Miracle-dz/UniFAR-FTUs huggingface dataset:
A temperature-sensitive Mycobacterium smegmatis glgE mutation leads to a loss of GlgE enzyme activity and thermostability and the accumulation of α-maltose-1-phosphate

Background The bacterial GlgE pathway is the third known route to glycogen and is the only one present in mycobacteria. It contributes to the virulence of Mycobacterium tuberculosis. The involvement of GlgE in glycogen biosynthesis was discovered twenty years ago when the phenotype of a temperature-sensitive Mycobacterium smegmatis mutation was rescued by the glgE gene. The evidence at the time suggested glgE coded for a glucanase responsible for the hydrolysis of glycogen, in stark contrast with recent evidence showing GlgE to be a polymerase responsible for its biosynthesis. Methods We reconstructed and examined the temperature-sensitive mutant and characterised the mutated GlgE enzyme. Results The mutant strain accumulated the substrate for GlgE, α-maltose-1-phosphate, at the non-permissive temperature. The glycogen assay used in the original study was shown to give a false positive result with α-maltose-1-phosphate. The accumulation of α-maltose-1-phosphate was due to the lowering of the kcat of GlgE as well as a loss of stability 42 ºC. The reported rescue of the phenotype by GarA could potentially involve an interaction with GlgE, but none was detected. Conclusions We have been able to reconcile apparently contradictory observations and shed light on the basis for the phenotype of the temperature-sensitive mutation. General Significance This study highlights how the lowering of flux through the GlgE pathway can slow the growth mycobacteria.
Drosophila Sex Peptide controls the assembly of lipid microcarriers in seminal fluid

Significance Seminal fluid plays a critical role in reprogramming female physiology and behavior to promote male reproductive success. We show, in the fruit fly, that specific seminal proteins, including the archetypal “female-reprogramming” molecule Sex Peptide, are stored in male seminal secretions in association with large neutral lipid-containing microcarriers, which rapidly disperse in females. Related structures are also observed in other Sex Peptide-expressing Drosophila species. Males lacking Sex Peptide have structurally defective microcarriers and exhibit abnormal transfer of many seminal proteins to females. Our data reveal that this key signaling molecule in Drosophila seminal fluid is also a microcarrier assembly factor that modulates transfer of other seminal factors and that this may be a more evolutionarily ancient role of this protein. Seminal fluid plays an essential role in promoting male reproductive success and modulating female physiology and behavior. In the fruit fly, Drosophila melanogaster, Sex Peptide (SP) is the best-characterized protein mediator of these effects. It is secreted from the paired male accessory glands (AGs), which, like the mammalian prostate and seminal vesicles, generate most of the seminal fluid contents. After mating, SP binds to spermatozoa and is retained in the female sperm storage organs. It is gradually released by proteolytic cleavage and induces several long-term postmating responses, including increased ovulation, elevated feeding, and reduced receptivity to remating, primarily signaling through the SP receptor (SPR). Here, we demonstrate a previously unsuspected SPR-independent function for SP. We show that, in the AG lumen, SP and secreted proteins with membrane-binding anchors are carried on abundant, large neutral lipid-containing microcarriers, also found in other SP-expressing Drosophila species. These microcarriers are transferred to females during mating where they rapidly disassemble. Remarkably, SP is a key microcarrier assembly and disassembly factor. Its absence leads to major changes in the seminal proteome transferred to females upon mating. Males expressing nonfunctional SP mutant proteins that affect SP’s binding to and release from sperm in females also do not produce normal microcarriers, suggesting that this male-specific defect contributes to the resulting widespread abnormalities in ejaculate function. Our data therefore reveal a role for SP in formation of seminal macromolecular assemblies, which may explain the presence of SP in Drosophila species that lack the signaling functions seen in D. melanogaster.
Adoptive transfer of nuclear factor-κB-inactive macrophages to the glomerulus

Adoptive transfer of nuclear factor-κB–inactive macrophages to the glomerulus. Background Macrophages have been regarded as “blackguards” in the generation of glomerular injury. However, it is still unclear what kind of cellular machinery is responsible for their pathogenic actions. To explore this issue, this investigation aims at developing a novel strategy using adoptive transfer of “loss-of-function” macrophages to the glomerulus. As a prototypal investigation, this study examines a role for nuclear factor-κB (NF-κB) in effector actions of macrophages within the glomerular microenvironment. Methods NF-κB–inactive macrophages, NIKMAC NR , were created by transduction of NR8383 rat macrophages with retrovirus encoding a super-repressor mutant of IκBα, IκBαM. The effector functions of NIKMAC NR cells on resident cells were evaluated by coculture, cross-feeding, and in vivo macrophage transfer. Results Rat mesangial cells cocultured with control macrophages showed abundant expression of activation markers, including monocyte chemoattractant protein-1, stromelysin, and gelatinase B. In contrast, coculture with NIKMAC NR macrophages induced only modest gene expression. Similarly, culture medium conditioned by activated, control macrophages triggered mesangial cells and isolated glomeruli to express the activation markers, whereas the stimulatory effect was not observed in medium conditioned by NIKMAC NR macrophages. To evaluate effector actions of NIKMAC NR macrophages in the glomerulus, control macrophages and NIKMAC NR cells were transferred into normal rat glomeruli via renal artery injection. After the transfer of control macrophages, substantial induction of the activation marker stromelysin was observed in resident glomerular cells. This induction was dramatically diminished in the glomeruli transferred with NIKMAC NR macrophages. Conclusions Inactivation of NF-κB in macrophages effectively disrupted paracrine, stimulatory loops from macrophages to resident glomerular cells. A combination of “loss-of-function” strategies with the technique for adoptive cell transfer is thus useful to explore pathophysiologic roles for certain machinery of macrophages within the glomerulus.
Recent elucidation of the expression and function of developmental genes in different animal groups has made it possible to determine the molecular developmental mechanisms underlying the evolution of various animal body

Recent elucidation of the expression and function of developmental genes in different animal groups has made it possible to determine the molecular developmental mechanisms underlying the evolution of various animal body plans. Among numerous evolutionary developmental processes, we have been focusing on the evolution of chordate body plans (Satoh and Jeffery, 1995; Satoh, 1995; Yasuo et al., 1995). The phylum Chordata comprises the subphylum groups urochordates, cephalochordates and vertebrates (cf. Fig. 8). They share several characteristic features, including a notochord, a dorsal hollow neural tube, pharyngeal gill slits and an endostyle (e.g., Brusca and Brusca, 1990; Nielsen, 1995; Gee, 1996; Hall, 1998). In addition, chordates form a superphyletic group of deuterostomes together with two other non-chordate invertebrate groups, echinoderms and hemichordates (cf. Fig. 8). Recent molecular phylogenic studies support the idea that echinoderms, hemichordates and chordates form a monophyletic group (Wada and Satoh, 1994; Turbeville et al., 1994). Therefore, chordate body plans evolved from the ancestor by developing their characteristic features mentioned above. This suggests that the elucidation of molecular developmental mechanisms underlying the formation of these organs will lead to a better understanding of the evolution of chordate body plans. Several studies have focused on developmental mechanisms underlying the formation of the notochord (Yasuo and Satoh, 1993; Harada et al., 1995; Tagawa et al., 1998) and neural tube (e.g., Wada et al., 1998). For example, Brachyury is a key developmental gene in the formation of the notochord (reviewed by Di Gregorio and Levine, 1998; Satoh et al., 1999). The pharyngeal gill slits and endostyle are organs characteristic of filter feeding, which might has arisen when primitive chordates shifted to internal feeding. Therefore, the pharyngeal gill is also an important structure for understanding the evolution of chordate body plans. In a previous study, we characterized two pharyngeal gill (endodermally derived 2539 Development 126, 2539-2550 (1999) Printed in Great Britain © The Company of Biologists Limited 1999 DEV2400
Holoprosencephaly‐diencephalic hamartoma: Sequence or pleiotropy?

Holoprosencephaly-Diencephalic Hamartoma: Sequence or Pleiotropy? Fabien Guimiot, Pascale Marcorelles, Anne-lise Delezoide, and Annie Laquerri ere* Department of Developmental Biology, Robert Debr e Hospital, AP-HP Paris, Denis Diderot University, Paris, France Department of Biology-Pathology, University Hospital of Brest, Brest, France Pathology Laboratory, University Hospital of Rouen, Rouen, France
A 3D packaging cover structure with optical filter and low signal-transmission loss for MEMS infrared detectors

This paper presents a wafer-level three-dimensional (3D) packaging cover structure for microelectromechanical systems (MEMS) infrared detectors. Subwavelength structures with an array of square coaxial apertures are designed on top of silicon substrate to obtain extraordinary optical transmission (EOT). The optical transmission is up to 58%, and its bandwidth is 4 μm. The vertical silicon vias, insulated by Pyrex glass, are used for electrical interconnections. The thickness of the insulation is optimized, such that the feed-through level is lower than -93 dB and the transmission coefficient is more than -0.032 dB at a frequency from 0 to 2 GHz. Those above results demonstrated that the proposed 3D packaging cover structure is suitable for MEMS infrared detectors.
Research of Low-profile High Performance new AMC Antenna for 5G mm-Wave AiP Application

A new AMC based broadband low-profile antenna is presented. The proposed antenna is composed by a patch, finite AMC cells and a slotted ground plane, and fed by a microstrip line under the ground plane. The structure of the proposed antenna is simple and compact, which can be realized by a three-layer printed circuit board (PCB) substrate. To verify the performance of the new AMC antenna, a reference patch antenna with the same thickness and feeding method is used for comparison. The new AMC antenna realizes a wide impedance bandwidth of 23% and a high gain up to 8.75dBi with an overall size of 1λ0×1λ0×0. 047λ0 (λ0 is the free space wavelength at 28GHz). In addition, it solves the inherent disadvantage of backward radiation induced by aperture coupling while utilizes the advantage of low cross polarization property. The good performance suggests that the proposed novel AMC antenna is fully capable for 5G mm-wave AiP application.
A Novel Neuro-Fuzzy GmpptAlgorithm based on Generalized Global Sliding Mode Concept for Variable-Shaded Photovoltaic System

This research article reports the designing of neuro-fuzzy based nonlinear generalized global sliding mode control (GGSMC) to track the globally maximum power point tracking (GMPPT) approach for partially-shaded photovoltaic system (PV) using buck-boost converter. In order to extract the possible maximum power (MP), it is compulsory to operate the PV system at maximum power point (MPP). GGSMC control scheme major advantages are faster convergence, high efficiency and robustness against the rapidly varying climatic conditions. The soft computing based technique neuro-fuzzy is utilized to generate the reference voltage for developed GMPPT control method. MATLAB/Simulink tool is used for simulations. The tracking performance of the proposed controller is compared with the previously conventional proportional integral derivative (CPID) controller.
Process Variation-Resilient STT-MTJ based TRNG using Linear Correcting Codes

With the increasing applications of artificial intelligence (AI) attacks, the requirement for high-quality security system becomes urgent. True random number generator (TRNG) is the core block of many cryptographic systems, of which the security is determined by the randomness source of TRNG. In this paper, stochastic switching behavior of spin transfer torque magnetic tunnel junction (STT-MTJ) device is exploited for generation of random numbers. Stochastic switching of STT-MTJ provides an excellent physical randomness source. However, due to the limited technology and correlation between different process steps, process variation has a significant impact on the randomness of MTJ based TRNG. Therefore, post processing-based control mechanism is also necessary to guarantee reliable randomness. The method of linear corrector is integrated into STT-MTJ based TRNG, resulting in improved entropy of randomness. The design is implemented by a 40nm CMOS technology and a compact model of the MTJ. By using the output random bitstream with and without process variations, the efficiency of linear corrector is demonstrated by passing the National Institute of Standards and Technology (NIST) statistical test suite.
Robust and Low-Overhead Hybrid Beamforming Design With Imperfect Phase Shifters in Multi-User Millimeter Wave Systems

Phase shifters, often applied for analog beamforming in hybrid millimeter wave systems, are usually imperfect with random phase and gain errors brought by manufacture imperfections. Due to the uncertainty and nonreciprocity of random phase and gain errors, the digital precoder cannot eliminate the inter-user interference, which leads to system performance degradation. In our previous works [1], [2], we have analyzed the degradation of the achievable sum rate caused by imperfect phase shifters. The results show that the impact of random phase and gain errors is indeed very severe and they lead to performance ceiling. In this paper, we propose a novel channel estimation and Hybrid BeamForming (HBF) design method considering the structures both with and without switches. More specifically, we apply the discrete Fourier transform interpolation algorithm to estimate the downlink angle-of-departure of the strongest path, which avoids the exhaustive search of the narrow beam codebook and greatly saves the training overhead. Then, the downlink equivalent channel is estimated at the users and fed back for the digital precoder design, which guarantees the robustness against imperfect phase shifters. Finally, we derive a closed-form expression to make a better tradeoff between the estimation performance and training overhead. We show that our proposed method outperforms other state-of-the-art beam training methods with much less training overhead both theoretically and numerically.
Human Genome Encodes Many Proteins with Charge Periodicity of 28 Residues

The human genome includes more than 36,000 open reading frames that are translated to amino acid sequences of proteins. When the charge distribution in amino acid sequences from the total human genome was analyzed by the autocorrelation function, a surprisingly sharp periodicity of 28 residues was observed. Every protein with the charge periodicity of 28 residues (PCP28) could be discriminated by a simple algorithm, and the number of PCP28 amounted to about 3% of the total open reading frames of the human genome. The net charge of most PCP28 was highly positive. The possible structural and functional features of this type of protein were discussed in terms of the electric repulsion within molecules.
Male Preference for Large Females and Female Reproductive Condition in the Japanese Beetle, Popillia japonica Newman (Coleoptera: Scarabaeidae)

Abstract In the field, paired (in copula) female Japanese beetles (Popillia japonica Newman) tend to be larger than unpaired females. In this study, we investigated whether this size pattern could be explained by a male preference for large females, and whether larger females tended to have more and/or larger eggs than smaller females. In a laboratory study, both small and large males, when given a choice of a large and small female, tended to choose the large female. We dissected field-caught paired and unpaired females, measured their body size, and counted and measured their eggs. Larger females tended to have more and larger eggs than smaller females, indicating that males may benefit from choosing larger females due to the egg characteristics of these larger females. Paired females in the field were consistently larger than single females; paired females also had more and larger eggs, even when body width was statistically controlled. Thus, although body width of the female correlates with her fecundity, males may either use cues in addition to a female's body width to determine her immediate fecundity or fecund females may be more available for or less resistant to male mating attempts.
Changes in the soil’s biological and chemical properties due to the land use

Increasing the soil productivity is challenged by the increasing biotic threat to plants and microorganisms, by the resistance to agrochemicals, and by the declining soil health. Soil management strategy is, therefore, aimed at erosion prevention and the minimisation of soil organic matter losses. A key factor in an agroecosystem is the appropriate biological stability. It is essential not only at present, but also for further sustainable agriculture. This study was based on the hypothesis that afforestation and conversion from arable land to permanent grassland improves the organic matter status and biological stability in the agroecosystem. The experiment was conducted from 2014 to 2018 in the Uhřice bio-corridor (Kroměříž region, the Czech Republic). Haplic Luvisol has been investigated for its basic biological and chemical properties after the arable land was converted to a natural vegetation system. The afforested segment (F), permanent grassland segment (G), and arable land segment (A) have been sampled in the upper soil horizon (0–0.30 m). Standard analytical methods were applied for the determination of the basic soil properties. A principal component analysis and factor analysis were used for interpreting the connection between the parameters of the soil organic carbon, the humic substances, the humic acids, and the fulvic acids, the agrochemical properties of the soil (the pH, the content of the nitrogen, phosphorus and potassium, etc.), and the soil biological properties (basal soil respiration (BSR), the ratios of the N/BSR, NG/BSR, etc.). After five years of investigation, the differences in the studied parameters were evident. The factor analysis and multivariate exploratory techniques showed that the soil properties were grouped based on the management into three different categories – F, G and A. The different land use directly influenced the quality and stability of the humic substances, basal soil respiration, and carbon and nitrogen utilisation. In comparison to the arable land, the forest and grassland were considered to have a higher accumulation potential of carbon and nitrogen. A negative correlation between the soil basal respiration (r = –0.95); total nitrogen (r = –0.93); total organic carbon (Cox) content (r = –0.82); and partial Ca (r = –0.82) was found. A positive correlation (r = 0.80) between the humic substances (C-HS) and soil reaction (pH) was determined.
Tracking via context-aware regression correlation filter with a spatial–temporal regularization

Abstract. Correlation filters are known to have superior performance in tracking speed. To improve tracking results, we propose a context-aware regression correlation filter with a spatial–temporal regularization for tracking. First, the spatial regularization parameters are computed by the spatial correlation between the target and the surrounding information. Meanwhile, the filter weight distribution is also computed to highlight the target region and suppress the background region. Next, a context-aware model is proposed to adaptively expand the search area of the target with the original regression analysis. Due to the introduction of the context-aware information, the target structure will be changed and the regression model will not be adapted to the Gaussian function. Therefore, an optimized regression objective function is constructed according to the context-aware model. In the tracking process, under rotation, out-of-view, deformation, etc., the tracker still can continue the tracking of subsequent frames according to partial background information. In addition, time variables for online updating of the spatial–temporal model employ the similarity of adjacent frames to achieve more accurate tracking. According to the model form, the alternative direction method of multipliers is used to optimize the model optimization. Extensive experimental results on the OTB-2013 and OTB-2015 dataset object tracking benchmarks prove that the proposed algorithm is superior to other state-of-the-art algorithms in terms of success, accuracy, and robustness.
Sprint interval training in young adult males with ampamp; without elevated worry

Using a pre-post design, we investigated state anxiety and worry responses to a single Wingate, three weeks of sprint interval training (SIT), and, change in response to a single Wingate. Differences between males with and without elevated worry were explored. Thirty-eight young adult males, 18 with elevated worry (Penn State Worry Questionnaire [PSWQ] ≥45), completed a single 30s Wingate at 7.5% body mass before and after three weeks of SIT (nine sessions of 4–6 sprints). The state subscale of the State-Trait Anxiety Inventory assessed state anxiety; the PSWQ measured worry and worry engagement. A single Wingate increased state anxiety (d = -0.37, [-0.82, 0.09]) and decreased worry engagement (d = 0.16, [-0.29, 0.61]). SIT resulted in non-significant reductions in state anxiety (d = 0.20, [-0.25, 0.65]) and worry (d = 0.09, [-0.36, 0.54]). SIT non-significantly attenuated state anxiety response to a single Wingate (d = 0.23, [-0.22, 0.68]), approximating a 2.5-fold reduction from pre(d = -0.37, [-0.82, 0.09]) to post-SIT (d = -0.16, [-0.61, 0.29]). Improvements in worry (d = 0.61, [-0.04, 1.26]) and worry engagement (d = 0.60, [-0.05, 1.25]) were moderately larger among males with elevated worry. Findings indicated that a single Wingate may acutely perturb state anxiety and improve worry. Three weeks of SIT may improve anxiety and worry and response to a single Wingate. Responses were moderately larger among males with elevated worry.
Study of Spurious Passbands of Ridged Hollow Waveguide Filters

Spurious passbands are a severe problem of distributed filter structures. In contrast to rectangular hollow waveguides, ridged waveguides can help to push the parasitic passbands to considerably higher frequencies. In this paper a closer look is given at the spurious behaviour of ridged hollow waveguide filters. The main focus lies on the reasons for the improved stopband behaviour and on the influence of a filter's bandwidth on the spurious passband. The performed investigations are based on the theory of coupled resonators and a series of illustrative results are given.