LDL induced lipid raft formation, in order to gain further insight into LDL oxidation. Confocal microscopic analysis revealed that lipid rafts were aggregated or clustered in the membrane, which were colocalized with myeloperoxidase (MPO) upon native LDL stimulation; however, in the presence of methyl-β-cyclodextrin (MβCD), LDL-stimulated aggregation, translocation, and colocalization of lipid rafts components was abolished. In addition, lipid raft disruptors MβCD and filipin decreased malondialdehyde expression levels. Density gradient centrifugation coupled to label-free quantitative proteomic analysis identified 1,449 individual proteins, of which 203 were significantly upregulated following native-LDL stimulation. Functional classification of the proteins identified in the lipid rafts revealed that the expression levels of translocation proteins were upregulated. In conclusion, the results of the present study indicated that native-LDL induced lipid raft clustering in macrophages, and the expression levels of several proteins were altered in the stimulated macrophages, which provided novel insights into the mechanism underlying LDL oxidation.
Memorization in Recurrent Neural Networks

We present work in progress on understanding generalization in deep networks by analyzing differences in learning behaviour of recurrent neural networks (RNNs) on noise data vs. real data i.e., by investigating memorization. There has been a recent surge of interest in explaining the generalization performance of deep neural networks (DNNs), partially spurred by the observation that feedforward DNNs can fit random noise datasets with 0 training error. RNNs are typically extremely deep; analyzing learning behaviour in RNNs thus gives an interesting perspective for understanding memorization, generalization, and effective capacity in deep networks. We demonstrate that fitting noise with RNNs is more difficult than in feedforward networks; standard gradientbased optimization fails to reach 0 training error. We make several other observations comparing and contrasting our results with previous work, and suggest a suite of experiments for future work.
Factors Affecting Early Surgical Intervention After Uterine Artery Embolization

Uterine artery embolization (UAE) is an effective technique for the management of uterine myoma. However, complications of this procedure can be serious, including uterine infection and bowel necrosis in conjunction with necrosis of subserous or pedunculated myomas. Treatment failure is more likely to occur in the presence of submucosal myoma associated with a uterine infection or a large myoma of more than 8 cm. Accordingly, patients whose primary symptoms include submucosal myoma and menorrhagia are best treated with a hysteroscopic myomectomy or hysterectomy. The role of the gynecologist is crucial for most effective management and safe use of uterine artery embolization. Target Audience: Obstetricians & Gynecologists, Family Physicians Learning Objectives: After completion of this article, the reader will be able to list the complications of uterine artery embolization for fibroids, to describe postembolization syndrome, and identify the myomas that are more likely to fail uterine artery embolization.
Susceptibility-Diffusion Mismatch Predicts Thrombolytic Outcomes: A Retrospective Cohort Study

The benefit of thrombolytic therapy was assessed in 54 patients with a mismatch between infarct core as seen on DWI and penumbra as seen on SWI. Favorable outcomes were significantly higher in patients with DWI-SWI mismatch than in those without it. The accuracy of the DWI-SWI mismatch for predicting good outcome was higher than that for the more traditional DWI-perfusion mismatch. BACKGROUND AND PURPOSE: Asymmetric hypointensity of cerebral veins on susceptibility-weighted imaging has been shown to indirectly reflect tissue hypoxia after cerebral ischemia. We therefore investigated whether patients with prominent asymmetry of the cerebral veins on SWI and a relatively small diffusion-weighted imaging lesion (SWI-DWI mismatch), representing the presence of salvageable tissue, were more likely to benefit from thrombolytic therapy. MATERIALS AND METHODS: We conducted a retrospective study of the anterior circulation of patients with ischemic stroke with SWI/DWI acquired before thrombolysis. The asymmetry index was defined as the ratio of cerebral vein voxel count between the ischemic and normal hemisphere on the SWI phase map. We defined SWI-DWI mismatch as an asymmetry index score of ≥1.75 with a DWI lesion volume of ≤25 mL. Favorable outcome was defined as modified Rankin Scale 0–2 at 3 months. Univariate and multivariate logistic regression analyses were used to examine the association between the mismatch profile and favorable outcome. RESULTS: Fifty-four patients undergoing thrombolytic treatment were enrolled in this study. The rate of favorable outcome was significantly higher among patients with baseline SWI-DWI mismatch compared with those without (78% versus 44%; adjusted odds ratio, 6.317; 95% CI, 1.12–35.80; P = .037). Patients with SWI-DWI mismatch were also more likely to have a favorable outcome from reperfusion (91% versus 43%, P = .033) or recanalization (100% versus 40%, P = .013). The accuracy of SWI-DWI mismatch for predicting favorable outcome was higher than that of perfusion-diffusion mismatch (63% versus 48.1%). CONCLUSIONS: The presence of SWI-DWI mismatch may identify patients with ischemia who would benefit from early reperfusion therapy.
Crystal structure of N′′-(2-ethoxy-2-oxoethyl)-N,N,N′,N′-tetramethyl-N′′-[3-(1,3,3-trimethylureido)propyl]guanidinium tetraphenylborate

In the title salt, C16H34N5O3 +·C24H20B−, the C—N bond lengths in the cation are 1.3368 (16), 1.3375 (18) and 1.3594 (17) Å, indicating partial double-bond character. The central C atom is bonded to the three N atoms in a nearly ideal trigonal–planar geometry and the positive charge is delocalized in the CN3 plane. In the crystal, weak C—H⋯O contacts are observed between neighbouring guanidinium ions and between guanidinium ions and tetraphenylborate anions. In addition, C—H⋯π interactions involving guanidinium H atoms and aromatic rings of the anion are present. The phenyl rings form aromatic pockets, in which the cations are embedded. This leads to the formation of a two-dimensional supramolecular pattern along the ab plane.
Nonlinear Levy and nonlinear Feller processes : an analytic introduction

The program of studying general nonlinear Markov processes was put forward in V. N. Kolokoltsov "Nonlinear Markov Semigroups and Interacting L\'evy Type Processes" (Journ. Stat. Physics 126:3 (2007), 585-642), and was developed by the author in monograph "Nonlinear Markov processes and kinetic equations". Cambridge University Press, 2010, where, in particular, nonlinear L\'evy processes were introduced. The present paper is an invitation to the rapidly developing topic of noninear Markov processes. We provide a quick (and at the same time more abstract) introduction to the basic analytical aspects of the theory developed in Part II of the above mentioned book.
What we have learned about fighting defects

The Center for Empirically Based Software Engineering helps improve software development by providing guidelines for selecting development techniques, recommending areas for further research, and supporting software engineering education. A central activity toward achieving this goal has been the running of "e- Workshops" that capture expert knowledge with a minimum of overhead effort to formulate heuristics on a particular topic. The resulting heuristics are a useful summary of the current state of knowledge in an area based on expert opinion. This paper discusses the results to date of a series of e-Workshops on software defect reduction. The original discussion items are presented along with an encapsulated summary of the expert discussion. The reformulated heuristics can be useful both to researchers (for pointing out gaps in the current state of the knowledge requiring further investigation) and to practitioners (for benchmarking or setting expectations about development practices).
DIM (3,3′-diindolylmethane) confers protection against ionizing radiation by a unique mechanism

Significance DIM (3,3′-diindolylmethane) is a small molecule compound under investigation as a cancer preventive agent. This research addresses a potential usage of DIM as a medical countermeasure to prevent or mitigate acute radiation syndrome due to whole body exposure. In this regard, DIM can be administered safely to humans and animals by oral or subcutaneous routes. DIM may also be useful in preventing or mitigating late normal tissue damage due to partial body radiation exposure during cancer treatment. DIM works, in part, by a mechanism distinct from other radioprotectors and mitigators involving stimulation of the DNA damage response, including DNA repair, and activation of cell survival signaling through the transcription factor NF-κB. DIM (3,3′-diindolylmethane), a small molecule compound, is a proposed cancer preventive agent that can be safely administered to humans in repeated doses. We report that administration of DIM in a multidose schedule protected rodents against lethal doses of total body irradiation up to 13 Gy, whether DIM dosing was initiated before or up to 24 h after radiation. Physiologic submicromolar concentrations of DIM protected cultured cells against radiation by a unique mechanism: DIM caused rapid activation of ataxia-telangiectasia mutated (ATM), a nuclear kinase that regulates responses to DNA damage (DDR) and oxidative stress. Subsequently, multiple ATM substrates were phosphorylated, suggesting that DIM induces an ATM-dependent DDR-like response, and DIM enhanced radiation-induced ATM signaling and NF-κB activation. DIM also caused activation of ATM in rodent tissues. Activation of ATM by DIM may be due, in part, to inhibition of protein phosphatase 2A, an upstream regulator of ATM. In contrast, DIM did not protect human breast cancer xenograft tumors against radiation under the conditions tested. In tumors, ATM was constitutively phosphorylated and was not further stimulated by radiation and/or DIM. Our findings suggest that DIM is a potent radioprotector and mitigator that functions by stimulating an ATM-driven DDR-like response and NF-κB survival signaling.
Programming Abstractions for Software-Defined Wireless Networks

Software-Defined Networking (SDN) has received, in the last years, significant interest from the academic and the industrial communities alike. The decoupled control and data planes found in an SDN allows for logically centralized intelligence in the control plane and generalized network hardware in the data plane. Although the current SDN ecosystem provides a rich support for wired packet-switched networks, the same cannot be said for wireless networks where specific radio data-plane abstractions, controllers, and programming primitives are still yet to be established. In this work, we present a set of programming abstractions modeling the fundamental aspects of a wireless network, namely state management, resource provisioning, network monitoring, and network reconfiguration. The proposed abstractions hide away the implementation details of the underlying wireless technology providing programmers with expressive tools to control the state of the network. We also present a Software-Defined Radio Access Network Controller for Enterprise WLANs and a Python--based Software Development Kit implementing the proposed abstractions. Finally, we experimentally evaluate the usefulness, efficiency and flexibility of the platform over a real 802.11-based WLAN.
Whole Cell Cryo-Electron Tomography Reveals Distinct Disassembly Intermediates of Vaccinia Virus

At each round of infection, viruses fall apart to release their genome for replication, and then reassemble into stable particles within the same host cell. For most viruses, the structural details that underlie these disassembly and assembly reactions are poorly understood. Cryo-electron tomography (cryo-ET), a unique method to investigate large and asymmetric structures at the near molecular resolution, was previously used to study the complex structure of vaccinia virus (VV). Here we study the disassembly of VV by cryo-ET on intact, rapidly frozen, mammalian cells, infected for up to 60 minutes. Binding to the cell surface induced distinct structural rearrangements of the core, such as a shape change, the rearrangement of its surface spikes and de-condensation of the viral DNA. We propose that the cell surface induced changes, in particular the decondensation of the viral genome, are a prerequisite for the subsequent release of the vaccinia DNA into the cytoplasm, which is followed by its cytoplasmic replication. Generally, this is the first study that employs whole cell cryo-ET to address structural details of pathogen-host cell interaction.
A novel equation to estimate glomerular filtration rate using beta-trace protein.

BACKGROUND Beta-trace protein (BTP) is a low molecular weight glycoprotein that is a more sensitive marker of glomerular filtration rate (GFR) than serum creatinine. The utility of BTP has been limited by the lack of an equation to translate BTP into an estimate of GFR. The objectives of this study were to develop a BTP-based GFR estimation equation. METHODS We measured BTP and GFR by (99m)technetium-diethylenetriaminepentaacetic acid in 163 stable adult renal transplant recipients. Stepwise multiple regression models were created to predict GFR corrected for body surface area. The following variables were considered for entry into the model: BTP, urea, sex, albumin, creatinine, age, and race. RESULTS BTP alone accounted for 75.6% of variability in GFR. The model that included all the predictor variables had the largest coefficient of determination (R(2)) at 0.821. The model with only BTP, urea, and sex had only a slightly lower R(2) of 0.81 and yielded the following equation: GFR mL . min(-1) . (1.73 m(2))(-1) = 112.1 x BTP(-0.662) x Urea(-0.280) x (0.88 if female). A 2nd equation (R(2) = 0.79) using creatinine instead of urea was also developed: GFR mL . min(-1) . (1.73 m(2))(-1) = 1.678 x BTP(-0.758) x creatinine(-0.204) x (0.871 if female). CONCLUSIONS We have shown that BTP can be used in a simple equation to estimate GFR. Further study is needed in other populations to determine accuracy and clinical utility of this equation.
A new technique for maintaining and monitoring conscious, stress-free rabbits in a steady state: its use in the determination of glucose kinetics.

1. A new technique is described for maintaining and monitoring conscious rabbits in a steady state. Solutions were infused and blood samples were withdrawn without major surgery and without causing stress. Cannulation, for infusion and blood sampling, was via the ear veins and arteries. 2. The validity of the technique is discussed with special reference to: the amount of blood removed from the animal; the use of a plasma substitute solution; the use of heparin; and assessing whether the animal was in a steady-state with respect to glucose. 3. The technique was used to determine glucose kinetics in the fasted rabbit after an injection of [2-(3)H]glucose with subsequent blood sampling over 2 h. A two compartment model was used to calculate certain physiological values, the two principal ones being the glucose uptake rate (3.30 +/- 0.24 (13) mg.kg-1.min-1) and the initial volume of distribution (74.8 +/- 7.8 (13) ml.kg-1). 4. The accuracy and precision of the results obtained from this study are discussed and shown to be more reliable than other published values.
Contribution of mutations in gyrA and parC genes to fluoroquinolone resistance of mutants of Streptococcus pneumoniae obtained in vivo and in vitro

We have analyzed by gene amplification and sequencing mutations in the quinolone resistance-determining regions of the gyrA, gyrB, and parC genes of fluoroquinolone-resistant Streptococcus pneumoniae mutants obtained during therapy or in vitro. Mutations leading to substitutions in ParC were detected in the two mutants obtained in vivo, BM4203-R (substitution of a histidine for an aspartate at position 84 [Asp-84-->His]; Staphylococcus aureus coordinates) and BM4204-R (Ser-80-->Phe), and in two mutants obtained in vitro (Ser-80-->Tyr). An additional mutant obtained in vitro, BM4205-R3, displayed a higher level of fluoroquinolone resistance and had a mutation in gyrA leading to a Ser-84-->Phe change. We could not detect any mutation in the three remaining mutants obtained in vitro. Total DNA from BM4203-R, BM4204-R, and BM4205-R3 was used to transform S. pneumoniae CP1000 by selection on fluoroquinolones. For the parC mutants, transformants with phenotypes indistinguishable from those of the donors were obtained at frequencies (5 x 10(-3) to 8 x 10(-3)) compatible with monogenic transformation. By contrast, transformants were obtained at a low frequency (4 x 10(-5)), compatible with the transformation of two independent genes, for the gyrA mutant. Resistant transformants of CP1000 were also obtained with an amplified fragment of parC from BM4203-R and BM4204-R but not with a gyrA fragment from BM4205-R3. All transformants had mutations identical to those in the donors. These data strongly suggest that ParC is the primary target for fluoroquinolones in S. pneumoniae and that BM4205-R3 is resistant to higher levels of the drugs following the acquisition of two mutations, including one in gyrA.
The Pseudosynchronization of Binary Stars Undergoing Strong Tidal Interactions

Eccentric binaries known as heartbeat stars experience strong dynamical tides as the stars pass through periastron, providing a laboratory to study tidal interactions. We measure the rotation periods of 24 heartbeat systems, using the Kepler light curves to identify rotation peaks in the Fourier transform. Where possible, we compare the rotation period to the pseudosynchronization period derived by Hut. Few of our heartbeat stars are pseudosynchronized with the orbital period. For four systems, we were able to identify two sets of rotation peaks, which we interpret as the rotation from both stars in the binary. Most stars in our sample have rotation rates larger than the pseudosynchronization period while a single target rotates much faster than this rate. The majority of the systems have a rotation period that is approximately times the pseudosynchronization period, suggesting that other physical mechanisms strongly influence the star’s evolution.
Relocation of the plastid rbcL gene to the nucleus yields functional ribulose-1,5-bisphosphate carboxylase in tobacco chloroplasts.

The conserved plastid localization of rbcL suggests that biosynthesis of the large subunit of ribulose-1,5-bisphosphate carboxylase [Rubisco; 3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1. 1.39] in chloroplasts is required to obtain functional enzyme. To examine the validity of this hypothesis, we relocated the plastid rbcL gene to the nucleus. First, we deleted the rbcL gene from the tobacco plastid genome by targeted insertion of a selectable aadA gene encoding spectinomycin resistance. The rbcL coding region was then inserted into an expression cassette and introduced into the nuclear genome of these plants by Agrobacterium-mediated transformation. We report that the nuclear rbcL functionally complements the defective plastids when the Rubisco large subunit is targeted to chloroplasts by a transit peptide. Therefore, the evolutionary process that relocates functional plastid genes to the nucleus has not yet occurred in the case of the rbcL gene. Targeted deletion of plastid genes, combined with their allotopic expression, will provide opportunities for studying the function of plastid enzyme complexes.