Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantum Resources Required to Block-Encode a Matrix of Classical Data

We provide a modular circuit-level implementation and resource estimates for several methods of block-encoding a dense <inline-formula><tex-math notation="LaTeX">$N\times N$</tex-math></inline-formula> matrix of classical data to precision <inline-formula><tex-math notation="LaTeX">$\epsilon$</tex-math></inline-formula>; the minimal-depth method achieves a <inline-formula><tex-math notation="LaTeX">$T$</tex-math></inline-formula>-depth of <inline-formula><tex-math notation="LaTeX">$\mathcal {O}(\log (N/\epsilon)),$</tex-math></inline-formula> while the minimal-count method achieves a <inline-formula><tex-math notation="LaTeX">$T$</tex-math></inline-formula>-count of <inline-formula><tex-math notation="LaTeX">$\mathcal{O} (N \log(\log(N)/\epsilon))$</tex-math></inline-formula>. We examine resource tradeoffs between the different approaches, and we explore implementations of two separate models of quantum random access memory. As a part of this analysis, we provide a novel state preparation routine with <inline-formula><tex-math notation="LaTeX">$T$</tex-math></inline-formula>-depth <inline-formula><tex-math notation="LaTeX">$\mathcal {O}(\log (N/\epsilon))$</tex-math></inline-formula>, improving on previous constructions with scaling <inline-formula><tex-math notation="LaTeX">$\mathcal {O}(\log ^{2} (N/\epsilon))$</tex-math></inline-formula>. Our results go beyond simple query complexity and provide a clear picture into the resource costs when large amounts of classical data are assumed to be accessible to quantum algorithms.
Construction of a Spike-Based Memory Using Neural-Like Logic Gates Based on Spiking Neural Networks on SpiNNaker

Neuromorphic engineering concentrates the efforts of a large number of researchers due to its great potential as a field of research, in a search for the exploitation of the advantages of the biological nervous system and the brain as a whole for the design of more efficient and real-time capable applications. For the development of applications as close to biology as possible, Spiking Neural Networks (SNNs) are used, which are considered biologically-plausible and constitute the third generation of Artificial Neural Networks. This work presents a spiking implementation of a memory, which is one of the most important components in computer architecture. In the process of designing this spiking memory, different intermediate components were also implemented and tested. The tests were carried out on the SpiNNaker neuromorphic platform. This work goes into the development of spiking blocks using a logic gate approach based on previous work and includes a comparison between other works in the state of the art related to spiking memories and the one proposed here. All the implemented blocks and developed tests are available in a public repository.
Oxygenation-Controlled Collective Dynamics in Aquatic Worm Blobs.

Many organisms utilize group aggregation as a method for survival. The freshwater oligochaete, Lumbriculus variegatus (California blackworms) form tightly entangled structures, or worm "blobs", that have adapted to survive in extremely low levels of dissolved oxygen (DO). Individual blackworms adapt to hypoxic environments through respiration via their mucous body wall and posterior ciliated hindgut, which they wave above them. However, the change in collective behavior at different levels of DO is not known. Using a closed-loop respirometer with flow, we discover that the relative tail reaching activity flux in low DO is ∼75x higher than in the high DO condition. Additionally, when flow rate is increased to suspend the worm blobs upward, we find that the average exposed surface area of a blob in low DO is ∼1.4x higher than in high DO. Furthermore, we observe emergent properties that arise when a worm blob is exposed to extreme DO levels. We demonstrate that internal mechanical stress is generated when worm blobs are exposed to high DO levels, allowing them to be physically lifted off from the bottom of a conical container using a serrated endpiece. Our results demonstrate how both collective behavior and the emergent generation of internal mechanical stress in worm blobs change to accommodate differing levels of oxygen. From an engineering perspective, this could be used to model and simulate swarm robots, self-assembly structures, or soft material entanglements.
A regression tree method for longitudinal and clustered data with multivariate responses

RE-EM tree is a tree-based method that combines the regression tree and the linear mixed effects model for modeling univariate response longitudinal or clustered data. In this paper, we generalize the RE-EM tree method to multivariate response data, by adopting the Multivariate Regression Tree method proposed by De'Ath [2002]. The Multivariate RE-EM tree method estimates a population-level single tree structure that is driven by the multiple responses simultaneously and object-level random effects for each response variable, where correlation between the response variables and between the associated random effects are each allowed. Through simulation studies, we verify the advantage of the Multivariate RE-EM tree over the use of multiple univariate RE-EM trees and the Multivariate Regression Tree. We apply the Multivariate RE-EM tree to analyze a real data set that contains multidimensional nonfinancial characteristics of poverty of different countries as responses, and various potential causes of poverty as predictors.
Gate-Tunable Spin-Orbit Coupling in a Germanium Hole Double Quantum Dot

Hole spins confined in semiconductor quantum dot systems have gained considerable interest for their strong spin-orbit interactions (SOIs) and relatively weak hyperfine interactions. Here we experimentally demonstrate a tunable SOI in a double quantum dot in a Germanium (Ge) hut wire (HW), which could help enable fast all-electric spin manipulations while suppressing unwanted decoherence. Specifically, we measure the transport spectra in the Pauli spin blockade regime in the double quantum dot device. By adjusting the interdot tunnel coupling, we obtain an electric-field-tuned spin-orbit length l SO = 2.0–48.9 nm. This tunability of the SOI could pave the way toward the realization of high-fidelity qubits in Ge HW systems.
Towards Bridging Algorithm and Theory for Unbiased Recommendation

This work studies the problem of learning unbiased algorithms from biased feedback for recommender systems. We address this problem from both theoretical and algorithmic perspectives. Recent works in unbiased learning have advanced the state-of-the-art with various techniques such as meta-learning, knowledge distillation, and information bottleneck. Despite their empirical successes, most of them lack theoretical guarantee, forming non-negligible gaps between the theories and recent algorithms. To this end, we ﬁrst view the unbiased recommendation problem from a distribution shift perspective. We theoretically analyze the generalization bounds of unbiased learning and suggest their close relations with recent unbiased learning objectives. Based on the theoretical analysis, we further propose a principled framework, Adversarial Self-Training (AST), for unbiased recommendation. Empirical evaluation on real-world and semi-synthetic datasets demonstrate the effectiveness of the proposed AST.
IL-21 and cellular activation concurrently induce potent cytotoxic function and promote antiviral activity in human CD8 T cells

Infection with HIV-1 induces a progressive deterioration of the immune system that ultimately leads to AIDS. Mouse models indicate that the common gamma chain ( γ c )- sharing cytokine interleukin (IL)-21 and its receptor (IL-21R) play a crucial role in maintaining polyfunctional T cell responses during chronic viral infections. Therefore, we analyzed the ability of this cytokine to modulate the properties of human CD8 T cells in comparison to other γ c -sharing cytokines (IL-2, IL-7 and IL-15). CD8 T cells from healthy volunteers were stimulated in vitro via T cell receptor signals to mimic the heightened status of immune activation of HIV-infected patients. The administration of IL-21 up-regulated cytotoxic effector function and the expression of the costimulatory molecule CD28. Notably, this outcome was not accompanied by increased cellular proliferation or activation. Moreover, IL-21 promoted antiviral activity while not inducing HIV-1 replication in vitro . Thus, IL-21 may be a favorable molecule for immunotherapy and a suitable vaccine adjuvant in HIV-infected individuals.
The interaction between sleep-disordered breathing and ApoE genotype on cerebrospinal fluid biomarkers for Alzheimer's disease in cognitively normal elderly

Background— Previous studies have suggested a link between Sleep Disordered Breathing (SDB) and dementia risk. In the present study, we analyzed the relationship between SDB severity, cerebrospinal fluid (CSF) Alzheimer's disease (AD) biomarkers, and the ApoE alleles. Methods— 95 cognitively normal elderly participants were analyzed for SDB severity, CSF measures of phosphorylated-tau (P-Tau), total-tau (T-Tau), and amyloid beta 42 (A β 42), as well as ApoE allele status. Findings— In ApoE3+ subjects, significant differences were found between sleep groups for P-Tau (F[df2]=4.3, p=0.017), and T-Tau (F[df2]=3.3, p=0.043). Additionally, among ApoE3+ subjects, the apnea/hypopnea with 4% O2-desaturation index (AHI4%) was positively correlated with P-Tau (r=0.30, p=0.023), T-Tau (r=0.31, p=0.021), and A β 42 (r=0.31, p=0.021). In ApoE2+ subjects, AHI4% was correlated with lower levels of CSF A β 42 (r=−0.71, p=0.004), similarly to ApoE4+ subjects where there was also a trend towards lower CSF A β 42 levels Interpretation— Our observations suggest that there is an association between SDB and CSF AD- biomarkers in cognitively normal elderly. Existing therapies for SDB such as CPAP could delay the onset to mild cognitive impairment or dementia in normal elderly.
Effect of hyperoxygenation on tissue pO 2 and its consequence on radiotherapeutic efficacy of orthotopic F98 gliomas

Purpose— Lack of methods for repeated assessment of tumor pO 2 limits the ability to test and optimize hypoxia modifying procedures being developed for clinical applications. We report the repeated measurements of orthotopic F98 tumor pO 2 , and relate this to the effect of carbogen inhalation on tumor growth when combined with hypofractionated radiotherapy. Methods and Materials— Electron Paramagnetic Resonance (EPR) oximetry was used for repeated measurements of tumor and contralateral brain pO 2 in rats during 30% O 2 and carbogen inhalation for 5 consecutive days. The T 1 enhanced volumes and diffusion coefficients of the tumors were assessed by MRI. The tumors were irradiated with 9.3 Gy × 4 in rats breathing 30% O 2 or carbogen to determine the effect on tumor growth. Results— The pre-treatment F98 tumor pO 2 varied between 8 – 16 mmHg, while the contralateral brain had 41 – 45 mmHg pO 2 during repeated measurements. Carbogen breathing led to a significant increase in tumor and contralateral brain pO 2 ; however this effect declined over days. Irradiation of the tumors in rats breathing carbogen resulted in a significant decrease in tumor growth and an increase in the diffusion coefficient measured by MRI. Conclusions— The results provide quantitative measurements of the effect of carbogen inhalation on intracerebral tumor pO 2 and its consequence on therapeutic outcome. Such direct repeated pO 2 measurements by EPR oximetry can provide temporal information that could be used to improve therapeutic outcome by scheduling doses at times of improved tumor oxygenation. EPR oximetry is currently being tested for clinical applications. repeated non-invasive tissue pO 2 of orthotopic tumors and could be used to investigate and optimize hypoxia modifying procedures for clinical applications.
Pro-Inflammatory Effects of Cook Stove Emissions on Human Bronchial Epithelial Cells

Approximately half the world’s population uses biomass fuel for indoor cooking and heating. This form of combustion typically occurs in open fires or primitive stoves. Human exposure to emissions from indoor biomass combustion is a global health concern, causing an estimated 1.5 million premature deaths each year. Many ‘improved’ stoves have been developed to address this concern; however, studies that examine exposure-response with cleaner-burning, more efficient stoves are few. The objective of this research was to evaluate the effects of traditional and cleaner burning stove emissions on an established model of the bronchial epithelium. We exposed well-differentiated, normal human bronchial epithelial (NHBE) cells to emissions from a single biomass combustion event using either a traditional three-stone fire or one of two energy-efficient stoves. Air-liquid interface cultures were exposed using a novel, aerosol-to-cell deposition system. Cellular expression of a panel of three pro-inflammatory markers was evaluated at 1 and 24 hours following exposure. Cells exposed to emissions from the cleaner burning stoves generated significantly fewer amounts of pro-inflammatory markers than cells exposed to emissions from a traditional, three stone fire. Particulate matter emissions from each cookstove were substantially different, with the three-stone fire producing the largest concentrations of particles (by both number and mass). This study supports emerging evidence that more efficient cookstoves have the potential to reduce respiratory inflammation in settings where solid fuel combustion is used to meet basic domestic needs.
Nucleic Acids Research

The origin of lagging strand synthesis in pUBllO, oriL, has been localized within 140 bases outside the pUBllO minimal replicon. The oriL DNA sequence is a cis-acting and orientation dependent determinant required for normal plasmid replication. Rearrange-ments affecting oriL cause plasmid instability, lead to the accumulation of replication intermediates and result in a marked reduction of the plasmid copy number in some recombination deficient mutant strains. In addition, deletion of oriL triggers a dnaB-dependent mode of replication. the accumulation of single-stranded DNA during the repli- cation of this plasmid.
Technical Advance Measurement of Gene Expression in Archival Paraffin-Embedded Tissues Development and Performance of a 92-Gene Reverse Transcriptase-Polymerase Chain Reaction Assay

Throughout the last decade many laboratories have shown that mRNA levels in formalin-fixed and paraf-fin-embedded (FPE) tissue specimens can be quanti-fied by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques despite the extensive RNA fragmentation that occurs in tissues so preserved. We have developed RT-PCR methods that are sensitive, precise, and that have multianalyte capability for potential wide use in clinical research and diagnostic assays. Here it is shown that the extent of fragmentation of extracted FPE tissue RNA significantly increases with archive storage time. Probe and primer sets for RT-PCR assays based on amplicons that are both short and homogeneous in length enable effec-tive reference gene-based data normalization for cross comparison of specimens that differ substantially in age. A 48-gene assay used to compare gene expression profiles from the same breast cancer tissue that had been either frozen or FPE showed very similar profiles after reference gene-based normalization. A 92-gene assay, using RNA extracted from three 10- (cid:1) m FPE sections of archival breast cancer specimens (dating from 1985 to 2001) yielded analyzable data for these genes in all 62 tested specimens. The results were substantially concordant when estrogen receptor, progesterone receptor, and HER2 receptor status determined by RT-PCR was compared with immunohistochemistry assays for these receptors. Fur-thermore, the results highlight the advantages of RT-PCR over immunohistochemistry with respect to quantitation
3D carotid plaque MR Imaging

There has been significant progress made in 3D carotid plaque magnetic resonance imaging techniques in recent years. 3D plaque imaging clearly represents the future in clinical use. With effective flow suppression techniques, choices of different contrast weighting acquisitions, and time-efficient imaging approaches, 3D plaque imaging offers flexible imaging plane and view angle analysis, large coverage, multi-vascular beds capability, and even can be used in fast screening.
Isolation of cDNA clones for human erythrocyte membrane sialoglycoproteins a and 6

We have isolated almost full-length cDNA clones corresponding to human erythrocyte membrane sialoglycoproteins a (glycophorin A) and (glycophorin B). The predicted amino acid sequence of differs at two amino acid residues from the sequence determined by peptide sequencing. The sialoglycoprotein clone we have isolated contains an interrupting sequence within the region that gives rise to the cleaved N-terminal leader sequence for the protein and represents a product that is unlikely to be inserted into the erythrocyte membrane. Comparison of the cDNA sequences of a and shows very strong homology at the DNA level within the coding regions. The two mRNA sequences are closely related and differ by a number of clearly defined insertions and deletions.
al-Antitrypsin NullbL.d . An al-Antitrypsin Deficiency Allele Caused by Deletion of All al-Antitrypsin Coding Exons

Summary al-Antitrypsin (alAT) deficiency, a common hereditary disorder responsible for emphysema in Caucasians of northern European descent, is caused by single base substitutions, deletions, or additions in the seven exons (IA-Ic and II-V), of the 12.2-kb alAT gene located on chromosome 14 at q31-32.3. Of the five known representatives of the "null" group of alAT-deficiency alleles (alAT genes incapable of producing alAT protein detectable in serum) evaluated at the gene level, all result from mutations causing the formation of stop codons in coding exons of the alAT gene. The present study identifies an alAT allele (referred to as "Nullisola di procida") caused by complete deletion of the alAT coding exons. The Nullisola di procida allele was identified in an individual with heterozygous inheritance of Mprcida (an allele associated with alAT deficiency) and a null allele. Although results of karyotypic analysis were normal, quantification of the copies of alAT genes in this individual revealed that the index case had only half the normal copies of alAT genes. Cloning and mapping of the Nullisola di procida gene demonstrated a deletion of a 17-kb fragment that included exons 11-V of the alAT structural gene. As a consequence of the deletion, the normal noncoding exons (IA-Ic) were followed by exons II-V of the downstream alAT-like gene. Sequence analysis of the deletion demonstrated a 7-bp repeat sequence (GAGGACA) both 5' to the deletion and at the 3' end of the deletion, a 4-bp palindromic sequence (ACAG vs. CTGT) bracketing the deletion, and a novel inserted 4-bp sequence (CCTG) at the breakpoint, suggesting that the mechanism of the deletion may have been "slipped mispairing. "
Estimation of the Range Between the Interceptor and the Target During Infrared Terminal Guidance of Space Interception

Abstract : A proper mathematical model is constructed according to the kinematic equations of space interception. After the component of the relative velocity normal to the line of sight is observed using a nonlinear observer design method with two canonical forms, the problem of estimating the range between interceptor and the target during infrared terminal guidance of space interception is solved. Numerical simulation verifies the above results.
Molecular Imaging of GSK3 β and CK1 α kinases

Glycogen synthase kinase-3 (GSK3 β ) and casein kinase-1 alpha (CK-1 α ) are multifunctional kinases that play critical role in the regulation of a number of cellular processes. In spite of their importance, molecular imaging tools for non-invasive and real-time monitoring of their kinase activities have not been devised. Here, we report development of bioluminescent GSK3 β and CK-1 α reporter (BGCR) based on firefly luciferase complementation. Treatment of SW620 cells stably expressing the reporter with inhibitors of GSK3 β (SB415286 and LiCl) or CK1 α (CKI-7) resulted in dose and time dependent increase in BGCR activity which were validated using western blotting. No increase in bioluminescence was observed in case of S37A mutant (GSK3 β inhibitors) or with S45A mutant (CKI-7) demonstrating the specificity of the reporter. Imaging of mice tumor xenograft generated with BGCR expressing SW620 cells following treatment with LiCl showed unique oscillations in GSK3 β activity which were corroborated by phospho-GSK3 β immunoblotting. Taken together, BGCR is novel molecular imaging tool that reveals unique insight into GSK3 β and CK1 α kinase activities and may provide powerful tool in experimental therapeutics for rapid optimization of dose and schedule of targeted therapies and for monitoring therapeutic response.
Nucleic Acids Research

Physical properties of the DNA duplex, poly(dA) -poly(dT) differ considerably from the alternating copolymer poly(dAT). A number of molecular models have been used to describe these structures obtained from fiber X-ray diffraction data. The recent solutions of single crystal DNA dodecamer structures with segments of oligo-A-oligo-T have revealed the presence of a high propeller twist in the AT regions which is stabilized by the formation of bifurcated (three-center) hydrogen bonds on the floor of the major groove, involving the N6 amino group of adenine hydrogen bonding to two 04 atoms of adjacent thymine residues on the opposite strand. Here we show that it is possible to incorporate the features of the single crystal analysis, specifically high propeller twist, bifurcated hydrogen bonds, and a narrow minor groove, as well as the close interstrand NMR signal between adenine HC2 and ribose HC1' of the opposite strand, into a model that is fully compatible with the diffraction data obtained from poly(dA) poly(dT).